GGCTTCACTT	0.483																																																0			7											282	237	252					7																	127953300		2203	4300	6503	127740536	SO:0001819	synonymous_variant	55131			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.2073C>T	7.37:g.127953300G>A			127740536	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	Silent	SNP	ENST00000223073.2	37	CCDS5801.1																																																																																				0.483	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		A	127953300	G	A	127953300	2	1	120	1	0	0	0	0	0	0	0	1	13165	1103	39	1		1	RBM28	7	127953300	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	29459889	127953300	31185363	73	31654										
TRIM24	8805	hgsc.bcm.edu	37	chr7	138235871	138235871	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	catccccagtgaccaacaacAccatccaatttcactgtgat	4	15	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:138235871A>C	ENST00000343526.4	+	8	1422	c.1207A>C	c.(1207-1209)Acc>Ccc	p.T403P	TRIM24_ENST00000497516.1_3'UTR|TRIM24_ENST00000415680.2_Missense_Mutation_p.T403P			O15164	TIF1A_HUMAN	tripartite motif containing 24	403			T -> N (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						GACCAACAACACCATCCAATT	0.418																																					Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)											0			7											244	211	222					7																	138235871		2203	4300	6503	137886411	SO:0001583	missense	8805			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.1207A>C	7.37:g.138235871A>C	ENSP00000340507:p.Thr403Pro		137886411	A4D1R7|A4D1R8|O95854	Missense_Mutation	SNP	ENST00000343526.4	37	CCDS5847.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.085788	0.76642	.	.	ENSG00000122779	ENST00000343526;ENST00000536822;ENST00000415680;ENST00000378381	T;T	0.76968	-1.02;-1.06	4.9	4.9	0.64082	.	0.180145	0.49305	D	0.000141	T	0.78972	0.4368	L	0.44542	1.39	0.38470	D	0.947444	B;D	0.56521	0.158;0.976	B;P	0.56127	0.07;0.792	T	0.78209	-0.2293	10	0.27785	T	0.31	-6.3172	13.0416	0.58901	1.0:0.0:0.0:0.0	.	403;403	O15164;O15164-2	TIF1A_HUMAN;.	P	403;314;403;361	ENSP00000340507:T403P;ENSP00000390829:T403P	ENSP00000340507:T403P	T	+	1	0	TRIM24	137886411	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.630000	0.61297	1.956000	0.56807	0.482000	0.46254	ACC		0.418	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		C	138235871	A	C	138235871	3	2	120	1	0	0	0	0	1	0	0	0	16538	159	6	4	1237	4	TRIM24	7	138235871	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	10282571	138235871	20902792	74	31655										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140269505	140269505	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cacccgtttctttcctctccGgacctcataaatggcgttga	7	14	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:140269505G>A	ENST00000275884.6	-	6	1897	c.1480C>T	c.(1480-1482)Cgg>Tgg	p.R494W	DENND2A_ENST00000537639.1_Missense_Mutation_p.R494W|DENND2A_ENST00000492720.1_Missense_Mutation_p.R494W|DENND2A_ENST00000496613.1_Missense_Mutation_p.R494W			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	494					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)					TTTCCTCTCCGGACCTCATAA	0.567																																																0			7											133	134	134					7																	140269505		1952	4158	6110	139915974	SO:0001583	missense	27147			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.1480C>T	7.37:g.140269505G>A	ENSP00000275884:p.Arg494Trp		139915974	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	37	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986338	0.93044	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613;ENST00000492720	T;T;T;T	0.13420	3.3;3.3;3.3;2.59	4.74	4.74	0.60224	.	0.081588	0.50627	D	0.000106	T	0.32645	0.0836	L	0.46157	1.445	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.973	T	0.06899	-1.0801	10	0.87932	D	0	-19.0906	17.7358	0.88392	0.0:0.0:1.0:0.0	.	494;494	Q9ULE3-2;Q9ULE3	.;DEN2A_HUMAN	W	494	ENSP00000275884:R494W;ENSP00000442245:R494W;ENSP00000419654:R494W;ENSP00000419464:R494W	ENSP00000275884:R494W	R	-	1	2	DENND2A	139915974	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.875000	0.69660	2.184000	0.69523	0.462000	0.41574	CGG		0.567	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140269505	G	A	140269505	3	1	120	1	0	0	0	0	1	0	0	0	4440	1115	39	1	1605	1	DENND2A	7	140269505	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	2033634	140269505	18869158	75	31656										
BRAF	673	hgsc.bcm.edu	37	chr7	140453171	140453171	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aaatcacctatttttactgtGaggtcttcatgaagaaatat	6	6	3	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:140453171G>A	ENST00000288602.6	-	15	1824	c.1764C>T	c.(1762-1764)ctC>ctT	p.L588L		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	588	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TTTTTACTGTGAGGTCTTCAT	0.378		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											97	93	95					7																	140453171		2203	4299	6502	140099640	SO:0001819	synonymous_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1764C>T	7.37:g.140453171G>A			140099640	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	G	9.936	1.216034	0.22373	.	.	ENSG00000157764	ENST00000496384	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	T	0.76550	0.4003	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74529	-0.3635	4	.	.	.	.	19.7917	0.96461	0.0:0.0:1.0:0.0	.	.	.	.	L	196	.	.	S	-	2	0	BRAF	140099640	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.157000	0.50716	2.686000	0.91538	0.650000	0.86243	TCA		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		A	140453171	G	A	140453171	2	1	120	1	0	0	0	0	0	0	0	1	1499	1277	45	3		3	BRAF	7	140453171	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	183666	140453171	18685492	76	31657										
BRAF	673	hgsc.bcm.edu	37	chr7	140481428	140481428	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gatccagatccaattctttgTcccactgtaatctgcccatc	5	14	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:140481428T>C	ENST00000288602.6	-	11	1440	c.1380A>G	c.(1378-1380)ggA>ggG	p.G460G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	460	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G460G(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CAATTCTTTGTCCCACTGTAA	0.403		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	7											169	145	153					7																	140481428		2203	4300	6503	140127897	SO:0001819	synonymous_variant	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1380A>G	7.37:g.140481428T>C			140127897	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.330893	0.24167	.	.	ENSG00000157764	ENST00000496384	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	T	0.61489	0.2351	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60835	-0.7184	4	.	.	.	.	10.2132	0.43154	0.0:0.0741:0.0:0.9259	.	.	.	.	G	68	.	.	D	-	2	0	BRAF	140127897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.628000	0.24522	2.130000	0.65690	0.477000	0.44152	GAC		0.403	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140481428	T	C	140481428	2	2	120	1	0	0	0	0	0	0	0	1	1499	1654	58	4		4	BRAF	7	140481428	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	28257	140481428	18657235	77	31658										
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562019	142562019	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcacctcaaacgctggaccaAggtggacacaattgcagcag	11	12	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:142562019A>G	ENST00000392957.2	+	7	1248	c.461A>G	c.(460-462)aAg>aGg	p.K154R	EPHB6_ENST00000442129.1_Missense_Mutation_p.K154R|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	154	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CGCTGGACCAAGGTGGACACA	0.637																																																0			7											61	65	64					7																	142562019		2203	4300	6503	142272141	SO:0001583	missense	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.461A>G	7.37:g.142562019A>G	ENSP00000376684:p.Lys154Arg		142272141	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	A	27.4	4.828961	0.90955	.	.	ENSG00000106123	ENST00000392957;ENST00000442129	T;T	0.05258	3.47;3.47	5.6	5.6	0.85130	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.47455	D	0.000236	T	0.26521	0.0648	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00992	-1.1488	10	0.72032	D	0.01	.	14.969	0.71217	1.0:0.0:0.0:0.0	.	154	O15197	EPHB6_HUMAN	R	154	ENSP00000376684:K154R;ENSP00000410789:K154R	ENSP00000376684:K154R	K	+	2	0	EPHB6	142272141	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.334000	0.96470	2.133000	0.65898	0.533000	0.62120	AAG		0.637	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			G	142562019	A	G	142562019	3	3	120	1	0	0	0	0	1	0	0	0	5191	72	3	4	471	4	EPHB6	7	142562019	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	2080591	142562019	16576644	78	31659										
GIMAP7	168537	hgsc.bcm.edu	37	chr7	150217240	150217240	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aatggcaggggagagaccttCttgttgtagacactccaggg	14	8	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:150217240C>G	ENST00000313543.4	+	2	335	c.178C>G	c.(178-180)Ctt>Gtt	p.L60V		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	60	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGAGACCTTCTTGTTGTAGA	0.532																																																0			7											55	52	53					7																	150217240		2203	4300	6503	149848173	SO:0001583	missense	168537			BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"GTPases, IMAP"	22404	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 7"					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.178C>G	7.37:g.150217240C>G	ENSP00000315474:p.Leu60Val		149848173		Missense_Mutation	SNP	ENST00000313543.4	37	CCDS5903.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.649620	0.00785	.	.	ENSG00000179144	ENST00000313543	T	0.61158	0.13	5.09	-0.281	0.12882	AIG1 (1);	0.535498	0.18313	N	0.145049	T	0.32941	0.0846	N	0.13198	0.31	0.09310	N	1	P	0.38129	0.619	B	0.33890	0.172	T	0.23904	-1.0175	10	0.19590	T	0.45	.	11.8577	0.52449	0.1209:0.2359:0.6432:0.0	.	60	Q8NHV1	GIMA7_HUMAN	V	60	ENSP00000315474:L60V	ENSP00000315474:L60V	L	+	1	0	GIMAP7	149848173	0.000000	0.05858	0.024000	0.17045	0.058000	0.15608	-0.555000	0.05999	0.275000	0.22094	-0.165000	0.13383	CTT		0.532	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236		G	150217240	C	G	150217240	3	3	120	1	0	0	0	0	1	0	0	0	6404	913	32	5	180	5	GIMAP7	7	150217240	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	7655221	150217240	8921423	79	31660										
RHEB	6009	hgsc.bcm.edu	37	chr7	151167703	151167703	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aaaaagctgcattccaagatTctgccaaagctttcccttct	5	12	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr7:151167703T>C	ENST00000262187.5	-	7	828	c.416A>G	c.(415-417)gAa>gGa	p.E139G	RHEB_ENST00000472642.1_Missense_Mutation_p.E34G|RHEB_ENST00000496004.1_Missense_Mutation_p.E34G	NM_005614.3	NP_005605.1	Q15382	RHEB_HUMAN	Ras homolog enriched in brain	139			E -> K (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|positive regulation of TOR signaling (GO:0032008)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)	14			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		ATTCCAAGATTCTGCCAAAGC	0.333																																					Pancreas(98;671 892 8111 15140 36556 39178 39939 44184)											0			7											71	72	72					7																	151167703		2202	4299	6501	150798636	SO:0001583	missense	6009			D78132	CCDS5927.1	7q36	2014-05-09	2003-07-14	2003-07-14	ENSG00000106615	ENSG00000106615			10011	protein-coding gene	gene with protein product		601293	"Ras homolog enriched in brain 2"	RHEB2		8661031	Standard	NM_005614		Approved		uc003wkh.1	Q15382	OTTHUMG00000157330	ENST00000262187.5:c.416A>G	7.37:g.151167703T>C	ENSP00000262187:p.Glu139Gly		150798636	B3KWN6|D3DX13|Q53Y56|Q99444	Missense_Mutation	SNP	ENST00000262187.5	37	CCDS5927.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397020	0.62177	.	.	ENSG00000106615	ENST00000262187;ENST00000472642;ENST00000496004	T;T;T	0.78364	-1.17;-1.17;-1.17	4.9	4.9	0.64082	Small GTP-binding protein domain (1);	0.051891	0.85682	D	0.000000	T	0.75539	0.3863	M	0.76002	2.32	0.80722	D	1	P	0.41784	0.762	B	0.36504	0.226	T	0.77651	-0.2508	10	0.40728	T	0.16	.	13.9983	0.64416	0.0:0.0:0.0:1.0	.	139	Q15382	RHEB_HUMAN	G	139;34;34	ENSP00000262187:E139G;ENSP00000420726:E34G;ENSP00000418161:E34G	ENSP00000262187:E139G	E	-	2	0	RHEB	150798636	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.992000	0.70609	1.967000	0.57214	0.482000	0.46254	GAA		0.333	RHEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348468.2	NM_005614		C	151167703	T	C	151167703	3	2	120	1	0	0	0	0	1	0	0	0	13365	1783	62	4	146	4	RHEB	7	151167703	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	950463	151167703	7970960	80	31661										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39495141	39495141	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gatttccaccagtggggatgCtgatgatatattacaaagat	10	6	0	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr8:39495141C>T	ENST00000265707.5	+	9	791	c.746C>T	c.(745-747)gCt>gTt	p.A249V	ADAM18_ENST00000379866.1_Missense_Mutation_p.A225V|ADAM18_ENST00000541111.1_5'UTR	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	249	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)			AGTGGGGATGCTGATGATATA	0.383																																																0			8											101	98	99					8																	39495141		2203	4299	6502	39614298	SO:0001583	missense	8749			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.746C>T	8.37:g.39495141C>T	ENSP00000265707:p.Ala249Val		39614298	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.058862	0.36277	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.10573	2.86;2.86	5.3	2.49	0.30216	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.920785	0.09124	N	0.845347	T	0.15998	0.0385	M	0.64260	1.97	0.09310	N	0.999992	P;P	0.45986	0.648;0.87	P;P	0.53102	0.596;0.718	T	0.12243	-1.0555	10	0.02654	T	1	.	4.6337	0.12514	0.1731:0.6477:0.0:0.1792	.	225;249	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	V	249;225;181	ENSP00000265707:A249V;ENSP00000369195:A225V	ENSP00000265707:A249V	A	+	2	0	ADAM18	39614298	0.191000	0.23288	0.005000	0.12908	0.164000	0.22412	0.560000	0.23500	0.363000	0.24346	0.650000	0.86243	GCT		0.383	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39495141	C	T	39495141	3	4	120	1	0	0	0	0	1	0	0	0	239	797	28	3	780	3	ADAM18	8	39495141	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10		39495141	106868881	81	31662										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43027510	43027510	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggaggaaaatattggtacttCaaacatgcaagttggaatgg	12	4	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr8:43027510C>T	ENST00000458501.2	+	8	885	c.885C>T	c.(883-885)ttC>ttT	p.F295F	HGSNAT_ENST00000379644.4_Silent_p.F267F			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	295					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)			ATTGGTACTTCAAACATGCAA	0.398																																																0			8											182	178	180					8																	43027510		1878	4115	5993	43146667	SO:0001819	synonymous_variant	138050				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.885C>T	8.37:g.43027510C>T			43146667	B4E2V0	Silent	SNP	ENST00000458501.2	37																																																																																					0.398	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		T	43027510	C	T	43027510	2	4	120	1	0	0	0	0	0	0	0	1	7109	825	29	3		3	HGSNAT	8	43027510	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3532369	43027510	103336512	82	31663										
MOS	4342	hgsc.bcm.edu	37	chr8	57026021	57026021	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	acttgagacactttcccaaaCttaactgtcctccagtgcgg	7	13	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr8:57026021C>G	ENST00000311923.1	-	1	520	c.521G>C	c.(520-522)aGt>aCt	p.S174T		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	174	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			CTTTCCCAAACTTAACTGTCC	0.567																																					Esophageal Squamous(124;373 2870 4778)											0			8											63	59	60					8																	57026021		2203	4300	6503	57188575	SO:0001583	missense	55034				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.521G>C	8.37:g.57026021C>G	ENSP00000310722:p.Ser174Thr		57188575	Q3KPG9|Q3KPH0	Missense_Mutation	SNP	ENST00000311923.1	37	CCDS6164.1	.	.	.	.	.	.	.	.	.	.	C	0.304	-0.972068	0.02215	.	.	ENSG00000172680	ENST00000311923	D	0.93811	-3.29	5.82	2.48	0.30137	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.121610	0.06544	N	0.743821	D	0.87908	0.6296	N	0.17764	0.52	0.09310	N	1	B	0.06786	0.001	B	0.15484	0.013	T	0.76337	-0.2996	10	0.56958	D	0.05	.	8.4483	0.32856	0.0:0.666:0.1297:0.2042	.	174	P00540	MOS_HUMAN	T	174	ENSP00000310722:S174T	ENSP00000310722:S174T	S	-	2	0	MOS	57188575	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.221000	0.09202	0.304000	0.22809	-0.810000	0.03169	AGT		0.567	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372		G	57026021	C	G	57026021	3	3	120	1	0	0	0	0	1	0	0	0	9742	565	20	5	522	5	MOS	8	57026021	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	13998511	57026021	89338001	83	31664										
OTUD6B	51633	hgsc.bcm.edu	37	chr8	92082610	92082610	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtgtgctggggtacctggtcGtcatggaggcggtattgacc	17	8	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr8:92082610G>C	ENST00000285420.4	+	1	187	c.88G>C	c.(88-90)Gtc>Ctc	p.V30L	GS1-251I9.4_ENST00000524003.1_RNA|GS1-251I9.4_ENST00000522817.1_RNA|OTUD6B_ENST00000404789.3_5'UTR	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B	0							cysteine-type peptidase activity (GO:0008234)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11			BRCA - Breast invasive adenocarcinoma(11;0.0187)			GTACCTGGTCGTCATGGAGGC	0.587																																																0			8											95	95	95					8																	92082610		2203	4300	6503	92151786	SO:0001583	missense	51633				CCDS6253.2, CCDS69513.1	8q21.3	2013-01-21			ENSG00000155100	ENSG00000155100		"OTU domain containing"	24281	protein-coding gene	gene with protein product		612021					Standard	NM_016023		Approved	CGI-77, DUBA5	uc003yeu.4	Q8N6M0	OTTHUMG00000150758	ENST00000285420.4:c.88G>C	8.37:g.92082610G>C	ENSP00000285420:p.Val30Leu		92151786	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Missense_Mutation	SNP	ENST00000285420.4	37	CCDS6253.2	.	.	.	.	.	.	.	.	.	.	G	8.766	0.924869	0.18056	.	.	ENSG00000155100	ENST00000285420	D	0.95518	-3.73	5.65	0.931	0.19460	.	.	.	.	.	D	0.87935	0.6303	N	0.08118	0	0.20873	N	0.999835	.	.	.	.	.	.	T	0.79004	-0.1980	7	0.39692	T	0.17	0.9201	7.3886	0.26897	0.3219:0.1106:0.5675:0.0	.	.	.	.	L	30	ENSP00000285420:V30L	ENSP00000285420:V30L	V	+	1	0	OTUD6B	92151786	0.006000	0.16342	0.002000	0.10522	0.034000	0.12701	0.966000	0.29331	-0.212000	0.10109	-1.886000	0.00541	GTC		0.587	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023		C	92082610	G	C	92082610	3	2	120	1	0	0	0	0	1	0	0	0	11348	1145	40	5	90	5	OTUD6B	8	92082610	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	35056589	92082610	54281412	84	31665										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109240603	109240603	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gttctctgctgaagagactgAagtggagaactcacagacta	11	8	2	5			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr8:109240603A>G	ENST00000220849.5	-	7	677	c.615T>C	c.(613-615)ctT>ctC	p.L205L	EIF3E_ENST00000519030.1_Silent_p.L112L|RP11-35G22.1_ENST00000520037.1_RNA|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)			GAAGAGACTGAAGTGGAGAAC	0.348																																					GBM(15;360 410 8460 34179 52246)											0			8											75	75	75					8																	109240603		2203	4300	6503	109309779	SO:0001819	synonymous_variant	3646			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.615T>C	8.37:g.109240603A>G			109309779		Silent	SNP	ENST00000220849.5	37	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	A	8.734	0.917257	0.17982	.	.	ENSG00000104408	ENST00000522352	.	.	.	5.5	-3.03	0.05429	.	.	.	.	.	T	0.51126	0.1656	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44711	-0.9310	4	.	.	.	-11.5618	7.819	0.29276	0.2882:0.2755:0.4363:0.0	.	.	.	.	P	29	.	.	S	-	1	0	EIF3E	109309779	0.996000	0.38824	0.935000	0.37517	0.974000	0.67602	0.333000	0.19768	-0.844000	0.04184	-1.501000	0.00957	TCA		0.348	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		G	109240603	A	G	109240603	2	3	120	1	0	0	0	0	0	0	0	1	5028	233	9	4		4	EIF3E	8	109240603	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	17157993	109240603	37123419	85	31666										
TG	7038	hgsc.bcm.edu	37	chr8	133925509	133925509	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agtcaggacggactgggatgCggtaggtccactctctccct	13	12	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr8:133925509C>T	ENST00000220616.4	+	20	4417	c.4377C>T	c.(4375-4377)tgC>tgT	p.C1459C	TG_ENST00000377869.1_Splice_Site_p.C1459C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1459					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)		GACTGGGATGCGGTAGGTCCA	0.567																																																0			8											74	62	66					8																	133925509		2203	4300	6503	133994691	SO:0001630	splice_region_variant	7038			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.4378+1C>T	8.37:g.133925509C>T			133994691	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																				0.567	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	Silent	T	133925509	C	T	133925509	5	4	120	1	0	0	0	0	0	0	1	0	15852	782	27	1	4455	1	TG	8	133925509	Splice_Site	SNP	C	TCGA-F5-6813-01A-11D-1826-10	24684906	133925509	12438513	86	31667										
KLHL9	55958	hgsc.bcm.edu	37	chr9	21333629	21333629	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tctactgtggccagttcaccAgctgcactgcgcccaccaac	8	17	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr9:21333629A>G	ENST00000359039.4	-	1	1750	c.1230T>C	c.(1228-1230)gcT>gcC	p.A410A	KLHL9_ENST00000537938.1_Silent_p.A342A			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	410					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)		p.A410A(1)		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)		CCAGTTCACCAGCTGCACTGC	0.443																																																1	Substitution - coding silent(1)	ovary(1)	9											112	101	105					9																	21333629		2203	4300	6503	21323629	SO:0001819	synonymous_variant	55958			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.1230T>C	9.37:g.21333629A>G			21323629	Q8TCQ2	Silent	SNP	ENST00000359039.4	37	CCDS6503.1																																																																																				0.443	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		G	21333629	A	G	21333629	2	3	120	1	0	0	0	0	0	0	0	1	8417	175	7	4		4	KLHL9	9	21333629	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10		21333629	119879802	87	31668										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79824434	79824434	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aaatttccagtatccatattCgttatgaagatgatgtaagt	7	5	0	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr9:79824434C>A	ENST00000360280.3	+	6	741	c.481C>A	c.(481-483)Cgt>Agt	p.R161S	VPS13A_ENST00000376636.3_Missense_Mutation_p.R161S|VPS13A_ENST00000376634.4_Missense_Mutation_p.R161S|VPS13A_ENST00000357409.5_Missense_Mutation_p.R161S	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	161			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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						TATCCATATTCGTTATGAAGA	0.274																																																0			9											33	34	33					9																	79824434		2200	4291	6491	79014254	SO:0001583	missense	23230			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.481C>A	9.37:g.79824434C>A	ENSP00000353422:p.Arg161Ser		79014254	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.552299	0.86127	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.67523	-0.13;-0.27;-0.23;-0.13	5.71	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.84906	0.5576	M	0.91561	3.22	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;1.0	D	0.88380	0.3001	10	0.87932	D	0	.	14.2793	0.66200	0.0:0.9276:0.0:0.0724	.	161;161;161;161	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	S	161	ENSP00000365821:R161S;ENSP00000365823:R161S;ENSP00000353422:R161S;ENSP00000349985:R161S	ENSP00000349985:R161S	R	+	1	0	VPS13A	79014254	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.182000	0.77689	1.417000	0.47077	0.655000	0.94253	CGT		0.274	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79824434	C	A	79824434	3	1	120	1	0	0	0	0	1	0	0	0	17229	884	31	2	503	2	VPS13A	9	79824434	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	58490805	79824434	61388997	88	31669										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87563463	87563463	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctccagcatgagcacatcgtCaagttctatggcgtctgcgt	10	12	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr9:87563463C>G	ENST00000323115.4	+	14	2156	c.1803C>G	c.(1801-1803)gtC>gtG	p.V601V	NTRK2_ENST00000277120.3_Silent_p.V617V|NTRK2_ENST00000376214.1_Silent_p.V617V|NTRK2_ENST00000376213.1_Silent_p.V601V			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	601	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)	AGCACATCGTCAAGTTCTATG	0.572										TSP Lung(25;0.17)																																						0			9											115	84	95					9																	87563463		2203	4300	6503	86753283	SO:0001819	synonymous_variant	4915			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.1803C>G	9.37:g.87563463C>G			86753283	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Silent	SNP	ENST00000323115.4	37	CCDS35050.1																																																																																				0.572	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			G	87563463	C	G	87563463	2	3	120	1	0	0	0	0	0	0	0	1	10738	813	29	5		5	NTRK2	9	87563463	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	7739029	87563463	53649968	89	31670										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88247986	88247986	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aatattctgcaatgtaattcGgtccaaggcctttacaatat	6	8	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr9:88247986G>A	ENST00000357081.3	-	14	1750	c.1606C>T	c.(1606-1608)Cga>Tga	p.R536*	AGTPBP1_ENST00000432218.1_Nonsense_Mutation_p.R374*|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376083.3_Nonsense_Mutation_p.R496*|AGTPBP1_ENST00000376109.3_Nonsense_Mutation_p.R548*			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	536					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)	p.R496*(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AATGTAATTCGGTCCAAGGCC	0.383																																																1	Substitution - Nonsense(1)	large_intestine(1)	9											112	109	110					9																	88247986		2203	4300	6503	87437806	SO:0001587	stop_gained	23287			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.1606C>T	9.37:g.88247986G>A	ENSP00000349592:p.Arg536*		87437806	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Nonsense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	G	39	7.765935	0.98477	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	.	.	.	5.92	2.83	0.33086	.	0.595744	0.17512	N	0.171597	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.4962	14.1766	0.65546	0.0:0.0:0.3337:0.6663	.	.	.	.	X	536;496;548;374	.	ENSP00000349592:R536X	R	-	1	2	AGTPBP1	87437806	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.482000	0.35486	0.772000	0.33382	-0.188000	0.12872	CGA		0.383	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88247986	G	A	88247986	4	1	120	1	0	0	0	0	0	1	0	0	400	1124	39	1	2126	1	AGTPBP1	9	88247986	Nonsense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	684523	88247986	52965445	90	31671										
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136321303	136321303	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctcggggaggtggtgaccctCcgcgtccttgagagttctct	14	12	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr9:136321303C>T	ENST00000371929.3	+	26	4125	c.3681C>T	c.(3679-3681)ctC>ctT	p.L1227L	ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.L1140L|ADAMTS13_ENST00000355699.2_Silent_p.L1171L|ADAMTS13_ENST00000371910.1_Silent_p.L23L|ADAMTS13_ENST00000485925.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	1227	CUB 1.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TGGTGACCCTCCGCGTCCTTG	0.637																																																0			9											65	59	61					9																	136321303		2203	4300	6503	135311124	SO:0001819	synonymous_variant	11093			AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"ADAM metallopeptidases with thrombospondin type 1 motif"	1366	protein-coding gene	gene with protein product		604134	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.3681C>T	9.37:g.136321303C>T			135311124	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																				0.637	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		T	136321303	C	T	136321303	2	4	120	1	0	0	0	0	0	0	0	1	258	842	30	3		3	ADAMTS13	9	136321303	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	48073317	136321303	4892128	91	31672										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26385365	26385365	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	atgctggtttggctgaaaagAagaaactagcccattacaaa	9	7	0	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:26385365A>C	ENST00000265944.5	+	16	1784	c.1618A>C	c.(1618-1620)Aag>Cag	p.K540Q	MYO3A_ENST00000543632.1_Missense_Mutation_p.K540Q	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	540	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						GGCTGAAAAGAAGAAACTAGC	0.318																																																0			10											60	65	63					10																	26385365		2201	4300	6501	26425371	SO:0001583	missense	53904			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.1618A>C	10.37:g.26385365A>C	ENSP00000265944:p.Lys540Gln		26425371	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.034563	0.75617	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	T;D	0.87256	-0.58;-2.23	5.13	5.13	0.70059	Myosin head, motor domain (2);	0.045499	0.85682	D	0.000000	D	0.90150	0.6922	L	0.38531	1.155	0.52501	D	0.999955	D;D;D	0.89917	1.0;1.0;0.996	D;D;D	0.87578	0.997;0.998;0.969	D	0.91249	0.5028	10	0.66056	D	0.02	.	15.2533	0.73564	1.0:0.0:0.0:0.0	.	540;540;540	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	Q	540	ENSP00000265944:K540Q;ENSP00000445909:K540Q	ENSP00000265944:K540Q	K	+	1	0	MYO3A	26425371	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.925000	0.70062	2.069000	0.61940	0.533000	0.62120	AAG		0.318	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26385365	A	C	26385365	3	2	120	1	0	0	0	0	1	0	0	0	10106	247	9	4	1672	4	MYO3A	10	26385365	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10		26385365	109149382	92	31673										
EGR2	1959	hgsc.bcm.edu	37	chr10	64573435	64573435	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttggggtacttgcgaggcctCagaatgggccgcagtggcag	17	9	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:64573435C>T	ENST00000242480.3	-	2	1288	c.963G>A	c.(961-963)ctG>ctA	p.L321L	EGR2_ENST00000493899.2_5'Flank|EGR2_ENST00000411732.1_Silent_p.L271L|EGR2_ENST00000439032.1_Silent_p.L321L	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	321					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)					TGCGAGGCCTCAGAATGGGCC	0.697																																																0			10											28	32	31					10																	64573435		2203	4300	6503	64243441	SO:0001819	synonymous_variant	1959			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.963G>A	10.37:g.64573435C>T			64243441	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Silent	SNP	ENST00000242480.3	37	CCDS7267.1																																																																																				0.697	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		T	64573435	C	T	64573435	2	4	120	1	0	0	0	0	0	0	0	1	4983	813	29	3		3	EGR2	10	64573435	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	38188070	64573435	70961312	93	31674										
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68687507	68687507	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cagtgttttccagtgtgtccCgaatctgcagcgcctcaacc	9	14	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:68687507C>T	ENST00000361320.4	+	2	1411	c.833C>T	c.(832-834)cCg>cTg	p.P278L	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	278					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						CAGTGTGTCCCGAATCTGCAG	0.478																																																0			10											115	122	120					10																	68687507		2203	4300	6503	68357513	SO:0001583	missense	347731			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.833C>T	10.37:g.68687507C>T	ENSP00000355187:p.Pro278Leu		68357513	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.491874	0.64074	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.60299	0.2	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000002	T	0.76630	0.4014	M	0.70787	2.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.77408	-0.2599	10	0.66056	D	0.02	.	18.8147	0.92072	0.0:1.0:0.0:0.0	.	278;278	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	L	278	ENSP00000355187:P278L	ENSP00000355187:P278L	P	+	2	0	LRRTM3	68357513	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	7.818000	0.86416	2.740000	0.93945	0.650000	0.86243	CCG		0.478	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		T	68687507	C	T	68687507	3	4	120	1	0	0	0	0	1	0	0	0	9070	652	23	1	839	1	LRRTM3	10	68687507	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	4114072	68687507	66847240	94	31675										
TTC18	118491	hgsc.bcm.edu	37	chr10	75071621	75071621	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aggattgtgacttagaggggGttcaccttccaaaggagtat	13	6	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:75071621G>T	ENST00000310715.3	-	12	1465	c.1345C>A	c.(1345-1347)Ccc>Acc	p.P449T	TTC18_ENST00000355577.3_5'UTR|TTC18_ENST00000401621.2_Missense_Mutation_p.P449T|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000394865.1_Missense_Mutation_p.P449T	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		449						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)					CTTAGAGGGGGTTCACCTTCC	0.378																																																0			10											163	174	170					10																	75071621		2203	4300	6503	74741627	SO:0001583	missense	118491																														ENST00000310715.3:c.1345C>A	10.37:g.75071621G>T	ENSP00000310829:p.Pro449Thr		74741627	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	G	7.551	0.662634	0.14645	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000372928;ENST00000394865	D;D;D	0.93019	-3.15;-3.15;-3.15	4.72	-0.591	0.11675	.	1.569510	0.03559	N	0.226755	D	0.85111	0.5622	N	0.10874	0.06	0.09310	N	1	B;B	0.14012	0.009;0.003	B;B	0.12156	0.007;0.002	T	0.74016	-0.3800	10	0.30854	T	0.27	-7.3953	6.9229	0.24399	0.0:0.3475:0.3846:0.2678	.	449;449	Q5T0N1-2;Q5T0N1	.;TTC18_HUMAN	T	449	ENSP00000310829:P449T;ENSP00000384479:P449T;ENSP00000378334:P449T	ENSP00000310829:P449T	P	-	1	0	TTC18	74741627	0.002000	0.14202	0.268000	0.24571	0.619000	0.37552	-0.366000	0.07563	0.013000	0.14918	0.563000	0.77884	CCC		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75071621	G	T	75071621	3	4	120	1	0	0	0	0	1	0	0	0	16725	1261	44	2	2088	2	TTC18	10	75071621	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	6384114	75071621	60463126	95	31676										
PTEN	5728	hgsc.bcm.edu	37	chr10	89624303	89624303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tggattcgacttagacttgaCctgtatccatttctgcggct	9	10	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:89624303C>T	ENST00000371953.3	+	1	1434	c.77C>T	c.(76-78)aCc>aTc	p.T26I	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	26	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				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.?(13)|p.L25fs*28(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)		TTAGACTTGACCTGTATCCAT	0.458		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)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	51	Whole gene deletion(37)|Unknown(13)|Deletion - Frameshift(1)	prostate(14)|central_nervous_system(9)|skin(7)|lung(6)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|kidney(1)	10											159	151	154					10																	89624303		2203	4300	6503	89614283	SO:0001583	missense	5728	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.77C>T	10.37:g.89624303C>T	ENSP00000361021:p.Thr26Ile		89614283	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699536	0.88830	.	.	ENSG00000171862	ENST00000371953	D	0.98701	-5.08	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.054781	0.64402	D	0.000001	D	0.98346	0.9451	M	0.90650	3.135	0.80722	D	1	B	0.30455	0.28	B	0.30572	0.117	D	0.99433	1.0936	9	.	.	.	-0.0938	17.6706	0.88216	0.0:1.0:0.0:0.0	.	26	P60484	PTEN_HUMAN	I	26	ENSP00000361021:T26I	.	T	+	2	0	PTEN	89614283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.018000	0.76406	2.467000	0.83353	0.561000	0.74099	ACC		0.458	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89624303	C	T	89624303	3	4	120	1	0	0	0	0	1	0	0	0	12772	507	18	3	79	3	PTEN	10	89624303	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	14552682	89624303	45910444	96	31677										
BTRC	8945	hgsc.bcm.edu	37	chr10	103221777	103221777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	actgtaataatggcgaacccCctaggaagataataccagag	9	9	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:103221777C>T	ENST00000370187.3	+	3	314	c.196C>T	c.(196-198)Cct>Tct	p.P66S	BTRC_ENST00000393441.4_Intron|BTRC_ENST00000408038.2_Missense_Mutation_p.P30S	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	66					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)	p.P66S(1)		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)		TGGCGAACCCCCTAGGAAGAT	0.363																																																1	Substitution - Missense(1)	ovary(1)	10											97	103	100					10																	103221777		2203	4300	6503	103211767	SO:0001583	missense	8945			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.196C>T	10.37:g.103221777C>T	ENSP00000359206:p.Pro66Ser		103211767	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	37	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.048038	0.55110	.	.	ENSG00000166167	ENST00000370187;ENST00000408038;ENST00000370183	T;T	0.61274	0.31;0.12	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000005	T	0.65439	0.2691	N	0.19112	0.55	0.80722	D	1	D;D	0.67145	0.996;0.967	D;P	0.75484	0.986;0.901	T	0.63042	-0.6725	10	0.35671	T	0.21	-12.3347	20.5568	0.99304	0.0:1.0:0.0:0.0	.	30;66	Q9Y297-2;Q9Y297	.;FBW1A_HUMAN	S	66;30;48	ENSP00000359206:P66S;ENSP00000385339:P30S	ENSP00000359202:P48S	P	+	1	0	BTRC	103211767	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.664000	0.68045	2.861000	0.98227	0.655000	0.94253	CCT		0.363	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		T	103221777	C	T	103221777	3	4	120	1	0	0	0	0	1	0	0	0	1572	623	22	3	206	3	BTRC	10	103221777	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	13597474	103221777	32312970	97	31678										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105944783	105944783	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	actgtacgtacttccactttAggtagacaagggtgccatca	9	10	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:105944783A>T	ENST00000278064.2	-	16	2250	c.1925T>A	c.(1924-1926)cTa>cAa	p.L642Q	WDR96_ENST00000357060.3_Missense_Mutation_p.L711Q|WDR96_ENST00000428666.1_Missense_Mutation_p.L712Q																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						CTTCCACTTTAGGTAGACAAG	0.393																																																0			10											202	175	184					10																	105944783		2203	4300	6503	105934773	SO:0001583	missense	80217																														ENST00000278064.2:c.1925T>A	10.37:g.105944783A>T	ENSP00000278064:p.Leu642Gln		105934773		Missense_Mutation	SNP	ENST00000278064.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.32|16.32	3.091052|3.091052	0.55968|0.55968	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064|ENST00000434629	T;T;T|.	0.31247|.	1.5;1.5;1.5|.	5.18|5.18	5.18|5.18	0.71444|0.71444	WD40 repeat-like-containing domain (1);|.	0.235524|.	0.28354|.	N|.	0.015652|.	T|.	0.56949|.	0.2020|.	M|M	0.65498|0.65498	2.005|2.005	0.09310|0.09310	N|N	0.999993|0.999993	D;D;D|.	0.89917|.	0.997;1.0;0.999|.	D;D;D|.	0.87578|.	0.932;0.998;0.982|.	T|.	0.51988|.	-0.8635|.	10|.	0.30854|.	T|.	0.27|.	.|.	12.9672|12.9672	0.58492|0.58492	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	712;712;711|.	G5E9L1;B4DHB6;Q8NDM7|.	.;.;WDR96_HUMAN|.	Q|K	711;712;642|72	ENSP00000349568:L711Q;ENSP00000400289:L712Q;ENSP00000278064:L642Q|.	ENSP00000278064:L642Q|.	L|X	-|-	2|1	0|0	WDR96|WDR96	105934773|105934773	0.995000|0.995000	0.38212|0.38212	0.033000|0.033000	0.17914|0.17914	0.871000|0.871000	0.50021|0.50021	5.212000|5.212000	0.65225|0.65225	1.946000|1.946000	0.56461|0.56461	0.533000|0.533000	0.62120|0.62120	CTA|TAA		0.393	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			T	105944783	A	T	105944783	3	4	120	1	0	0	0	0	1	0	0	0	1622	420	15	5	2957	5	C10orf79	10	105944783	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	2723006	105944783	29589964	98	31679										
CHST15	51363	hgsc.bcm.edu	37	chr10	125780811	125780811	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtgttgttgtagacgcaggcGcgcagtgaataatcaagcat	13	7	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr10:125780811G>A	ENST00000346248.5	-	6	1950	c.1308C>T	c.(1306-1308)cgC>cgT	p.R436R	CHST15_ENST00000435907.1_Silent_p.R436R|CHST15_ENST00000421115.1_Silent_p.R436R	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	436					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						AGACGCAGGCGCGCAGTGAAT	0.537																																																0			10											72	65	67					10																	125780811		2203	4300	6503	125770801	SO:0001819	synonymous_variant	51363			AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"Sulfotransferases, membrane-bound"	18137	protein-coding gene	gene with protein product	"B cell RAG associated protein", "N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1308C>T	10.37:g.125780811G>A			125770801	O60338|O60474|Q86VM4	Silent	SNP	ENST00000346248.5	37	CCDS7638.1																																																																																				0.537	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		A	125780811	G	A	125780811	2	1	120	1	0	0	0	0	0	0	0	1	3409	1074	38	1		1	CHST15	10	125780811	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	19836028	125780811	9753936	99	31680										
MUC2	4583	hgsc.bcm.edu	37	chr11	1083833	1083833	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcagctgccagacgctggccGccggctatgtgcgtgttggg	16	12	1	1	rs199542148	byFrequency	TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:1083833G>A	ENST00000441003.2	+	18	2392	c.2365G>A	c.(2365-2367)Gcc>Acc	p.A789T	MUC2_ENST00000359061.5_Missense_Mutation_p.A789T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	789					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)	GACGCTGGCCGCCGGCTATGT	0.682													G|||	4	0.000798722	0.003	0	5008	,	,		13012	0		0	False		,,,				2504	0															0			11						G	THR/ALA	23,4175		0,23,2076	12	15	14		2365	2.2	0	11		14	0,8396		0,0,4198	yes	missense	MUC2	NM_002457.2	58	0,23,6274	AA,AG,GG		0.0,0.5479,0.1826	benign	789/2813	1083833	23,12571	2099	4198	6297	1073833	SO:0001583	missense	4583			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.2365G>A	11.37:g.1083833G>A	ENSP00000415183:p.Ala789Thr		1073833	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	2.660	-0.280043	0.05642	0.005479	0.0	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.17213	2.29;2.29	4.27	2.19	0.27852	.	0.599154	0.14709	U	0.303070	T	0.07413	0.0187	L	0.42581	1.335	0.09310	N	1	B	0.21905	0.062	B	0.19666	0.026	T	0.35226	-0.9797	10	0.08599	T	0.76	.	3.6344	0.08143	0.244:0.2095:0.5465:0.0	.	789	E7EUV1	.	T	789	ENSP00000415183:A789T;ENSP00000351956:A789T	ENSP00000351956:A789T	A	+	1	0	MUC2	1073833	0.000000	0.05858	0.007000	0.13788	0.018000	0.09664	0.415000	0.21181	1.005000	0.39183	0.455000	0.32223	GCC		0.682	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1083833	G	A	1083833	3	1	120	1	0	0	0	0	1	0	0	0	10005	1087	38	1	2435	1	MUC2	11	1083833	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		1083833	133922683	100	31681										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1263851	1263851	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cacaaagccgaccacaacagCcactacgactgcgtccactg	7	17	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:1263851C>T	ENST00000529681.1	+	31	5799	c.5741C>T	c.(5740-5742)gCc>gTc	p.A1914V	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.A1917V	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1914	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				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)		ACCACAACAGCCACTACGACT	0.652																																																0			11											111	137	128					11																	1263851		2158	4240	6398	1220427	SO:0001583	missense	727897			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.5741C>T	11.37:g.1263851C>T	ENSP00000436812:p.Ala1914Val		1220427	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	7.540	0.660573	0.14645	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.45	1.4	-2.17	0.07059	.	.	.	.	.	T	0.10809	0.0264	L	0.43923	1.385	0.09310	N	1	B;B	0.28324	0.207;0.207	B;B	0.16722	0.011;0.016	T	0.33292	-0.9874	9	0.87932	D	0	.	1.829	0.03126	0.3144:0.4317:0.0:0.2538	.	2607;1917	A7Y9J9;E9PBJ0	.;.	V	1914;1917;1915;1984	ENSP00000436812:A1914V;ENSP00000415793:A1917V	ENSP00000343037:A1915V	A	+	2	0	MUC5B	1220427	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	-0.611000	0.05622	-0.100000	0.12241	0.134000	0.15878	GCC		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1263851	C	T	1263851	3	4	120	1	0	0	0	0	1	0	0	0	10009	739	26	3	5872	3	MUC5B	11	1263851	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	180018	1263851	133742665	101	31682										
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5530440	5530440	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aatggagcttggctgagggaGtgatccaggacttgggccct	16	8	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:5530440G>C	ENST00000311659.4	-	2	496	c.349C>G	c.(349-351)Ctc>Gtc	p.L117V	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	117										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)		GGCTGAGGGAGTGATCCAGGA	0.607																																					Ovarian(72;684 1260 12332 41642 52180)											0			11											72	66	68					11																	5530440		2201	4297	6498	5487016	SO:0001583	missense	50613			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.349C>G	11.37:g.5530440G>C	ENSP00000347997:p.Leu117Val		5487016	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	G	1.961	-0.438879	0.04636	.	.	ENSG00000175520	ENST00000311659;ENST00000445998	T;T	0.50001	1.37;0.76	5.06	0.892	0.19230	.	0.522959	0.16106	N	0.229308	T	0.37320	0.0999	M	0.68317	2.08	0.09310	N	0.999997	B	0.18968	0.032	B	0.17098	0.017	T	0.27262	-1.0079	10	0.16896	T	0.51	.	3.9777	0.09481	0.2811:0.0:0.5571:0.1618	.	117	Q9H347	UBQL3_HUMAN	V	117	ENSP00000347997:L117V;ENSP00000412561:L117V	ENSP00000347997:L117V	L	-	1	0	UBQLN3	5487016	0.310000	0.24527	0.005000	0.12908	0.859000	0.49053	0.906000	0.28517	0.072000	0.16694	0.585000	0.79938	CTC		0.607	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		C	5530440	G	C	5530440	3	2	120	1	0	0	0	0	1	0	0	0	16938	1029	36	5	1622	5	UBQLN3	11	5530440	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	4266589	5530440	129476076	102	31683										
CTR9	9646	hgsc.bcm.edu	37	chr11	10789928	10789928	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aaggatattttcgtgaagctCgtgatgtatttgcccaagta	10	6	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:10789928C>T	ENST00000361367.2	+	16	2425	c.1999C>T	c.(1999-2001)Cgt>Tgt	p.R667C		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	667					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)		TCGTGAAGCTCGTGATGTATT	0.388																																																0			11											138	132	134					11																	10789928		2201	4294	6495	10746504	SO:0001583	missense	9646			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.1999C>T	11.37:g.10789928C>T	ENSP00000355013:p.Arg667Cys		10746504	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	37	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	C	32	5.184882	0.94885	.	.	ENSG00000198730	ENST00000361367	T	0.74209	-0.82	5.93	5.93	0.95920	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.86381	0.5919	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	P	0.61722	0.893	D	0.86205	0.1621	10	0.54805	T	0.06	-13.0065	20.3334	0.98727	0.0:1.0:0.0:0.0	.	667	Q6PD62	CTR9_HUMAN	C	667	ENSP00000355013:R667C	ENSP00000355013:R667C	R	+	1	0	CTR9	10746504	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.760000	0.85248	2.818000	0.97014	0.591000	0.81541	CGT		0.388	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633		T	10789928	C	T	10789928	3	4	120	1	0	0	0	0	1	0	0	0	4030	884	31	1	2061	1	CTR9	11	10789928	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	5259488	10789928	124216588	103	31684										
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40136960	40136960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gttgtgatgtaaatgtatccGctctagatgatgcaagggag	13	5	1	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:40136960G>A	ENST00000278198.2	-	2	2846	c.883C>T	c.(883-885)Cgg>Tgg	p.R295W	LRRC4C_ENST00000528697.1_Missense_Mutation_p.R295W|LRRC4C_ENST00000530763.1_Missense_Mutation_p.R295W|LRRC4C_ENST00000527150.1_Missense_Mutation_p.R295W			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	295					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)				AAATGTATCCGCTCTAGATGA	0.468																																																0			11											194	156	169					11																	40136960		2203	4300	6503	40093536	SO:0001583	missense	57689			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.883C>T	11.37:g.40136960G>A	ENSP00000278198:p.Arg295Trp		40093536	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371392	0.42003	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.75	-0.466	0.12153	.	0.000000	0.85682	D	0.000000	T	0.68384	0.2995	M	0.70595	2.14	0.58432	D	0.999997	D	0.89917	1.0	D	0.70716	0.97	T	0.73783	-0.3874	10	0.72032	D	0.01	.	16.3231	0.82958	0.0:0.0:0.2003:0.7997	.	295	Q9HCJ2	LRC4C_HUMAN	W	295	ENSP00000278198:R295W;ENSP00000436976:R295W;ENSP00000437132:R295W;ENSP00000434761:R295W	ENSP00000278198:R295W	R	-	1	2	LRRC4C	40093536	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	2.559000	0.45888	0.023000	0.15187	0.650000	0.86243	CGG		0.468	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		A	40136960	G	A	40136960	3	1	120	1	0	0	0	0	1	0	0	0	9037	1086	38	1	1043	1	LRRC4C	11	40136960	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	29347032	40136960	94869556	104	31685										
CHRM1	1128	hgsc.bcm.edu	37	chr11	62678246	62678246	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agattcatgacggaggcattGctggccacatagtccagggc	13	10	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:62678246G>A	ENST00000306960.3	-	2	868	c.327C>T	c.(325-327)agC>agT	p.S109S	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	109					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	CGGAGGCATTGCTGGCCACAT	0.617																																																0			11											69	61	63					11																	62678246		2201	4298	6499	62434822	SO:0001819	synonymous_variant	1128			Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.327C>T	11.37:g.62678246G>A			62434822	Q96RH1	Silent	SNP	ENST00000306960.3	37	CCDS8040.1																																																																																				0.617	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		A	62678246	G	A	62678246	2	1	120	1	0	0	0	0	0	0	0	1	3382	1310	46	3		3	CHRM1	11	62678246	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	22541286	62678246	72328270	105	31686										
UVRAG	7405	hgsc.bcm.edu	37	chr11	75590981	75590981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agaccgtcttgatacatctgTgtcttgtttcgtggtgaaga	11	7	3	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:75590981T>C	ENST00000356136.3	+	4	570	c.329T>C	c.(328-330)gTg>gCg	p.V110A	UVRAG_ENST00000528420.1_Missense_Mutation_p.V9A	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	110	C2.				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						GATACATCTGTGTCTTGTTTC	0.433																																																0			11											277	262	267					11																	75590981		2200	4293	6493	75268629	SO:0001583	missense	7405			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.329T>C	11.37:g.75590981T>C	ENSP00000348455:p.Val110Ala		75268629	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	37	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.616580	0.46736	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000528264	T	0.45668	0.89	5.65	5.65	0.86999	C2 calcium-dependent membrane targeting (1);	0.054145	0.64402	D	0.000001	T	0.35913	0.0948	L	0.41236	1.265	0.80722	D	1	B	0.26935	0.164	B	0.26517	0.07	T	0.11251	-1.0595	10	0.28530	T	0.3	-12.7328	14.7229	0.69320	0.0:0.0:0.0:1.0	.	110	Q9P2Y5	UVRAG_HUMAN	A	110;9;9	ENSP00000348455:V110A	ENSP00000348455:V110A	V	+	2	0	UVRAG	75268629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.890000	0.69774	2.163000	0.67991	0.533000	0.62120	GTG		0.433	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		C	75590981	T	C	75590981	3	2	120	1	0	0	0	0	1	0	0	0	17148	1696	59	4	343	4	UVRAG	11	75590981	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	12912735	75590981	59415535	106	31687										
ATM	472	hgsc.bcm.edu	37	chr11	108180939	108180939	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tctggctggatttaaattatCtagaagttgccaaggtagct	10	6	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:108180939C>A	ENST00000452508.2	+	40	6004	c.5815C>A	c.(5815-5817)Cta>Ata	p.L1939I	ATM_ENST00000278616.4_Missense_Mutation_p.L1939I|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1939					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)	p.L1939V(1)		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)	TTTAAATTATCTAGAAGTTGC	0.328			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Substitution - Missense(1)	kidney(1)	11											73	76	75					11																	108180939		2201	4297	6498	107686149	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	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.5815C>A	11.37:g.108180939C>A	ENSP00000388058:p.Leu1939Ile		107686149	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128731	0.77549	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.78595	-1.19;-1.19	5.7	3.51	0.40186	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86581	0.5967	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.931	D	0.86779	0.1978	10	0.42905	T	0.14	.	13.5657	0.61817	0.0:0.8526:0.0:0.1474	.	591;1939	E9PFP9;Q13315	.;ATM_HUMAN	I	1939	ENSP00000278616:L1939I;ENSP00000388058:L1939I	ENSP00000278616:L1939I	L	+	1	2	ATM	107686149	0.976000	0.34144	0.993000	0.49108	0.812000	0.45895	2.228000	0.42981	1.419000	0.47118	-0.252000	0.11476	CTA		0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108180939	C	A	108180939	3	1	120	1	0	0	0	0	1	0	0	0	1110	912	32	2	5965	2	ATM	11	108180939	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	32589958	108180939	26825577	107	31688										
ATM	472	hgsc.bcm.edu	37	chr11	108236072	108236072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgatattgaccagagtttcaAcaaagtagctgaacgtgtct	9	7	2	4	rs144636562		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:108236072A>G	ENST00000452508.2	+	64	9197	c.9008A>G	c.(9007-9009)aAc>aGc	p.N3003S	C11orf65_ENST00000526725.1_Intron|ATM_ENST00000525178.1_3'UTR|ATM_ENST00000278616.4_Missense_Mutation_p.N3003S|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	3003				N -> D (in Ref. 1; AAC50289, 2; AAB38309/ AAB38310 and 9; AAA86520). {ECO:0000305}.	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)	CAGAGTTTCAACAAAGTAGCT	0.393			"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)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11						A	SER/ASN	0,4402		0,0,2201	118	116	117		9008	5.2	1	11	dbSNP_134	117	1,8595	1.2+/-3.3	0,1,4297	no	missense	ATM	NM_000051.3	46	0,1,6498	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging	3003/3057	108236072	1,12997	2201	4298	6499	107741282	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	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.9008A>G	11.37:g.108236072A>G	ENSP00000388058:p.Asn3003Ser		107741282	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.452755	0.84209	0.0	1.16E-4	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.02103	4.45;4.45	5.22	5.22	0.72569	Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.048039	0.85682	D	0.000000	T	0.12902	0.0313	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.00298	-1.1837	10	0.56958	D	0.05	.	15.3219	0.74129	1.0:0.0:0.0:0.0	.	3003	Q13315	ATM_HUMAN	S	3003	ENSP00000278616:N3003S;ENSP00000388058:N3003S	ENSP00000278616:N3003S	N	+	2	0	ATM	107741282	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	8.903000	0.92573	2.202000	0.70862	0.529000	0.55759	AAC		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108236072	A	G	108236072	3	3	120	1	0	0	0	0	1	0	0	0	1110	43	2	4	9254	4	ATM	11	108236072	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	55133	108236072	26770444	108	31689										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110035171	110035171	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccgtgccatgtctagaaataCggcagccaaaactgcaaacg	9	12	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:110035171C>T	ENST00000278590.3	+	6	1412	c.1361C>T	c.(1360-1362)aCg>aTg	p.T454M	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.T455M|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.T423M	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	454							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)		TCTAGAAATACGGCAGCCAAA	0.498																																																0			11											59	61	60					11																	110035171		1928	4140	6068	109540381	SO:0001583	missense	85463				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.1361C>T	11.37:g.110035171C>T	ENSP00000278590:p.Thr454Met		109540381	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.587661	0.46110	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.31769	1.48;1.48;1.49	5.85	5.85	0.93711	.	0.179430	0.50627	D	0.000117	T	0.28665	0.0710	N	0.08118	0	0.37360	D	0.911184	D;D;D	0.67145	0.99;0.996;0.996	P;P;P	0.53689	0.572;0.732;0.732	T	0.32455	-0.9906	10	0.62326	D	0.03	-19.3538	15.635	0.76944	0.0:0.8634:0.1366:0.0	.	455;454;454	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	M	454;455;423	ENSP00000278590:T454M;ENSP00000431821:T455M;ENSP00000413094:T423M	ENSP00000278590:T454M	T	+	2	0	ZC3H12C	109540381	0.998000	0.40836	0.975000	0.42487	0.407000	0.30961	3.224000	0.51238	2.771000	0.95319	0.561000	0.74099	ACG		0.498	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		T	110035171	C	T	110035171	3	4	120	1	0	0	0	0	1	0	0	0	17602	536	19	1	1383	1	ZC3H12C	11	110035171	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	1799099	110035171	24971345	109	31690										
OR6X1	390260	hgsc.bcm.edu	37	chr11	123624877	123624877	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tggtgaggtagcggtcaaaaGacatgatagtgaggatcaag	15	4	2	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:123624877G>A	ENST00000327930.2	-	1	376	c.350C>T	c.(349-351)tCt>tTt	p.S117F		NM_001005188.1	NP_001005188.1	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X, member 1	117						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)		GCGGTCAAAAGACATGATAGT	0.562																																																0			11											164	160	161					11																	123624877		2202	4299	6501	123130087	SO:0001583	missense	390260			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.350C>T	11.37:g.123624877G>A	ENSP00000333724:p.Ser117Phe		123130087	B9EGW9|Q6IFA0	Missense_Mutation	SNP	ENST00000327930.2	37	CCDS31695.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199636	0.79015	.	.	ENSG00000221931	ENST00000327930	T	0.51071	0.72	4.34	4.34	0.51931	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.73814	0.3635	H	0.95504	3.68	0.44807	D	0.997816	D	0.67145	0.996	P	0.59703	0.862	T	0.82965	-0.0195	9	0.72032	D	0.01	-9.6481	14.3878	0.66958	0.0:0.0:1.0:0.0	.	117	Q8NH79	OR6X1_HUMAN	F	117	ENSP00000333724:S117F	ENSP00000333724:S117F	S	-	2	0	OR6X1	123130087	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.253000	0.72453	2.261000	0.74972	0.650000	0.86243	TCT		0.562	OR6X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387436.1	NM_001005188		A	123624877	G	A	123624877	3	1	120	1	0	0	0	0	1	0	0	0	11243	942	33	3	590	3	OR6X1	11	123624877	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	13589706	123624877	11381639	110	31691										
OR10G4	390264	hgsc.bcm.edu	37	chr11	123886824	123886824	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cactacttctgtgacgcaccGcccatcctgaaactggcctg	8	16	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:123886824G>T	ENST00000320891.4	+	1	543	c.543G>T	c.(541-543)ccG>ccT	p.P181P		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	181			P -> S (in dbSNP:rs1893764).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P181P(2)		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)		GTGACGCACCGCCCATCCTGA	0.542																																																2	Substitution - coding silent(2)	large_intestine(1)|central_nervous_system(1)	11											203	168	180					11																	123886824		2201	4298	6499	123392034	SO:0001819	synonymous_variant	390264			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.543G>T	11.37:g.123886824G>T			123392034	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																				0.542	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		T	123886824	G	T	123886824	2	4	120	1	0	0	0	0	0	0	0	1	10932	1074	38	2		2	OR10G4	11	123886824	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	261947	123886824	11119692	111	31692										
CDON	50937	hgsc.bcm.edu	37	chr11	125888238	125888238	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tacttacgactcacaaggagCtttcggccaataggttcaac	8	11	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr11:125888238C>A	ENST00000392693.3	-	5	754	c.627G>T	c.(625-627)aaG>aaT	p.K209N	CDON_ENST00000263577.7_Missense_Mutation_p.K209N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	209					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)		TCACAAGGAGCTTTCGGCCAA	0.363																																																0			11											134	121	126					11																	125888238		2201	4299	6500	125393448	SO:0001583	missense	50937			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.627G>T	11.37:g.125888238C>A	ENSP00000376458:p.Lys209Asn		125393448	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.55|17.55	3.417679|3.417679	0.62622|0.62622	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000534661|ENST00000392693;ENST00000263577	.|T;T	.|0.70986	.|-0.52;-0.53	5.53|5.53	4.62|4.62	0.57501|0.57501	.|Immunoglobulin-like fold (1);	.|0.000000	.|0.53938	.|D	.|0.000045	D|D	0.82967|0.82967	0.5152|0.5152	M|M	0.83223|0.83223	2.63|2.63	0.33349|0.33349	D|D	0.570777|0.570777	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.85962|0.85962	0.1471|0.1471	5|10	.|0.24483	.|T	.|0.36	-25.6977|-25.6977	12.4435|12.4435	0.55637|0.55637	0.0:0.8598:0.0:0.1402|0.0:0.8598:0.0:0.1402	.|.	.|209;209	.|Q4KMG0;Q4KMG0-2	.|CDON_HUMAN;.	S|N	185|209	.|ENSP00000376458:K209N;ENSP00000263577:K209N	.|ENSP00000263577:K209N	A|K	-|-	1|3	0|2	CDON|CDON	125393448|125393448	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	1.043000|1.043000	0.30316|0.30316	1.469000|1.469000	0.48083|0.48083	0.491000|0.491000	0.48974|0.48974	GCT|AAG		0.363	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		A	125888238	C	A	125888238	3	1	120	1	0	0	0	0	1	0	0	0	3176	796	28	2	3231	2	CDON	11	125888238	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	2001414	125888238	9118278	112	31693										
FGF23	8074	hgsc.bcm.edu	37	chr12	4481831	4481831	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cacacctgtaatcaccacaaAgccagcatcctctgatctga	5	15	3	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:4481831A>C	ENST00000237837.1	-	2	389	c.244T>G	c.(244-246)Ttt>Gtt	p.F82V		NM_020638.2	NP_065689.1	Q9GZV9	FGF23_HUMAN	fibroblast growth factor 23	82					cell differentiation (GO:0030154)|cellular phosphate ion homeostasis (GO:0030643)|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 bone mineralization (GO:0030502)|negative regulation of hormone secretion (GO:0046888)|negative regulation of osteoblast differentiation (GO:0045668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphate ion homeostasis (GO:0055062)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of phosphate transport (GO:0010966)|vitamin D catabolic process (GO:0042369)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	22			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)|STAD - Stomach adenocarcinoma(119;0.206)			ATCACCACAAAGCCAGCATCC	0.458																																																0			12											159	138	145					12																	4481831		2203	4300	6503	4352092	SO:0001583	missense	8074			AF263537	CCDS8526.1	12p13	2008-07-04			ENSG00000118972	ENSG00000118972			3680	protein-coding gene	gene with protein product		605380				11032749, 18310961	Standard	NM_020638		Approved		uc001qmq.1	Q9GZV9	OTTHUMG00000168241	ENST00000237837.1:c.244T>G	12.37:g.4481831A>C	ENSP00000237837:p.Phe82Val		4352092	Q4V758	Missense_Mutation	SNP	ENST00000237837.1	37	CCDS8526.1	.	.	.	.	.	.	.	.	.	.	A	7.504	0.653236	0.14580	.	.	ENSG00000118972	ENST00000237837	D	0.84298	-1.83	4.75	3.59	0.41128	.	0.336301	0.36167	N	0.002755	T	0.51635	0.1686	N	0.00493	-1.44	0.09310	N	0.999996	B	0.26120	0.142	B	0.24394	0.053	T	0.55062	-0.8199	10	0.02654	T	1	-16.9928	7.9433	0.29971	0.8309:0.0:0.1691:0.0	.	82	Q9GZV9	FGF23_HUMAN	V	82	ENSP00000237837:F82V	ENSP00000237837:F82V	F	-	1	0	FGF23	4352092	0.995000	0.38212	0.997000	0.53966	0.994000	0.84299	3.494000	0.53273	1.994000	0.58287	0.448000	0.29417	TTT		0.458	FGF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398936.1			C	4481831	A	C	4481831	3	2	120	1	0	0	0	0	1	0	0	0	5871	72	3	4	519	4	FGF23	12	4481831	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10		4481831	129370064	113	31694										
VWF	7450	hgsc.bcm.edu	37	chr12	6128300	6128300	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttctcaggggcctgcttctcGatgaggcggatctgcttgag	14	10	3	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:6128300G>A	ENST00000261405.5	-	28	4538	c.4284C>T	c.(4282-4284)atC>atT	p.I1428I		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1428	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)	CCTGCTTCTCGATGAGGCGGA	0.577																																																0			12											76	76	76					12																	6128300		2203	4300	6503	5998561	SO:0001819	synonymous_variant	7450				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.4284C>T	12.37:g.6128300G>A			5998561	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.577	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6128300	G	A	6128300	2	1	120	1	0	0	0	0	0	0	0	1	17286	1048	37	1		1	VWF	12	6128300	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	1646469	6128300	127723595	114	31695										
CLEC2B	9976	hgsc.bcm.edu	37	chr12	10010127	10010127	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcatgttgagtggaacagttGtatttacttgaattccaatc	9	6	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:10010127G>T	ENST00000228438.2	-	3	1116	c.183C>A	c.(181-183)taC>taA	p.Y61*	CLEC2B_ENST00000538152.1_5'Flank	NM_005127.2	NP_005118.2	Q92478	CLC2B_HUMAN	C-type lectin domain family 2, member B	61	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						TGGAACAGTTGTATTTACTTG	0.338																																																0			12											90	85	87					12																	10010127		2202	4297	6499	9901394	SO:0001587	stop_gained	51266			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.183C>A	12.37:g.10010127G>T	ENSP00000228438:p.Tyr61*		9901394	B2R9U1|Q8IZE9|Q9BS74|Q9UQB4	Nonsense_Mutation	SNP	ENST00000228438.2	37	CCDS8605.1	.	.	.	.	.	.	.	.	.	.	G	39	7.288455	0.98189	.	.	ENSG00000110852	ENST00000228438	.	.	.	2.79	-2.88	0.05682	.	2.271790	0.02440	N	0.084424	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	0.5183	0.00608	0.3671:0.1775:0.2752:0.1802	.	.	.	.	X	61	.	ENSP00000228438:Y61X	Y	-	3	2	CLEC2B	9901394	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.052000	0.11865	-0.778000	0.04566	0.591000	0.81541	TAC		0.338	CLEC2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399881.1	NM_005127		T	10010127	G	T	10010127	4	4	120	1	0	0	0	0	0	1	0	0	3513	1372	48	2	278	2	CLEC2B	12	10010127	Nonsense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	3881827	10010127	123841768	115	31696										
C12orf39	80763	hgsc.bcm.edu	37	chr12	21681996	21681996	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcagcaaccatcttactggcGtcccttcagaaatcaccaga	7	14	3	2	rs547568893		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:21681996G>A	ENST00000256969.2	+	5	436	c.270G>A	c.(268-270)gcG>gcA	p.A90A	C12orf39_ENST00000543800.1_3'UTR	NM_030572.2	NP_085049.1	Q9BT56	SPXN_HUMAN		90					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						TCTTACTGGCGTCCCTTCAGA	0.438													G|||	1	0.000199681	0	0.0014	5008	,	,		18861	0		0	False		,,,				2504	0															0			12											152	150	150					12																	21681996		2203	4300	6503	21573263	SO:0001819	synonymous_variant	80763																														ENST00000256969.2:c.270G>A	12.37:g.21681996G>A			21573263	B3KND6	Silent	SNP	ENST00000256969.2	37	CCDS31757.1																																																																																				0.438	C12orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402389.1			A	21681996	G	A	21681996	2	1	120	1	0	0	0	0	0	0	0	1	1688	1132	40	1		1	C12orf39	12	21681996	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	11671869	21681996	112169899	116	31697										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43777717	43777717	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	catttcttcaaccacctgacCaacacctttcagtctgcagt	4	15	4	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:43777717C>A	ENST00000389420.3	-	30	4515	c.4516G>T	c.(4516-4518)Ggt>Tgt	p.G1506C		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1506	TSP type-1 12. {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)		ACCACCTGACCAACACCTTTC	0.493																																																0			12											130	103	112					12																	43777717		2203	4300	6503	42063984	SO:0001583	missense	80070			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.4516G>T	12.37:g.43777717C>A	ENSP00000374071:p.Gly1506Cys		42063984	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809801	0.90707	.	.	ENSG00000173157	ENST00000389420	T	0.56444	0.46	4.25	4.25	0.50352	.	0.123269	0.36268	N	0.002682	T	0.79275	0.4418	M	0.93808	3.46	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.85196	0.1012	10	0.66056	D	0.02	.	17.9573	0.89073	0.0:1.0:0.0:0.0	.	1506	P59510	ATS20_HUMAN	C	1506	ENSP00000374071:G1506C	ENSP00000374071:G1506C	G	-	1	0	ADAMTS20	42063984	0.997000	0.39634	0.206000	0.23566	0.745000	0.42441	6.073000	0.71245	2.650000	0.89964	0.655000	0.94253	GGT		0.493	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		A	43777717	C	A	43777717	3	1	120	1	0	0	0	0	1	0	0	0	266	594	21	2	1255	2	ADAMTS20	12	43777717	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	22095721	43777717	90074178	117	31698										
KRT81	3887	hgsc.bcm.edu	37	chr12	52681070	52681070	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gagggccgcctcaccctgctGctcagactgggccaccgcgg	14	17	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:52681070G>T	ENST00000327741.5	-	7	1131	c.1063C>A	c.(1063-1065)Cag>Aag	p.Q355K	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	355	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)		TCACCCTGCTGCTCAGACTGG	0.602																																																0			12											25	28	27					12																	52681070		2201	4298	6499	50967337	SO:0001583	missense	3887			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.1063C>A	12.37:g.52681070G>T	ENSP00000369349:p.Gln355Lys		50967337	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Missense_Mutation	SNP	ENST00000327741.5	37	CCDS31805.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.172818	0.57584	.	.	ENSG00000205426	ENST00000327741;ENST00000389388	D	0.88509	-2.39	5.1	3.23	0.37069	Filament (1);	0.000000	0.39834	U	0.001258	D	0.93291	0.7862	M	0.89095	3.005	0.30276	N	0.791801	P	0.48503	0.911	P	0.57244	0.816	D	0.90755	0.4660	10	0.87932	D	0	.	9.9183	0.41448	0.0735:0.3824:0.5441:0.0	.	355	Q14533	KRT81_HUMAN	K	355	ENSP00000369349:Q355K	ENSP00000369349:Q355K	Q	-	1	0	KRT81	50967337	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	1.093000	0.30939	1.125000	0.41998	-0.304000	0.09214	CAG		0.602	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		T	52681070	G	T	52681070	3	4	120	1	0	0	0	0	1	0	0	0	8516	1328	46	2	466	2	KRT81	12	52681070	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	8903353	52681070	81170825	118	31699										
KRT77	374454	hgsc.bcm.edu	37	chr12	53091627	53091627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gttgaggtgttcacctgctgCagcaactcccattttgtttg	10	10	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:53091627C>T	ENST00000341809.3	-	2	625	c.597G>A	c.(595-597)ctG>ctA	p.L199L	KRT77_ENST00000537195.1_5'UTR|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	199	Coil 1A.|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						TCACCTGCTGCAGCAACTCCC	0.567																																																0			12											182	168	173					12																	53091627		2203	4300	6503	51377894	SO:0001819	synonymous_variant	374454			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.597G>A	12.37:g.53091627C>T			51377894	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																				0.567	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		T	53091627	C	T	53091627	2	4	120	1	0	0	0	0	0	0	0	1	8511	697	25	3		3	KRT77	12	53091627	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	410557	53091627	80760268	119	31700										
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57648643	57648643	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cgactcacggagttgttgagAcgaagggaggcattttgggc	16	7	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:57648643A>G	ENST00000347140.3	-	24	3234	c.2844T>C	c.(2842-2844)cgT>cgC	p.R948R	R3HDM2_ENST00000403821.2_Silent_p.R982R|RP11-123K3.4_ENST00000548184.1_Intron|R3HDM2_ENST00000441731.2_Silent_p.R643R|R3HDM2_ENST00000413953.2_Intron|R3HDM2_ENST00000358907.2_Silent_p.R948R|R3HDM2_ENST00000402412.1_Silent_p.R962R			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	948						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						AGTTGTTGAGACGAAGGGAGG	0.567																																																0			12											80	74	76					12																	57648643		2203	4300	6503	55934910	SO:0001819	synonymous_variant	22864			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.2844T>C	12.37:g.57648643A>G			55934910	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	37	CCDS8937.2																																																																																				0.567	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		G	57648643	A	G	57648643	2	3	120	1	0	0	0	0	0	0	0	1	12925	262	10	4		4	R3HDM2	12	57648643	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	4557016	57648643	76203252	120	31701										
FGD6	55785	hgsc.bcm.edu	37	chr12	95604081	95604081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agtatctacacacttttggcGtaacagacgagcagttcgtg	10	9	1	1	rs138823345	byFrequency	TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:95604081G>A	ENST00000343958.4	-	2	1202	c.979C>T	c.(979-981)Cgc>Tgc	p.R327C	FGD6_ENST00000546711.1_Missense_Mutation_p.R327C|FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.R327C	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	327					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						CACTTTTGGCGTAACAGACGA	0.408													G|||	4	0.000798722	0	0.0043	5008	,	,		19824	0		0.001	False		,,,				2504	0															0			12						G	CYS/ARG	3,4403	6.2+/-15.9	0,3,2200	121	124	123		979	5.7	0.9	12	dbSNP_134	123	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FGD6	NM_018351.3	180	0,8,6495	AA,AG,GG		0.0581,0.0681,0.0615	probably-damaging	327/1431	95604081	8,12998	2203	4300	6503	94128212	SO:0001583	missense	55785			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.979C>T	12.37:g.95604081G>A	ENSP00000344446:p.Arg327Cys		94128212	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	15.09	2.731183	0.48939	6.81E-4	5.81E-4	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.80304	-1.22;-1.33;-1.36	5.71	5.71	0.89125	.	0.000000	0.47093	D	0.000242	D	0.86410	0.5926	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88126	0.2835	10	0.87932	D	0	-6.6615	19.8647	0.96799	0.0:0.0:1.0:0.0	.	327	Q6ZV73	FGD6_HUMAN	C	327	ENSP00000344446:R327C;ENSP00000450342:R327C;ENSP00000449005:R327C	ENSP00000344446:R327C	R	-	1	0	FGD6	94128212	1.000000	0.71417	0.885000	0.34714	0.188000	0.23474	4.914000	0.63348	2.684000	0.91462	0.561000	0.74099	CGC		0.408	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		A	95604081	G	A	95604081	3	1	120	1	0	0	0	0	1	0	0	0	5856	1145	40	1	3393	1	FGD6	12	95604081	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	37955438	95604081	38247814	121	31702										
UTP20	27340	hgsc.bcm.edu	37	chr12	101759291	101759291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggaaagttcatgaaactttaCgccgaatcacagtgggatta	10	7	2	1	rs143153802	byFrequency	TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:101759291C>T	ENST00000261637.4	+	46	6187	c.6013C>T	c.(6013-6015)Cgc>Tgc	p.R2005C		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2005					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						TGAAACTTTACGCCGAATCAC	0.378													C|||	9	0.00179712	0.0068	0	5008	,	,		16849	0		0	False		,,,				2504	0															0			12						C	CYS/ARG	21,4385	28.1+/-56.4	0,21,2182	71	69	70		6013	5.9	1	12	dbSNP_134	70	0,8600		0,0,4300	no	missense	UTP20	NM_014503.2	180	0,21,6482	TT,TC,CC		0.0,0.4766,0.1615	probably-damaging	2005/2786	101759291	21,12985	2203	4300	6503	100283422	SO:0001583	missense	27340			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.6013C>T	12.37:g.101759291C>T	ENSP00000261637:p.Arg2005Cys		100283422	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	19.59	3.855545	0.71834	0.004766	0.0	ENSG00000120800	ENST00000261637	T	0.22945	1.93	5.92	5.92	0.95590	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.69824	0.966	T	0.65553	-0.6140	10	0.72032	D	0.01	-7.4616	20.3206	0.98668	0.0:1.0:0.0:0.0	.	2005	O75691	UTP20_HUMAN	C	2005	ENSP00000261637:R2005C	ENSP00000261637:R2005C	R	+	1	0	UTP20	100283422	1.000000	0.71417	0.999000	0.59377	0.225000	0.24961	4.998000	0.63927	2.809000	0.96659	0.655000	0.94253	CGC		0.378	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101759291	C	T	101759291	3	4	120	1	0	0	0	0	1	0	0	0	17139	536	19	1	6195	1	UTP20	12	101759291	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	6155210	101759291	32092604	122	31703										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123042001	123042001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttctgtggatgccagtgaacAgaccgaatggcaacaacttg	11	9	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:123042001A>G	ENST00000333479.7	+	17	1520	c.1343A>G	c.(1342-1344)cAg>cGg	p.Q448R	KNTC1_ENST00000450485.2_Missense_Mutation_p.Q411R	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	448					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)				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)		GCCAGTGAACAGACCGAATGG	0.383																																																0			12											126	116	119					12																	123042001		1884	4124	6008	121607954	SO:0001583	missense	9735				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.1343A>G	12.37:g.123042001A>G	ENSP00000328236:p.Gln448Arg		121607954	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	A	8.153	0.787834	0.16258	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.22945	1.93;2.5	5.74	-1.3	0.09259	.	0.332014	0.32357	N	0.006218	T	0.18383	0.0441	L	0.51422	1.61	0.54753	D	0.999989	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.09314	-1.0680	10	0.23891	T	0.37	-0.5724	8.5362	0.33364	0.5957:0.3205:0.0838:0.0	.	411;448	E7ES84;P50748	.;KNTC1_HUMAN	R	411;448	ENSP00000397992:Q411R;ENSP00000328236:Q448R	ENSP00000328236:Q448R	Q	+	2	0	KNTC1	121607954	0.971000	0.33674	0.055000	0.19348	0.117000	0.20001	2.392000	0.44433	-0.062000	0.13088	0.460000	0.39030	CAG		0.383	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			G	123042001	A	G	123042001	3	3	120	1	0	0	0	0	1	0	0	0	8449	188	7	4	1405	4	KNTC1	12	123042001	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	21282710	123042001	10809894	123	31704										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124821682	124821682	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtgggcagtgggtggcaggtGggaatgtggcagccgggcga	23	6	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr12:124821682G>A	ENST00000405201.1	-	38	5732	c.5732C>T	c.(5731-5733)cCa>cTa	p.P1911L	NCOR2_ENST00000404621.1_Missense_Mutation_p.P1901L|NCOR2_ENST00000356219.3_Missense_Mutation_p.P1918L|NCOR2_ENST00000404121.2_Missense_Mutation_p.P1472L|NCOR2_ENST00000397355.1_Missense_Mutation_p.P1902L|NCOR2_ENST00000429285.2_Missense_Mutation_p.P1901L			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1922					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)		GGTGGCAGGTGGGAATGTGGC	0.697																																																0			12											11	15	14					12																	124821682		1932	4039	5971	123387635	SO:0001583	missense	9612			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.5732C>T	12.37:g.124821682G>A	ENSP00000384018:p.Pro1911Leu		123387635	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	g	16.10	3.027368	0.54683	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.21361	2.01;2.28;2.01;2.28;2.02;2.27	4.36	4.36	0.52297	.	0.325215	0.25598	U	0.029567	T	0.29976	0.0750	N	0.24115	0.695	0.39660	D	0.970597	D;D;P	0.69078	0.997;0.96;0.932	P;P;P	0.60789	0.879;0.737;0.573	T	0.18524	-1.0334	10	0.52906	T	0.07	-11.2733	16.894	0.86095	0.0:0.0:1.0:0.0	.	1902;1911;1922	C9J239;C9JFD3;Q9Y618	.;.;NCOR2_HUMAN	L	1911;1901;1918;1902;1910;1472;1901	ENSP00000384018:P1911L;ENSP00000384202:P1901L;ENSP00000348551:P1918L;ENSP00000380513:P1902L;ENSP00000385618:P1472L;ENSP00000400281:P1901L	ENSP00000348551:P1918L	P	-	2	0	NCOR2	123387635	.	.	0.984000	0.44739	0.903000	0.53119	.	.	1.958000	0.56883	0.556000	0.70494	CCA		0.697	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124821682	G	A	124821682	3	1	120	1	0	0	0	0	1	0	0	0	10267	1348	47	3	1852	3	NCOR2	12	124821682	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	1779681	124821682	9030213	124	31705										
SLC7A1	6541	hgsc.bcm.edu	37	chr13	30104812	30104812	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	atacaagtgaatattttgttGaccatggccgactctttcac	7	9	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr13:30104812G>A	ENST00000380752.5	-	5	953	c.567C>T	c.(565-567)gtC>gtT	p.V189V		NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	189					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	ATATTTTGTTGACCATGGCCG	0.438																																																0			13											131	126	128					13																	30104812		2203	4300	6503	29002812	SO:0001819	synonymous_variant	6541			AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"Solute carriers"	11057	protein-coding gene	gene with protein product	"ecotropic retroviral receptor", "amino acid transporter, cationic 1"	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.567C>T	13.37:g.30104812G>A			29002812	Q5JR50	Silent	SNP	ENST00000380752.5	37	CCDS9333.1																																																																																				0.438	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		A	30104812	G	A	30104812	2	1	120	1	0	0	0	0	0	0	0	1	14729	1277	45	3		3	SLC7A1	13	30104812	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10		30104812	85065066	125	31706										
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111545497	111545497	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccccatttaagatgccattgTtatagaaatggttcagatga	8	7	1	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr13:111545497T>C	ENST00000267339.2	-	4	703	c.569A>G	c.(568-570)aAc>aGc	p.N190S	ANKRD10_ENST00000375758.5_Silent_p.*221*|ANKRD10_ENST00000489973.2_5'UTR|ANKRD10-IT1_ENST00000426991.1_RNA|ANKRD10_ENST00000310847.4_Silent_p.*221*	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	190								p.N190S(1)		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)			GATGCCATTGTTATAGAAATG	0.428																																																1	Substitution - Missense(1)	central_nervous_system(1)	13											127	127	127					13																	111545497		2203	4300	6503	110343498	SO:0001583	missense	55608			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.569A>G	13.37:g.111545497T>C	ENSP00000267339:p.Asn190Ser		110343498	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	37	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	T	0.372	-0.933221	0.02359	.	.	ENSG00000088448	ENST00000267339	T	0.52754	0.65	5.67	-5.51	0.02568	Ankyrin repeat-containing domain (1);	0.950216	0.08927	N	0.873485	T	0.19846	0.0477	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27571	-1.0070	10	0.18710	T	0.47	0.0706	7.7453	0.28864	0.0:0.2932:0.4296:0.2772	.	190	Q9NXR5	ANR10_HUMAN	S	190	ENSP00000267339:N190S	ENSP00000267339:N190S	N	-	2	0	ANKRD10	110343498	0.013000	0.17824	0.000000	0.03702	0.656000	0.38851	0.431000	0.21444	-0.480000	0.06803	-0.290000	0.09829	AAC		0.428	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			C	111545497	T	C	111545497	3	2	120	1	0	0	0	0	1	0	0	0	638	1725	60	4	705	4	ANKRD10	13	111545497	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	81440685	111545497	3624381	126	31707										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23548783	23548784	+	In_Frame_Ins	INS	-	-	GAACGT													0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgttgcttgatgctgaacgaINSgaacgtgaacgtgaccttga					rs78164858|rs148403158|rs61741621|rs5807202|rs3077646	byFrequency	TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr14:23548783_23548784insGAACGT	ENST00000262710.1	-	6	2261_2262	c.1934_1935insACGTTC	c.(1933-1935)tct>tcACGTTCt	p.645_645S>SRS	ACIN1_ENST00000457657.1_In_Frame_Ins_p.605_605S>SRS|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_In_Frame_Ins_p.587_587S>SRS|ACIN1_ENST00000555053.1_In_Frame_Ins_p.645_645S>SRS	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	645	Ser-rich.				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)		ATGCTGAACGAGAACGTGAACG	0.485														1942	0.38778	0.5318	0.2637	5008	,	,		21370	0.4226		0.2664	False		,,,				2504	0.3701															0			14							,,	2635,143,113,3,1370		775,98,106,3,878,1,1,0,42,0,0,6,0,0,222					,,	-4.2	0.3		dbSNP_126	219	3073,1,288,0,4892		417,1,253,0,1985,0,0,0,0,0,0,35,0,0,1436	no	codingComplex,codingComplex,codingComplex	ACIN1	NM_014977.3,NM_001164815.1,NM_001164814.1	,,	1192,99,359,3,2863,1,1,0,42,0,0,41,0,0,1658	A1A1,A1A2,A1A3,A1A4,A1R,A2A2,A2A3,A2A4,A2R,A3A3,A3A4,A3R,A4A4,A4R,RR		40.7318,38.2036,49.976	,,	,,		5708,144,401,3,6262				22618624	SO:0001652	inframe_insertion	22985			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.1929_1934dupACGTTC	14.37:g.23548784_23548789dupGAACGT	ENSP00000262710:p.ArgSer647dup		22618623	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Ins	INS	ENST00000262710.1	37	CCDS9587.1																																																																																				0.485	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		GAACGT	23548784	-	GAACGT	23548783	7	5	120	1	0	1	1	0	0	0	0	0	142	291	11	0	2293	0	ACIN1	14	23548783	In_Frame_Ins	INS	-	TCGA-F5-6813-01A-11D-1826-10		23548783	83800757	127	31708										
MBIP	51562	hgsc.bcm.edu	37	chr14	36777342	36777342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gatgccttccaattcaaggaTtttatcctcaagttttttaa	5	8	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr14:36777342T>C	ENST00000416007.4	-	7	931	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	MBIP_ENST00000359527.7_Intron|MBIP_ENST00000318473.7_Missense_Mutation_p.I282V	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	282	Interaction with MAP3K12.|Leucine-zipper 1. {ECO:0000255}.				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)		AATTCAAGGATTTTATCCTCA	0.289																																																0			14											68	76	73					14																	36777342		2203	4290	6493	35847093	SO:0001583	missense	51562			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.844A>G	14.37:g.36777342T>C	ENSP00000399718:p.Ile282Val		35847093	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Missense_Mutation	SNP	ENST00000416007.4	37	CCDS9658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.93|16.93	3.257307|3.257307	0.59321|0.59321	.|.	.|.	ENSG00000151332|ENSG00000151332	ENST00000416007;ENST00000318473|ENST00000553977	T;T|.	0.52057|.	0.68;0.69|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67353|0.67353	0.2884|0.2884	L|L	0.52364|0.52364	1.645|1.645	0.80722|0.80722	D|D	1|1	P;P;P|.	0.46784|.	0.884;0.884;0.778|.	P;P;P|.	0.46253|.	0.509;0.509;0.472|.	T|T	0.65821|0.65821	-0.6075|-0.6075	10|5	0.72032|.	D|.	0.01|.	-17.3379|-17.3379	14.9313|14.9313	0.70916|0.70916	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	256;282;282|.	B4DE55;Q9NS73-5;Q9NS73|.	.;.;MBIP1_HUMAN|.	V|S	282|278	ENSP00000399718:I282V;ENSP00000324444:I282V|.	ENSP00000324444:I282V|.	I|N	-|-	1|2	0|0	MBIP|MBIP	35847093|35847093	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.664000|0.664000	0.39144|0.39144	5.299000|5.299000	0.65716|0.65716	1.983000|1.983000	0.57843|0.57843	0.254000|0.254000	0.18369|0.18369	ATC|AAT		0.289	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586		C	36777342	T	C	36777342	3	2	120	1	0	0	0	0	1	0	0	0	9379	1493	52	4	202	4	MBIP	14	36777342	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	13228559	36777342	70572198	128	31709										
MDGA2	161357	hgsc.bcm.edu	37	chr14	47600963	47600963	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	accatcttatcaggaatattAcatacattcctcactgaagc	4	11	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr14:47600963A>G	ENST00000399232.2	-	5	1036	c.672T>C	c.(670-672)tgT>tgC	p.C224C	MDGA2_ENST00000357362.3_5'UTR|MDGA2_ENST00000439988.3_Silent_p.C293C|MDGA2_ENST00000426342.1_5'UTR	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	224	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						CAGGAATATTACATACATTCC	0.333																																																0			14											123	111	115					14																	47600963		1863	4097	5960	46670713	SO:0001819	synonymous_variant	161357			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.672T>C	14.37:g.47600963A>G			46670713	F6W3S7|J3KPX6	Silent	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	A	10.30	1.311970	0.23821	.	.	ENSG00000139915	ENST00000554762	.	.	.	5.34	1.75	0.24633	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0329	0.24977	0.5833:0.0:0.4167:0.0	.	.	.	.	Q	27	.	.	X	-	1	0	MDGA2	46670713	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	1.675000	0.37555	0.434000	0.26340	0.477000	0.44152	TAA		0.333	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		G	47600963	A	G	47600963	2	3	120	1	0	0	0	0	0	0	0	1	9437	389	14	4		4	MDGA2	14	47600963	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	10823621	47600963	59748577	129	31710										
FRMD6	122786	hgsc.bcm.edu	37	chr14	52186866	52186866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcgggccagcgggagcagtgCgggcagcatgaaacacaagc	17	11	0	1	rs371612348		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr14:52186866C>T	ENST00000344768.5	+	11	1314	c.1118C>T	c.(1117-1119)gCg>gTg	p.A373V	FRMD6_ENST00000553556.1_Missense_Mutation_p.A15V|FRMD6_ENST00000554167.1_Missense_Mutation_p.A296V|FRMD6_ENST00000356218.4_Missense_Mutation_p.A365V|FRMD6_ENST00000395718.2_Missense_Mutation_p.A365V			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	373					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.A365V(1)		breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					GGGAGCAGTGCGGGCAGCATG	0.607																																																1	Substitution - Missense(1)	lung(1)	14						C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	66	62	64		1094,1094	5.1	0.5	14		64	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FRMD6	NM_001042481.1,NM_152330.3	64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	365/615,365/615	52186866	1,13005	2203	4300	6503	51256616	SO:0001583	missense	122786			BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1118C>T	14.37:g.52186866C>T	ENSP00000343899:p.Ala373Val		51256616	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Missense_Mutation	SNP	ENST00000344768.5	37	CCDS58318.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.574223	0.45902	0.0	1.16E-4	ENSG00000139926	ENST00000356218;ENST00000395718;ENST00000344768;ENST00000554167;ENST00000555197;ENST00000555703;ENST00000553556	T;T;T;T	0.78003	-1.14;-1.14;-0.91;-0.72	5.98	5.1	0.69264	.	0.056465	0.64402	N	0.000001	T	0.62756	0.2454	N	0.14661	0.345	0.80722	D	1	P;B;P	0.37038	0.579;0.443;0.579	B;B;B	0.33392	0.163;0.078;0.104	T	0.65907	-0.6054	10	0.46703	T	0.11	.	15.226	0.73352	0.0:0.9327:0.0:0.0673	.	296;373;365	G3V4T7;Q96NE9;Q96NE9-2	.;FRMD6_HUMAN;.	V	365;365;373;296;103;15;15	ENSP00000348550:A365V;ENSP00000379068:A365V;ENSP00000343899:A373V;ENSP00000451977:A296V	ENSP00000343899:A373V	A	+	2	0	FRMD6	51256616	0.208000	0.23494	0.510000	0.27712	0.148000	0.21650	0.918000	0.28678	1.538000	0.49270	0.591000	0.81541	GCG		0.607	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		T	52186866	C	T	52186866	3	4	120	1	0	0	0	0	1	0	0	0	6073	768	27	1	1132	1	FRMD6	14	52186866	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	4585903	52186866	55162674	130	31711										
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64886575	64886575	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggttgcaactggtcagcctgAaatggttaaaggggagtgga	16	5	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr14:64886575A>G	ENST00000545908.1	+	8	1056	c.827A>G	c.(826-828)gAa>gGa	p.E276G	MTHFD1_ENST00000216605.8_Missense_Mutation_p.E220G			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	220	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.|Substrate binding.				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)	p.E220G(1)		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)	GGTCAGCCTGAAATGGTTAAA	0.443																																					Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)											1	Substitution - Missense(1)	ovary(1)	14											123	114	117					14																	64886575		2203	4300	6503	63956328	SO:0001583	missense	4522			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.827A>G	14.37:g.64886575A>G	ENSP00000438588:p.Glu276Gly		63956328	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		.	.	.	.	.	.	.	.	.	.	A	18.14	3.558735	0.65538	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605;ENST00000555252	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	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	T	0.43612	0.1255	L	0.31065	0.9	0.80722	D	1	B;B;B	0.18610	0.029;0.029;0.006	B;B;B	0.20184	0.017;0.028;0.01	T	0.31308	-0.9948	10	0.49607	T	0.09	-26.7219	14.6068	0.68486	1.0:0.0:0.0:0.0	.	276;220;220	F5H2F4;P11586;G3V2B8	.;C1TC_HUMAN;.	G	276;220;276;200	ENSP00000438588:E276G;ENSP00000450560:E220G;ENSP00000216605:E276G;ENSP00000451309:E200G	ENSP00000216605:E220G	E	+	2	0	MTHFD1	63956328	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.339000	0.96797	2.192000	0.70111	0.528000	0.53228	GAA		0.443	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			G	64886575	A	G	64886575	3	3	120	1	0	0	0	0	1	0	0	0	9957	246	9	4	689	4	MTHFD1	14	64886575	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	12699709	64886575	42462965	131	31712										
ADCK1	57143	hgsc.bcm.edu	37	chr14	78285426	78285426	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttggaccctaatgactttggCgctgtcagggtgggcagagc	15	9	1	2	rs370327529		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr14:78285426C>T	ENST00000238561.5	+	2	204	c.105C>T	c.(103-105)ggC>ggT	p.G35G	Y_RNA_ENST00000362570.1_RNA|ADCK1_ENST00000341211.5_Silent_p.G35G	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	35						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)		ATGACTTTGGCGCTGTCAGGG	0.512																																																0			14						C	,	0,4406		0,0,2203	140	123	129		105,105	-9.6	0.9	14		129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	35/456,35/524	78285426	1,13005	2203	4300	6503	77355179	SO:0001819	synonymous_variant	57143			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.105C>T	14.37:g.78285426C>T			77355179	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																				0.512	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		T	78285426	C	T	78285426	2	4	120	1	0	0	0	0	0	0	0	1	288	755	27	1		1	ADCK1	14	78285426	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	13398851	78285426	29064114	132	31713										
TJP1	7082	hgsc.bcm.edu	37	chr15	30010973	30010973	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	acgtggaaagtaccctcgttCtgaggactcttcgggatgct	12	10	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr15:30010973C>G	ENST00000346128.6	-	21	3847	c.3373G>C	c.(3373-3375)Gaa>Caa	p.E1125Q	TJP1_ENST00000545208.2_Missense_Mutation_p.E1045Q|TJP1_ENST00000356107.6_Missense_Mutation_p.E1125Q|TJP1_ENST00000400011.2_Missense_Mutation_p.E1049Q	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1125					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)		TACCCTCGTTCTGAGGACTCT	0.527																																					Melanoma(77;681 1843 6309 6570)											0			15											183	182	182					15																	30010973		2080	4205	6285	27798265	SO:0001583	missense	7082				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.3373G>C	15.37:g.30010973C>G	ENSP00000281537:p.Glu1125Gln		27798265	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046205	0.93740	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.08634	3.07;3.07	6.06	6.06	0.98353	.	0.045285	0.85682	D	0.000000	T	0.22003	0.0530	M	0.61703	1.905	0.80722	D	1	P;P;P;P	0.51791	0.944;0.948;0.944;0.933	P;P;P;P	0.53185	0.528;0.72;0.663;0.623	T	0.00023	-1.2329	10	0.35671	T	0.21	.	20.6282	0.99521	0.0:1.0:0.0:0.0	.	1118;1045;1125;1049	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	Q	1125;1049;1125;1045;1045	ENSP00000281537:E1125Q;ENSP00000382890:E1049Q	ENSP00000281537:E1125Q	E	-	1	0	TJP1	27798265	1.000000	0.71417	0.987000	0.45799	0.960000	0.62799	5.235000	0.65348	2.871000	0.98454	0.655000	0.94253	GAA		0.527	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		G	30010973	C	G	30010973	3	3	120	1	0	0	0	0	1	0	0	0	15968	922	32	5	1905	5	TJP1	15	30010973	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10		30010973	72520419	133	31714										
TRIM69	140691	hgsc.bcm.edu	37	chr15	45047513	45047513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctttcaatgcaaggatgctcGgttgtctgtggggcagtcta	13	8	3	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr15:45047513G>A	ENST00000559390.1	+	3	1350	c.422G>A	c.(421-423)cGg>cAg	p.R141Q	TRIM69_ENST00000558329.1_Intron|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000338264.4_Intron|TRIM69_ENST00000329464.4_Missense_Mutation_p.R141Q|TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000560442.1_Intron			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	141	Necessary for nuclear localization. {ECO:0000250}.				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)			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)		AAGGATGCTCGGTTGTCTGTG	0.493																																					Pancreas(84;519 1450 1802 20427 34706)											0			15											72	67	69					15																	45047513		2198	4298	6496	42834805	SO:0001583	missense	140691			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.422G>A	15.37:g.45047513G>A	ENSP00000453177:p.Arg141Gln		42834805	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684451	0.47991	.	.	ENSG00000185880	ENST00000329464	T	0.37058	1.22	5.32	4.39	0.52855	.	0.165039	0.32204	N	0.006427	T	0.15652	0.0377	N	0.25380	0.74	0.29866	N	0.827226	P	0.41313	0.745	B	0.26202	0.067	T	0.08827	-1.0703	10	0.10111	T	0.7	.	7.461	0.27296	0.18:0.0:0.82:0.0	.	141	Q86WT6	TRI69_HUMAN	Q	141	ENSP00000332284:R141Q	ENSP00000332284:R141Q	R	+	2	0	TRIM69	42834805	0.799000	0.28903	0.992000	0.48379	0.964000	0.63967	2.446000	0.44908	2.648000	0.89879	0.563000	0.77884	CGG		0.493	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1			A	45047513	G	A	45047513	3	1	120	1	0	0	0	0	1	0	0	0	16582	1116	39	1	428	1	TRIM69	15	45047513	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	15036540	45047513	57483879	134	31715										
AAGAB	79719	hgsc.bcm.edu	37	chr15	67495195	67495196	+	Frame_Shift_Del	DEL	AT	AT	-													0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gatgaaaggccttcaatttcAtctctgtctcccccgattgc					rs371502228		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr15:67495195_67495196delAT	ENST00000261880.5	-	10	1015_1016	c.911_912delAT	c.(910-912)gatfs	p.D304fs	AAGAB_ENST00000561452.1_Frame_Shift_Del_p.D195fs|AAGAB_ENST00000538028.1_5'UTR|AAGAB_ENST00000542650.1_Frame_Shift_Del_p.D195fs	NM_001271885.1|NM_001271886.1|NM_024666.3	NP_001258814.1|NP_001258815.1|NP_078942.3	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin binding protein	304					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9						CTTCAATTTCATCTCTGTCTCC	0.431																																																0			15																																								65282250	SO:0001589	frameshift_variant	0			AL136715	CCDS42050.1, CCDS61679.1	15q22.33-q23	2014-02-12	2009-07-20		ENSG00000103591	ENSG00000103591			25662	protein-coding gene	gene with protein product		614888				11230166, 10477754	Standard	NM_024666		Approved	FLJ11506, p34	uc002aqk.5	Q6PD74	OTTHUMG00000172246	ENST00000261880.5:c.911_912delAT	15.37:g.67495195_67495196delAT	ENSP00000261880:p.Asp304fs		65282249	B4DG44|Q6FI86|Q7Z5X9|Q9H0P1|Q9HAK0	Frame_Shift_Del	DEL	ENST00000261880.5	37	CCDS42050.1																																																																																				0.431	AAGAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417472.1	NM_024666		-	67495196	AT	-	67495195	7	5	120	1	0	1	0	1	0	0	0	0	15	214	8	0	39	0	AAGAB	15	67495195	Frame_Shift_Del	DEL	AT	TCGA-F5-6813-01A-11D-1826-10	22447682	67495195	35036197	135	31716										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82443978	82443978	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cctttctgtgatgtcctcttCtcaaaggcctcagagcagcc	8	14	4	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr15:82443978C>T	ENST00000268206.7	-	18	2985	c.2817G>A	c.(2815-2817)gaG>gaA	p.E939E	EFTUD1_ENST00000359445.3_Silent_p.E888E	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	939					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						ATGTCCTCTTCTCAAAGGCCT	0.473																																																0			15											140	141	141					15																	82443978		2003	4177	6180	80231033	SO:0001819	synonymous_variant	79631			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.2817G>A	15.37:g.82443978C>T			80231033	A6NKY5|B7Z6I0|Q9H8Z6	Silent	SNP	ENST00000268206.7	37	CCDS42071.1																																																																																				0.473	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		T	82443978	C	T	82443978	2	4	120	1	0	0	0	0	0	0	0	1	4971	912	32	3		3	EFTUD1	15	82443978	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	14948783	82443978	20087414	136	31717										
TM2D3	80213	hgsc.bcm.edu	37	chr15	102191956	102191956	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcccggatcctttattgactGagccagcgcctgcgattgct	11	13	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr15:102191956G>C	ENST00000333202.3	-	2	117	c.112C>G	c.(112-114)Cag>Gag	p.Q38E	TM2D3_ENST00000561373.1_5'Flank|TM2D3_ENST00000559107.1_Missense_Mutation_p.Q38E|TARSL2_ENST00000559492.1_5'Flank|TM2D3_ENST00000347970.3_Intron|TM2D3_ENST00000428002.2_Intron	NM_078474.2	NP_510883.2	Q9BRN9	TM2D3_HUMAN	TM2 domain containing 3	38						integral component of membrane (GO:0016021)		p.Q38*(1)		central_nervous_system(1)|endometrium(2)|lung(6)|ovary(1)	10	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)			TTTATTGACTGAGCCAGCGCC	0.448																																																1	Substitution - Nonsense(1)	lung(1)	15											150	156	154					15																	102191956		2203	4300	6503	100009479	SO:0001583	missense	80213			AK094955	CCDS10392.1, CCDS10393.1	15q26.3	2014-02-12			ENSG00000184277	ENSG00000184277			24128	protein-coding gene	gene with protein product		610014				11278849	Standard	XM_005254980		Approved	BLP2, FLJ22604	uc002bxi.3	Q9BRN9	OTTHUMG00000149872	ENST00000333202.3:c.112C>G	15.37:g.102191956G>C	ENSP00000330433:p.Gln38Glu		100009479	B2RDK9|Q9H046|Q9H651	Missense_Mutation	SNP	ENST00000333202.3	37	CCDS10393.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420067	0.25552	.	.	ENSG00000184277	ENST00000333202	T	0.76839	-1.05	4.58	3.66	0.41972	.	0.571542	0.17637	N	0.167178	T	0.63260	0.2496	L	0.47716	1.5	0.33182	D	0.549674	B;B	0.31817	0.341;0.118	B;B	0.26770	0.058;0.073	T	0.61907	-0.6966	10	0.02654	T	1	-7.1736	9.2398	0.37489	0.1036:0.0:0.8964:0.0	.	38;38	B4DKG4;Q9BRN9	.;TM2D3_HUMAN	E	38	ENSP00000330433:Q38E	ENSP00000330433:Q38E	Q	-	1	0	TM2D3	100009479	0.706000	0.27856	0.065000	0.19835	0.419000	0.31324	1.265000	0.33027	1.248000	0.43934	-0.262000	0.10625	CAG		0.448	TM2D3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313623.1	NM_078474		C	102191956	G	C	102191956	3	2	120	1	0	0	0	0	1	0	0	0	16004	1299	45	5	651	5	TM2D3	15	102191956	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	19747978	102191956	339436	137	31718										
MEFV	4210	hgsc.bcm.edu	37	chr16	3293377	3293377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tagcaggcgggtcgggggaaCgctggacgcctggtactcat	17	10	1	0	rs104895096		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:3293377C>T	ENST00000219596.1	-	10	2149	c.2110G>A	c.(2110-2112)Gtt>Att	p.V704I	MEFV_ENST00000339854.4_Missense_Mutation_p.V524I|MEFV_ENST00000536379.1_Missense_Mutation_p.V493I|MEFV_ENST00000541159.1_3'UTR	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	704	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		V -> I (in arFMF). {ECO:0000269|PubMed:16730661}.		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						GTCGGGGGAACGCTGGACGCC	0.517																																																0			16	GRCh37	CM012154	MEFV	M	rs104895096						115	108	110					16																	3293377		2197	4300	6497	3233378	SO:0001583	missense	4210			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.2110G>A	16.37:g.3293377C>T	ENSP00000219596:p.Val704Ile		3233378	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	37	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.702155	0.00719	.	.	ENSG00000103313	ENST00000219596;ENST00000339854;ENST00000536379	T;T;T	0.69306	-0.39;-0.39;-0.39	5.06	-10.1	0.00402	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	2.267920	0.01763	N	0.030660	T	0.38374	0.1038	N	0.14661	0.345	0.09310	N	1	B	0.16603	0.018	B	0.06405	0.002	T	0.16958	-1.0385	10	0.20046	T	0.44	-32.5872	2.8611	0.05588	0.2072:0.2652:0.0676:0.46	.	704	O15553	MEFV_HUMAN	I	704;524;493	ENSP00000219596:V704I;ENSP00000339639:V524I;ENSP00000445079:V493I	ENSP00000219596:V704I	V	-	1	0	MEFV	3233378	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.010000	0.01454	-1.745000	0.01337	-0.271000	0.10264	GTT		0.517	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3293377	C	T	3293377	3	4	120	1	0	0	0	0	1	0	0	0	9489	536	19	1	239	1	MEFV	16	3293377	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10		3293377	87061376	138	31719										
MYH11	4629	hgsc.bcm.edu	37	chr16	15869986	15869986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtagtaaaagatgtggaatgTcctctcgtctctggcttggc	12	8	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:15869986T>C	ENST00000300036.5	-	8	947	c.838A>G	c.(838-840)Aca>Gca	p.T280A	MYH11_ENST00000396324.3_Missense_Mutation_p.T287A|MYH11_ENST00000576790.2_Missense_Mutation_p.T280A|MYH11_ENST00000452625.2_Missense_Mutation_p.T287A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	280	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						ATGTGGAATGTCCTCTCGTCT	0.483			T	CBFB	AML																																		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	0			16											347	310	322					16																	15869986		2197	4300	6497	15777487	SO:0001583	missense	4629			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.838A>G	16.37:g.15869986T>C	ENSP00000300036:p.Thr280Ala		15777487	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.607373	0.46527	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.91	5.91	0.95273	Myosin head, motor domain (2);	0.060749	0.64402	D	0.000003	T	0.62648	0.2445	L	0.33753	1.03	0.54753	D	0.999988	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001	B;B;B;B;B	0.12837	0.008;0.005;0.005;0.005;0.005	T	0.59220	-0.7495	10	0.56958	D	0.05	.	15.1666	0.72833	0.0:0.0:0.0:1.0	.	287;280;287;280;287	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	A	280;280;287;287;287	ENSP00000300036:T280A;ENSP00000345136:T280A;ENSP00000379616:T287A;ENSP00000407821:T287A	ENSP00000300036:T280A	T	-	1	0	MYH11	15777487	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	2.256000	0.43231	2.263000	0.75096	0.379000	0.24179	ACA		0.483	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		C	15869986	T	C	15869986	3	2	120	1	0	0	0	0	1	0	0	0	10061	1667	58	4	5251	4	MYH11	16	15869986	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	12576609	15869986	74484767	139	31720										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27509109	27509109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgactgtcttcttctgcctcCccttggggcactggaggctg	12	13	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:27509109C>T	ENST00000356183.4	-	14	2214	c.2199G>A	c.(2197-2199)ggG>ggA	p.G733G	GTF3C1_ENST00000561623.1_Silent_p.G733G	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	733					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						CTTCTGCCTCCCCTTGGGGCA	0.468																																																0			16											100	94	96					16																	27509109		2197	4300	6497	27416610	SO:0001819	synonymous_variant	2975			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.2199G>A	16.37:g.27509109C>T			27416610	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	37	CCDS32414.1																																																																																				0.468	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27509109	C	T	27509109	2	4	120	1	0	0	0	0	0	0	0	1	6893	610	22	3		3	GTF3C1	16	27509109	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	11639123	27509109	62845644	140	31721										
SPNS1	83985	hgsc.bcm.edu	37	chr16	28989308	28989308	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aatcggaagtatctcatgtgCgggggcattgccttctggtc	13	9	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:28989308C>T	ENST00000311008.11	+	3	764	c.387C>T	c.(385-387)tgC>tgT	p.C129C	RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000561868.1_Intron|SPNS1_ENST00000352260.7_Silent_p.C107C|SPNS1_ENST00000565975.1_Silent_p.C174C|SPNS1_ENST00000334536.8_Silent_p.C129C|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000323081.8_Silent_p.C56C	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	129					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						ATCTCATGTGCGGGGGCATTG	0.577											OREG0023711	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			16											240	191	207					16																	28989308		2197	4300	6497	28896809	SO:0001819	synonymous_variant	83985			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.387C>T	16.37:g.28989308C>T		806	28896809	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																				0.577	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		T	28989308	C	T	28989308	2	4	120	1	0	0	0	0	0	0	0	1	15113	776	27	1		1	SPNS1	16	28989308	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	1480199	28989308	61365445	141	31722										
MMP2	4313	hgsc.bcm.edu	37	chr16	55519570	55519570	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtactgcaagttccccttctTgttcaatggcaaggagtaca	9	10	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:55519570T>A	ENST00000219070.4	+	5	1222	c.713T>A	c.(712-714)tTg>tAg	p.L238*	MMP2_ENST00000543485.1_Nonsense_Mutation_p.L162*|MMP2_ENST00000437642.2_Nonsense_Mutation_p.L188*|MMP2_ENST00000570308.1_Nonsense_Mutation_p.L162*	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	238	Collagen-binding.|Fibronectin type-II 1. {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)	TTCCCCTTCTTGTTCAATGGC	0.542																																																0			16											154	131	139					16																	55519570		2198	4300	6498	54077071	SO:0001587	stop_gained	4313				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.713T>A	16.37:g.55519570T>A	ENSP00000219070:p.Leu238*		54077071	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Nonsense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.869640	0.91587	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	.	.	.	4.66	3.54	0.40534	.	0.311094	0.30556	N	0.009379	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	11.2718	0.49144	0.0:0.0:0.3104:0.6896	.	.	.	.	X	238;162;188	.	ENSP00000219070:L238X	L	+	2	0	MMP2	54077071	1.000000	0.71417	0.972000	0.41901	0.673000	0.39480	2.442000	0.44873	0.636000	0.30508	0.358000	0.22013	TTG		0.542	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			A	55519570	T	A	55519570	4	1	120	1	0	0	0	0	0	1	0	0	9688	1821	63	5	738	5	MMP2	16	55519570	Nonsense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	26530262	55519570	34835183	142	31723										
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55729245	55729245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccagcttcgtctctgggttcGccatcttctccatccttggt	8	15	3	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:55729245G>A	ENST00000379906.2	+	7	1333	c.1078G>A	c.(1078-1080)Gcc>Acc	p.A360T	SLC6A2_ENST00000566163.1_Missense_Mutation_p.A315T|SLC6A2_ENST00000561820.1_Missense_Mutation_p.A360T|SLC6A2_ENST00000414754.3_Missense_Mutation_p.A360T|SLC6A2_ENST00000219833.8_Missense_Mutation_p.A360T|SLC6A2_ENST00000568943.1_Missense_Mutation_p.A360T|SLC6A2_ENST00000567238.1_Missense_Mutation_p.A255T	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	360					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)	CTCTGGGTTCGCCATCTTCTC	0.577																																																0			16											185	126	146					16																	55729245		2198	4300	6498	54286746	SO:0001583	missense	6530				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.1078G>A	16.37:g.55729245G>A	ENSP00000369237:p.Ala360Thr		54286746	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051799	0.75960	.	.	ENSG00000103546	ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833	T;T;T	0.75367	-0.93;-0.93;-0.93	4.64	4.64	0.57946	.	0.049763	0.85682	D	0.000000	T	0.66528	0.2798	L	0.33753	1.03	0.58432	D	0.999999	P;P;P;P	0.37176	0.586;0.531;0.586;0.586	B;B;B;B	0.35770	0.21;0.133;0.21;0.21	T	0.72200	-0.4362	10	0.66056	D	0.02	.	17.4501	0.87589	0.0:0.0:1.0:0.0	.	360;74;255;360	Q96KH8;F5H0T4;B4DX48;P23975	.;.;.;SC6A2_HUMAN	T	360;74;360;360	ENSP00000394956:A360T;ENSP00000369237:A360T;ENSP00000219833:A360T	ENSP00000219833:A360T	A	+	1	0	SLC6A2	54286746	1.000000	0.71417	0.961000	0.40146	0.959000	0.62525	9.107000	0.94261	2.300000	0.77407	0.650000	0.86243	GCC		0.577	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			A	55729245	G	A	55729245	3	1	120	1	0	0	0	0	1	0	0	0	14720	1087	38	1	1195	1	SLC6A2	16	55729245	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	209675	55729245	34625508	143	31724										
C16orf57	79650	hgsc.bcm.edu	37	chr16	58048187	58048188	+	Frame_Shift_Ins	INS	-	-	CTGC													0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aaatttcagattcttctttaINSctgccaaccaggtaaagatt							TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:58048187_58048188insCTGC	ENST00000219281.3	+	4	571_572	c.460_461insCTGC	c.(460-462)actfs	p.-155fs	USB1_ENST00000561743.1_Frame_Shift_Ins_p.-104fs|USB1_ENST00000565662.1_3'UTR|USB1_ENST00000539737.2_Intron	NM_024598.3	NP_078874.2			U6 snRNA biogenesis 1																		ATTCTTCTTTACTGCCAACCAG	0.351																																																0			16																																								56605689	SO:0001589	frameshift_variant	79650			AK023216	CCDS10791.1, CCDS55997.1, CCDS55998.1	16q13	2014-09-17	2012-08-21	2012-08-21	ENSG00000103005	ENSG00000103005			25792	protein-coding gene	gene with protein product	"HVSL motif containing 1", "poikiloderma with neutropenia", "U six biogenesis 1", "mutated in poikiloderma with neutropenia protein 1"	613276	"chromosome 16 open reading frame 57"	C16orf57		20004881, 20503306, 22899009	Standard	NM_024598		Approved	FLJ13154, HVSL1, Mpn1	uc002emz.3	Q9BQ65	OTTHUMG00000133456	ENST00000219281.3:c.461_464dupCTGC	16.37:g.58048188_58048191dupCTGC	ENSP00000219281:p.Ala155fs		56605688		Frame_Shift_Ins	INS	ENST00000219281.3	37	CCDS10791.1																																																																																				0.351	USB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257331.3	NM_024598		CTGC	58048188	-	CTGC	58048187	7	5	120	1	0	1	1	0	0	0	0	0	1825	391	14	0	474	0	C16orf57	16	58048187	Frame_Shift_Ins	INS	-	TCGA-F5-6813-01A-11D-1826-10	2318942	58048187	32306566	144	31725										
CDH8	1006	hgsc.bcm.edu	37	chr16	61854860	61854860	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cttataatgccatcctgggcCtgggcatcagaagtgatttc	10	10	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:61854860C>T	ENST00000577390.1	-	6	1947	c.993G>A	c.(991-993)caG>caA	p.Q331Q	CDH8_ENST00000584337.1_Silent_p.Q331Q|CDH8_ENST00000577730.1_Silent_p.Q331Q|CDH8_ENST00000299345.6_Silent_p.Q331Q	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	331	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)|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)		CATCCTGGGCCTGGGCATCAG	0.383																																																0			16											143	121	129					16																	61854860		2203	4300	6503	60412361	SO:0001819	synonymous_variant	1006			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.993G>A	16.37:g.61854860C>T			60412361	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																				0.383	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61854860	C	T	61854860	2	4	120	1	0	0	0	0	0	0	0	1	3122	680	24	3		3	CDH8	16	61854860	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3806673	61854860	28499893	145	31726										
NAE1	8883	hgsc.bcm.edu	37	chr16	66842915	66842915	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tttcatccttgttaattgtaTccaaaccatattcttcagct	3	10	3	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:66842915T>C	ENST00000290810.3	-	16	1311	c.1214A>G	c.(1213-1215)gAt>gGt	p.D405G	NAE1_ENST00000394074.2_Missense_Mutation_p.D316G|NAE1_ENST00000359087.4_Missense_Mutation_p.D408G|NAE1_ENST00000379463.2_Missense_Mutation_p.D399G			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1	405					mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)	p.D405A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	GTTAATTGTATCCAAACCATA	0.308																																																1	Substitution - Missense(1)	ovary(1)	16											88	83	85					16																	66842915		2200	4300	6500	65400416	SO:0001583	missense	8883			U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"Ubiquitin-like modifier activating enzymes"	621	protein-coding gene	gene with protein product		603385	"amyloid beta precursor protein binding protein 1, 59kDa"	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.1214A>G	16.37:g.66842915T>C	ENSP00000290810:p.Asp405Gly		65400416	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Missense_Mutation	SNP	ENST00000290810.3	37	CCDS10820.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.453660	0.43531	.	.	ENSG00000159593	ENST00000359087;ENST00000290810;ENST00000379463;ENST00000394074	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.14	5.14	0.70334	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.217835	0.45361	D	0.000361	T	0.31451	0.0797	N	0.25647	0.755	0.58432	D	0.999999	B;B;B	0.13145	0.0;0.007;0.0	B;B;B	0.15870	0.001;0.014;0.0	T	0.06752	-1.0809	10	0.27785	T	0.31	-12.7033	14.6507	0.68794	0.0:0.0:0.0:1.0	.	408;405;399	A6NCK0;Q13564;A6NFN4	.;ULA1_HUMAN;.	G	408;405;399;316	ENSP00000351990:D408G;ENSP00000290810:D405G;ENSP00000368776:D399G;ENSP00000377637:D316G	ENSP00000290810:D405G	D	-	2	0	NAE1	65400416	1.000000	0.71417	0.976000	0.42696	0.882000	0.50991	5.892000	0.69790	1.938000	0.56188	0.528000	0.53228	GAT		0.308	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905		C	66842915	T	C	66842915	3	2	120	1	0	0	0	0	1	0	0	0	10169	1435	50	4	410	4	NAE1	16	66842915	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	4988055	66842915	23511838	146	31727										
WDR59	79726	hgsc.bcm.edu	37	chr16	74908248	74908248	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gacgatccccgcacagccacGtgacagatggcacactggaa	11	14	0	2	rs372404261		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:74908248G>A	ENST00000262144.6	-	26	2914	c.2784C>T	c.(2782-2784)caC>caT	p.H928H		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	928										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						GCACAGCCACGTGACAGATGG	0.607																																																0			16						G		0,4396		0,0,2198	77	60	66		2784	0.7	1	16		66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WDR59	NM_030581.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		928/975	74908248	1,12995	2198	4300	6498	73465749	SO:0001819	synonymous_variant	79726			AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"WD repeat domain containing"	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.2784C>T	16.37:g.74908248G>A			73465749	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	37	CCDS32488.1																																																																																				0.607	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		A	74908248	G	A	74908248	2	1	120	1	0	0	0	0	0	0	0	1	17348	1136	40	1		1	WDR59	16	74908248	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	8065333	74908248	15446505	147	31728										
GAN	8139	hgsc.bcm.edu	37	chr16	81385237	81385237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	atgatggatcaacttataagAttgaacttgaagggatatcg	10	4	1	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr16:81385237A>G	ENST00000568107.2	+	2	379	c.217A>G	c.(217-219)Att>Gtt	p.I73V		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	73	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)				AACTTATAAGATTGAACTTGA	0.343																																					GBM(106;1239 1507 7582 9741 33976)											0			16											121	113	116					16																	81385237		2202	4300	6502	79942738	SO:0001583	missense	8139			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.217A>G	16.37:g.81385237A>G	ENSP00000476795:p.Ile73Val		79942738		Missense_Mutation	SNP	ENST00000568107.2	37	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.294312	0.40594	.	.	ENSG00000127688	ENST00000248272	T	0.69806	-0.43	5.88	5.88	0.94601	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.56934	0.2019	N	0.25426	0.745	0.80722	D	1	P	0.35575	0.51	B	0.42625	0.393	T	0.54337	-0.8309	10	0.02654	T	1	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	73	Q9H2C0	GAN_HUMAN	V	73	ENSP00000248272:I73V	ENSP00000248272:I73V	I	+	1	0	GAN	79942738	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.246000	0.74042	0.533000	0.62120	ATT		0.343	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			G	81385237	A	G	81385237	3	3	120	1	0	0	0	0	1	0	0	0	6252	333	12	4	223	4	GAN	16	81385237	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	6476989	81385237	8969516	148	31729										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3935538	3935538	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tccatataaacgcagcgggtTcccacacagaggacctagaa	9	12	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:3935538T>C	ENST00000381638.2	-	42	6898	c.6774A>G	c.(6772-6774)ggA>ggG	p.G2258G		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2258							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						CGCAGCGGGTTCCCACACAGA	0.443																																																0			17											88	85	86					17																	3935538		2203	4300	6503	3882287	SO:0001819	synonymous_variant	23140			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.6774A>G	17.37:g.3935538T>C			3882287	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																				0.443	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		C	3935538	T	C	3935538	2	2	120	1	0	0	0	0	0	0	0	1	18294	1770	62	4		4	ZZEF1	17	3935538	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10		3935538	77259672	149	31730										
TP53	7157	hgsc.bcm.edu	37	chr17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agcgctcatggtgggggcagCgcctcacaacctccgtcatg	13	14	3	0	rs28934578		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR	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	175	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 LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and 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).		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.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(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)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	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)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50	50	50					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	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.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His		7519131	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	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578406	C	T	7578406	3	4	120	1	0	0	0	0	1	0	0	0	16421	768	27	1	774	1	TP53	17	7578406	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3642868	7578406	73616804	150	31731										
MYH2	4620	hgsc.bcm.edu	37	chr17	10436604	10436604	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	taaacatattttttatacctTctctccaccatcctctggta	2	12	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:10436604T>C	ENST00000245503.5	-	21	2823	c.2439A>G	c.(2437-2439)agA>agG	p.R813R	MYH2_ENST00000532183.2_Intron|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000397183.2_Silent_p.R813R	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	813	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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						TTTTATACCTTCTCTCCACCA	0.428																																																0			17											83	84	83					17																	10436604		2203	4300	6503	10377329	SO:0001819	synonymous_variant	4620				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.2439A>G	17.37:g.10436604T>C			10377329	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																				0.428	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		C	10436604	T	C	10436604	2	2	120	1	0	0	0	0	0	0	0	1	10065	1780	62	4		4	MYH2	17	10436604	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	2858198	10436604	70758606	151	31732										
NF1	4763	hgsc.bcm.edu	37	chr17	29486045	29486045	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tagagaatatttggagaagcTgctgaaaaaaatttatatct	8	3	1	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:29486045T>C	ENST00000358273.4	+	3	605	c.222T>C	c.(220-222)gcT>gcC	p.A74A	NF1_ENST00000431387.4_Silent_p.A74A|NF1_ENST00000356175.3_Silent_p.A74A	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	74			A -> D (in mismatch repair deficient cancer cells; dbSNP:rs199474726). {ECO:0000269|PubMed:12522551}.		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)		TTGGAGAAGCTGCTGAAAAAA	0.328			"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)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	17											58	64	62					17																	29486045		2202	4299	6501	26510171	SO:0001819	synonymous_variant	4763	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.222T>C	17.37:g.29486045T>C			26510171	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.328	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29486045	T	C	29486045	2	2	120	1	0	0	0	0	0	0	0	1	10387	1567	55	4		4	NF1	17	29486045	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	19049441	29486045	51709165	152	31733										
NF1	4763	hgsc.bcm.edu	37	chr17	29684001	29684001	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctcagaggatttcctcatcaCaacagcacccacatttacgt	5	14	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:29684001C>T	ENST00000358273.4	+	53	8145	c.7762C>T	c.(7762-7764)Caa>Taa	p.Q2588*	NF1_ENST00000444181.2_Nonsense_Mutation_p.Q381*|NF1_ENST00000417592.2_3'UTR|NF1_ENST00000356175.3_Nonsense_Mutation_p.Q2567*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2588					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)|p.Q2588*(1)	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)		TTCCTCATCACAACAGCACCC	0.398			"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)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(3)|Substitution - Nonsense(1)	soft_tissue(8)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17	GRCh37	CM000820	NF1	M							195	185	188					17																	29684001		2203	4300	6503	26708127	SO:0001587	stop_gained	4763	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.7762C>T	17.37:g.29684001C>T	ENSP00000351015:p.Gln2588*		26708127	O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	35	5.468526	0.96274	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181	.	.	.	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	20.1745	0.98175	0.0:1.0:0.0:0.0	.	.	.	.	X	2588;2567;2233;381	.	ENSP00000348498:Q2567X	Q	+	1	0	NF1	26708127	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.032000	0.64140	2.941000	0.99782	0.655000	0.94253	CAA		0.398	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29684001	C	T	29684001	4	4	120	1	0	0	0	0	0	1	0	0	10387	479	17	3	8033	3	NF1	17	29684001	Nonsense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	197956	29684001	51511209	153	31734										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34072984	34072984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tccttcctggtgttggggggCgagcagggggcagccggatg	20	9	0	0	rs144024552		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:34072984C>T	ENST00000254466.6	-	6	1559	c.1532G>A	c.(1531-1533)cGc>cAc	p.R511H	GAS2L2_ENST00000587565.1_Missense_Mutation_p.R495H	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	511					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)		TGTTGGGGGGCGAGCAGGGGG	0.607													C|||	1	0.000199681	8e-04	0	5008	,	,		19127	0		0	False		,,,				2504	0															0			17						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	41	47	45		1532	-0.2	0	17	dbSNP_134	45	0,8600		0,0,4300	no	missense	GAS2L2	NM_139285.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	511/881	34072984	1,13005	2203	4300	6503	31097097	SO:0001583	missense	246176			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.1532G>A	17.37:g.34072984C>T	ENSP00000254466:p.Arg511His		31097097	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.302431	0.23736	2.27E-4	0.0	ENSG00000132139	ENST00000254466	T	0.20598	2.06	5.19	-0.158	0.13383	.	1.148570	0.06249	N	0.691803	T	0.13927	0.0337	N	0.17082	0.46	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.35251	-0.9796	10	0.36615	T	0.2	-0.0957	10.134	0.42695	0.0:0.6882:0.0:0.3118	.	511	Q8NHY3	GA2L2_HUMAN	H	511	ENSP00000254466:R511H	ENSP00000254466:R511H	R	-	2	0	GAS2L2	31097097	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.691000	0.00830	-0.109000	0.12044	-0.940000	0.02684	CGC		0.607	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		T	34072984	C	T	34072984	3	4	120	1	0	0	0	0	1	0	0	0	6267	768	27	1	1114	1	GAS2L2	17	34072984	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	4388983	34072984	47122226	154	31735										
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40823492	40823493	+	Frame_Shift_Del	DEL	CT	CT	-													0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tccgccagcgagggcaccagCtctctgccgcgcgtccggcc							TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	CT	CT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:40823492_40823493delCT	ENST00000591022.1	-	8	1547_1548	c.1160_1161delAG	c.(1159-1161)gagfs	p.E387fs	PLEKHH3_ENST00000293349.6_Frame_Shift_Del_p.E387fs|PLEKHH3_ENST00000412503.1_Frame_Shift_Del_p.E387fs|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	387	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)		AGGGCACCAGCTCTCTGCCGCG	0.668																																																0			17																																								38077019	SO:0001589	frameshift_variant	79990			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.1160_1161delAG	17.37:g.40823496_40823497delCT	ENSP00000468678:p.Glu387fs		38077018	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Frame_Shift_Del	DEL	ENST00000591022.1	37	CCDS11434.1																																																																																				0.668	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		-	40823493	CT	-	40823492	7	5	120	1	0	1	0	1	0	0	0	0	12109	796	28	0	1244	0	PLEKHH3	17	40823492	Frame_Shift_Del	DEL	CT	TCGA-F5-6813-01A-11D-1826-10	6750508	40823492	40371718	155	31736										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45368326	45368326	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccctttctgctcagaaaatcCgttctaaagtagagctggaa	8	10	3	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:45368326C>G	ENST00000559488.1	+	9	1148	c.1132C>G	c.(1132-1134)Cgt>Ggt	p.R378G	ITGB3_ENST00000560629.1_Missense_Mutation_p.P366R|ITGB3_ENST00000571680.1_Missense_Mutation_p.R378G|ITGB3_ENST00000435993.2_Missense_Mutation_p.R331G	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	378					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)	p.R378C(2)|p.R331C(1)		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)	TCAGAAAATCCGTTCTAAAGT	0.488																																																3	Substitution - Missense(3)	endometrium(2)|central_nervous_system(1)	17											130	119	123					17																	45368326		2203	4300	6503	42723325	SO:0001583	missense	3690				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.1132C>G	17.37:g.45368326C>G	ENSP00000452786:p.Arg378Gly		42723325	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.673586	0.67928	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.97772	-4.53	5.48	5.48	0.80851	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.98909	0.9630	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.983	D	0.99751	1.1018	10	0.72032	D	0.01	.	18.1076	0.89525	0.0:1.0:0.0:0.0	.	378;378	P05106;Q2YFE1	ITB3_HUMAN;.	G	378;331	ENSP00000407801:R331G	ENSP00000262017:R378G	R	+	1	0	C17orf57	42723325	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	7.783000	0.85696	2.566000	0.86566	0.455000	0.32223	CGT		0.488	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		G	45368326	C	G	45368326	3	3	120	1	0	0	0	0	1	0	0	0	7916	652	23	5	1166	5	ITGB3	17	45368326	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	4544834	45368326	35826884	156	31737										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901682	51901682	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccaggagccatgcagtgttcCagatcatcctgaagtcagga	11	11	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:51901682C>T	ENST00000268919.4	+	1	1444	c.1288C>T	c.(1288-1290)Cag>Tag	p.Q430*		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	430	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						TGCAGTGTTCCAGATCATCCT	0.507																																																0			17											81	65	70					17																	51901682		2203	4300	6503	49256681	SO:0001587	stop_gained	84643			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.1288C>T	17.37:g.51901682C>T	ENSP00000268919:p.Gln430*		49256681	Q96MA2|Q9BXG6	Nonsense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933291	0.92458	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	.	.	.	5.73	5.73	0.89815	.	0.000000	0.42682	D	0.000678	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.2577	0.93952	0.0:1.0:0.0:0.0	.	.	.	.	X	430;318	.	ENSP00000268919:Q430X	Q	+	1	0	KIF2B	49256681	1.000000	0.71417	1.000000	0.80357	0.084000	0.17831	7.675000	0.84002	2.854000	0.98071	0.655000	0.94253	CAG		0.507	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901682	C	T	51901682	4	4	120	1	0	0	0	0	0	1	0	0	8319	595	21	3	1290	3	KIF2B	17	51901682	Nonsense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	6533356	51901682	29293528	157	31738										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59761141	59761141	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cagaacagagcggatgttcaGaatgattttttctagtaagg	11	5	2	4			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:59761141G>C	ENST00000259008.2	-	20	3533	c.3266C>G	c.(3265-3267)tCt>tGt	p.S1089C		NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	1089					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						CGGATGTTCAGAATGATTTTT	0.368			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																														yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	0			17											152	154	153					17																	59761141		2203	4300	6503	57115923	SO:0001583	missense	83990			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.3266C>G	17.37:g.59761141G>C	ENSP00000259008:p.Ser1089Cys		57115923	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	G	4.624	0.115900	0.08831	.	.	ENSG00000136492	ENST00000259008	T	0.75938	-0.98	5.23	4.25	0.50352	.	1.396920	0.04580	N	0.394787	T	0.60287	0.2257	N	0.14661	0.345	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.45804	-0.9236	9	.	.	.	0.0804	9.287	0.37764	0.0:0.1574:0.6798:0.1629	.	1089	Q9BX63	FANCJ_HUMAN	C	1089	ENSP00000259008:S1089C	.	S	-	2	0	BRIP1	57115923	0.015000	0.18098	0.004000	0.12327	0.006000	0.05464	0.937000	0.28951	1.307000	0.44944	0.557000	0.71058	TCT		0.368	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		C	59761141	G	C	59761141	3	2	120	1	0	0	0	0	1	0	0	0	1517	942	33	5	487	5	BRIP1	17	59761141	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	7859459	59761141	21434069	158	31739										
ACE	1636	hgsc.bcm.edu	37	chr17	61574287	61574287	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gctggactggctccgcacggAgaacgagctgcatggggaga	17	10	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:61574287A>C	ENST00000290866.4	+	24	3656	c.3632A>C	c.(3631-3633)gAg>gCg	p.E1211A	ACE_ENST00000490216.2_Missense_Mutation_p.E637A|ACE_ENST00000421982.2_Missense_Mutation_p.E416A|ACE_ENST00000577647.1_Missense_Mutation_p.E637A|ACE_ENST00000413513.3_Missense_Mutation_p.E596A|ACE_ENST00000428043.1_Intron|ACE_ENST00000290863.6_Missense_Mutation_p.E637A	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1211	Peptidase M2 2.				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)	CTCCGCACGGAGAACGAGCTG	0.652																																																0			17											29	30	30					17																	61574287		2203	4298	6501	58928019	SO:0001583	missense	1636			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.3632A>C	17.37:g.61574287A>C	ENSP00000290866:p.Glu1211Ala		58928019	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	a	10.56	1.384597	0.25031	.	.	ENSG00000159640	ENST00000290866;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T	0.36520	1.25;1.25;1.32;1.32	4.86	4.86	0.63082	.	0.106337	0.64402	D	0.000008	T	0.54581	0.1867	M	0.71581	2.175	0.58432	D	0.999992	D;P;P;D	0.58970	0.97;0.645;0.844;0.984	P;P;B;P	0.58721	0.844;0.542;0.3;0.787	T	0.60796	-0.7192	10	0.87932	D	0	-27.5646	14.4689	0.67501	1.0:0.0:0.0:0.0	.	416;596;637;1211	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	A	1211;637;596;416	ENSP00000290866:E1211A;ENSP00000290863:E637A;ENSP00000392247:E596A;ENSP00000387760:E416A	ENSP00000290863:E637A	E	+	2	0	ACE	58928019	1.000000	0.71417	0.776000	0.31678	0.007000	0.05969	7.337000	0.79256	1.819000	0.53055	0.370000	0.22315	GAG		0.652	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			C	61574287	A	C	61574287	3	2	120	1	0	0	0	0	1	0	0	0	136	304	11	4	3929	4	ACE	17	61574287	Missense_Mutation	SNP	A	TCGA-F5-6813-01A-11D-1826-10	1813146	61574287	19620923	159	31740										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67079028	67079028	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tctcacctttcctgccctgcAgcctgtgggaaaagcttcag	9	14	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:67079028A>G	ENST00000284425.2	-	36	4776	c.4602T>C	c.(4600-4602)gcT>gcC	p.A1534A	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1534					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)					CCTGCCCTGCAGCCTGTGGGA	0.433																																																0			17											202	205	204					17																	67079028		2203	4300	6503	64590623	SO:0001819	synonymous_variant	23460			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.4602T>C	17.37:g.67079028A>G			64590623	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																				0.433	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		G	67079028	A	G	67079028	2	3	120	1	0	0	0	0	0	0	0	1	36	175	7	4		4	ABCA6	17	67079028	Silent	SNP	A	TCGA-F5-6813-01A-11D-1826-10	5504741	67079028	14116182	160	31741										
SLC39A11	201266	hgsc.bcm.edu	37	chr17	71027797	71027797	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcaccgaagcccccagaggaCgtggccatctcaactgctgg	12	15	1	1	rs34317750	byFrequency	TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr17:71027797C>T	ENST00000542342.2	-	4	292	c.204G>A	c.(202-204)acG>acA	p.T68T	SLC39A11_ENST00000579732.1_Silent_p.T68T|SLC39A11_ENST00000255559.3_Silent_p.T68T	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	68					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						CCCCAGAGGACGTGGCCATCT	0.532																																					NSCLC(95;736 1527 12296 39625 41839)											0			17											122	109	113					17																	71027797		2203	4300	6503	68539392	SO:0001819	synonymous_variant	201266			AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"Solute carriers"	14463	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 26"	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.204G>A	17.37:g.71027797C>T			68539392	B2R8H7|Q8WZ81	Silent	SNP	ENST00000542342.2	37	CCDS54160.1																																																																																				0.532	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1			T	71027797	C	T	71027797	2	4	120	1	0	0	0	0	0	0	0	1	14651	523	19	1		1	SLC39A11	17	71027797	Silent	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3948769	71027797	10167413	161	31742										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22807394	22807394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cggtgtggagttttatgtggCgatctcggctgcgcttgtgt	16	7	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr18:22807394C>T	ENST00000361524.3	-	4	636	c.488G>A	c.(487-489)cGc>cAc	p.R163H	ZNF521_ENST00000584787.1_5'UTR|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.R163H	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	163					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)					TTTTATGTGGCGATCTCGGCT	0.483			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0			18											134	123	127					18																	22807394		2203	4300	6503	21061392	SO:0001583	missense	25925			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.488G>A	18.37:g.22807394C>T	ENSP00000354794:p.Arg163His		21061392	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.252790	0.39797	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.26810	1.71;1.71	5.98	5.98	0.97165	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	0.49762	0.1576	L	0.53249	1.67	0.46458	D	0.999057	D	0.89917	1.0	D	0.97110	1.0	T	0.22417	-1.0217	10	0.45353	T	0.12	-38.6733	20.4434	0.99119	0.0:1.0:0.0:0.0	.	163	Q96K83	ZN521_HUMAN	H	163;197;163	ENSP00000354794:R163H;ENSP00000382352:R163H	ENSP00000354794:R163H	R	-	2	0	ZNF521	21061392	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	7.487000	0.81328	2.838000	0.97847	0.655000	0.94253	CGC		0.483	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22807394	C	T	22807394	3	4	120	1	0	0	0	0	1	0	0	0	18004	768	27	1	3467	1	ZNF521	18	22807394	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10		22807394	55269854	162	31743										
CDH2	1000	hgsc.bcm.edu	37	chr18	25563001	25563001	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aaaagttgtttggcctggcgTtctttatcccggcgtttcat	10	9	2	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr18:25563001T>C	ENST00000269141.3	-	14	2679	c.2256A>G	c.(2254-2256)gaA>gaG	p.E752E	CDH2_ENST00000399380.3_Silent_p.E721E	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	752					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						TGGCCTGGCGTTCTTTATCCC	0.368																																																0			18											124	123	123					18																	25563001		2203	4300	6503	23816999	SO:0001819	synonymous_variant	1000			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.2256A>G	18.37:g.25563001T>C			23816999	A8MWK3|B0YIY6|Q14923|Q8N173	Silent	SNP	ENST00000269141.3	37	CCDS11891.1																																																																																				0.368	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		C	25563001	T	C	25563001	2	2	120	1	0	0	0	0	0	0	0	1	3111	1722	60	4		4	CDH2	18	25563001	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	2755607	25563001	52514247	163	31744										
ACAA2	10449	hgsc.bcm.edu	37	chr18	47311574	47311574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ttctagcaaataccttaattCgtgaaccaggtgtgcagtaa	8	8	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr18:47311574C>T	ENST00000285093.10	-	9	1577	c.1102G>A	c.(1102-1104)Gaa>Aaa	p.E368K	ACAA2_ENST00000589432.1_Missense_Mutation_p.E313K|ACAA2_ENST00000587994.1_Missense_Mutation_p.E365K	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	368					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						TACCTTAATTCGTGAACCAGG	0.403																																																0			18											93	84	87					18																	47311574		2203	4300	6503	45565572	SO:0001583	missense	10449			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.1102G>A	18.37:g.47311574C>T	ENSP00000285093:p.Glu368Lys		45565572	Q9BUT6	Missense_Mutation	SNP	ENST00000285093.10	37	CCDS11939.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.013385	0.93346	.	.	ENSG00000167315	ENST00000285093	D	0.83506	-1.73	5.6	5.6	0.85130	Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90960	0.7158	M	0.94142	3.5	0.80722	D	1	B;P	0.39940	0.1;0.696	B;P	0.45343	0.131;0.477	D	0.92657	0.6138	10	0.72032	D	0.01	-36.356	19.6297	0.95698	0.0:1.0:0.0:0.0	.	368;368	B2RB23;P42765	.;THIM_HUMAN	K	368	ENSP00000285093:E368K	ENSP00000285093:E368K	E	-	1	0	ACAA2	45565572	1.000000	0.71417	0.993000	0.49108	0.762000	0.43233	7.506000	0.81665	2.644000	0.89710	0.655000	0.94253	GAA		0.403	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111		T	47311574	C	T	47311574	3	4	120	1	0	0	0	0	1	0	0	0	105	893	31	1	99	1	ACAA2	18	47311574	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	21748573	47311574	30765674	164	31745										
DCC	1630	hgsc.bcm.edu	37	chr18	51025778	51025778	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccatccccacagcttgtgttCgaccaactcacccactccgc	5	20	1	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr18:51025778C>T	ENST00000442544.2	+	27	4625	c.4009C>T	c.(4009-4011)Cga>Tga	p.R1337*	DCC_ENST00000581580.1_Nonsense_Mutation_p.R970*|RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1337					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)		AGCTTGTGTTCGACCAACTCA	0.532																																																0			18											239	182	201					18																	51025778		2203	4300	6503	49279776	SO:0001587	stop_gained	1630			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.4009C>T	18.37:g.51025778C>T	ENSP00000389140:p.Arg1337*		49279776		Nonsense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	45	11.757825	0.99599	.	.	ENSG00000187323	ENST00000442544	.	.	.	6.17	5.28	0.74379	.	0.090025	0.43919	D	0.000517	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1816	15.6428	0.77020	0.1385:0.8615:0.0:0.0	.	.	.	.	X	1337	.	ENSP00000389140:R1337X	R	+	1	2	DCC	49279776	0.996000	0.38824	0.998000	0.56505	0.972000	0.66771	3.546000	0.53656	1.561000	0.49584	0.655000	0.94253	CGA		0.532	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	51025778	C	T	51025778	4	4	120	1	0	0	0	0	0	1	0	0	4288	876	31	1	4115	1	DCC	18	51025778	Nonsense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	3714204	51025778	27051470	165	31746										
STARD6	147323	hgsc.bcm.edu	37	chr18	51851242	51851242	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	actagtttggaatatgctggGtttctgtaagcaaaagaaga	11	4	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr18:51851242G>T	ENST00000581310.1	-	9	856	c.483C>A	c.(481-483)aaC>aaA	p.N161K	STARD6_ENST00000307844.3_Missense_Mutation_p.N161K|STARD6_ENST00000580990.2_Missense_Mutation_p.N37K			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	161	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)		AATATGCTGGGTTTCTGTAAG	0.328																																																0			18											80	79	80					18																	51851242		2197	4298	6495	50105240	SO:0001583	missense	147323			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.483C>A	18.37:g.51851242G>T	ENSP00000462349:p.Asn161Lys		50105240		Missense_Mutation	SNP	ENST00000581310.1	37	CCDS11955.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.376937	0.24857	.	.	ENSG00000174448	ENST00000307844	T	0.47528	0.84	5.53	1.32	0.21799	Lipid-binding START (3);START-like domain (1);	0.000000	0.64402	D	0.000001	T	0.57975	0.2090	M	0.74258	2.255	0.37388	D	0.912322	D	0.89917	1.0	D	0.91635	0.999	T	0.62364	-0.6870	10	0.09843	T	0.71	.	6.7166	0.23306	0.4457:0.0:0.5543:0.0	.	161	P59095	STAR6_HUMAN	K	161	ENSP00000310814:N161K	ENSP00000310814:N161K	N	-	3	2	STARD6	50105240	0.983000	0.35010	1.000000	0.80357	0.953000	0.61014	-0.070000	0.11523	0.164000	0.19529	0.411000	0.27672	AAC		0.328	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171		T	51851242	G	T	51851242	3	4	120	1	0	0	0	0	1	0	0	0	15300	1252	44	2	182	2	STARD6	18	51851242	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	825464	51851242	26226006	166	31747										
CCBE1	147372	hgsc.bcm.edu	37	chr18	57103325	57103325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cagctcagtgatgtcattgcGgatgtcagccagcataagta	11	9	3	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr18:57103325G>A	ENST00000439986.4	-	11	1073	c.1036C>T	c.(1036-1038)Cgc>Tgc	p.R346C	CCBE1_ENST00000398179.2_Missense_Mutation_p.R75C	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	346					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)	p.R346C(1)		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)				ATGTCATTGCGGATGTCAGCC	0.522																																					NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)											1	Substitution - Missense(1)	lung(1)	18											122	127	126					18																	57103325		2203	4300	6503	55254305	SO:0001583	missense	147372			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.1036C>T	18.37:g.57103325G>A	ENSP00000404464:p.Arg346Cys		55254305	Q6MZX5|Q86SS2|Q8TF19	Missense_Mutation	SNP	ENST00000439986.4	37	CCDS32838.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.360196	0.82353	.	.	ENSG00000183287	ENST00000439986;ENST00000398179	D;D	0.94576	-3.46;-3.46	5.79	4.87	0.63330	.	0.096988	0.64402	D	0.000002	D	0.96281	0.8787	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.999	D	0.95925	0.8934	10	0.87932	D	0	-29.0958	11.6681	0.51385	0.0:0.0:0.6816:0.3184	.	75;346;155	Q6UXH8-2;Q6UXH8;Q6UXH8-3	.;CCBE1_HUMAN;.	C	346;75	ENSP00000404464:R346C;ENSP00000381241:R75C	ENSP00000381241:R75C	R	-	1	0	CCBE1	55254305	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.175000	0.58263	2.731000	0.93534	0.650000	0.86243	CGC		0.522	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459		A	57103325	G	A	57103325	3	1	120	1	0	0	0	0	1	0	0	0	2737	1116	39	1	188	1	CCBE1	18	57103325	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	5252083	57103325	20973923	167	31748										
C3	718	hgsc.bcm.edu	37	chr19	6690729	6690729	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtctttctcgttgttgttccGtaatccaccctgagatagag	9	10	2	2	rs138900723		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr19:6690729G>A	ENST00000245907.6	-	27	3492	c.3400C>T	c.(3400-3402)Cgg>Tgg	p.R1134W		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1134					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)	TTGTTGTTCCGTAATCCACCC	0.532													G|||	1	0.000199681	0	0	5008	,	,		20290	0.001		0	False		,,,				2504	0															0			19						G	TRP/ARG	0,4406		0,0,2203	131	105	114		3400	0.4	0	19	dbSNP_134	114	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C3	NM_000064.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1134/1664	6690729	1,13005	2203	4300	6503	6641729	SO:0001583	missense	718			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.3400C>T	19.37:g.6690729G>A	ENSP00000245907:p.Arg1134Trp		6641729	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.26	1.883231	0.33255	0.0	1.16E-4	ENSG00000125730	ENST00000245907	T	0.38560	1.13	5.69	0.445	0.16597	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.918382	0.09060	N	0.854486	T	0.62307	0.2417	M	0.82323	2.585	0.09310	N	1	D	0.89917	1.0	D	0.64042	0.921	T	0.51036	-0.8756	10	0.66056	D	0.02	.	9.2829	0.37740	0.0791:0.0:0.2215:0.6994	.	1134	P01024	CO3_HUMAN	W	1134	ENSP00000245907:R1134W	ENSP00000245907:R1134W	R	-	1	2	C3	6641729	0.000000	0.05858	0.002000	0.10522	0.152000	0.21847	-0.416000	0.07097	0.101000	0.17610	0.491000	0.48974	CGG		0.532	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6690729	G	A	6690729	3	1	120	1	0	0	0	0	1	0	0	0	2210	1144	40	1	1651	1	C3	19	6690729	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		6690729	52438254	168	31749										
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8665923	8665923	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tagcgctctcggctgaccgaTcgcttcaggcctggctggcc	13	15	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr19:8665923T>C	ENST00000597188.1	-	6	969	c.699A>G	c.(697-699)cgA>cgG	p.R233R	ADAMTS10_ENST00000270328.4_Silent_p.R233R|ADAMTS10_ENST00000596709.1_5'UTR	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	233						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						GGCTGACCGATCGCTTCAGGC	0.647																																																0			19											70	62	65					19																	8665923		2203	4300	6503	8571923	SO:0001819	synonymous_variant	81794			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.699A>G	19.37:g.8665923T>C			8571923	M0QZE4	Silent	SNP	ENST00000597188.1	37	CCDS12206.1																																																																																				0.647	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		C	8665923	T	C	8665923	2	2	120	1	0	0	0	0	0	0	0	1	256	1422	50	4		4	ADAMTS10	19	8665923	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	1975194	8665923	50463060	169	31750										
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13928045	13928045	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tgcagagctgctccagaaggGctccacctgcatcaccaaca	9	15	1	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr19:13928045G>A	ENST00000254323.2	+	7	1385	c.1196G>A	c.(1195-1197)gGc>gAc	p.G399D	RN7SL619P_ENST00000581753.1_RNA|ZSWIM4_ENST00000440752.2_Missense_Mutation_p.G233D	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	399							zinc ion binding (GO:0008270)	p.G399V(1)		central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CTCCAGAAGGGCTCCACCTGC	0.627																																																1	Substitution - Missense(1)	endometrium(1)	19											79	76	77					19																	13928045		2203	4300	6503	13789045	SO:0001583	missense	65249			AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1196G>A	19.37:g.13928045G>A	ENSP00000254323:p.Gly399Asp		13789045		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.283454	0.59867	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.49720	0.77;0.99	4.79	3.68	0.42216	.	0.479287	0.17966	N	0.156015	T	0.55737	0.1939	L	0.40543	1.245	0.46564	D	0.999101	D;B	0.71674	0.998;0.185	D;B	0.71656	0.974;0.14	T	0.48768	-0.9006	10	0.30854	T	0.27	-4.7683	12.128	0.53926	0.0:0.1747:0.8252:0.0	.	233;399	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	D	399;233	ENSP00000254323:G399D;ENSP00000405278:G233D	ENSP00000254323:G399D	G	+	2	0	ZSWIM4	13789045	1.000000	0.71417	0.886000	0.34754	0.276000	0.26787	5.408000	0.66368	2.215000	0.71742	0.400000	0.26472	GGC		0.627	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		A	13928045	G	A	13928045	3	1	120	1	0	0	0	0	1	0	0	0	18282	1203	42	3	1222	3	ZSWIM4	19	13928045	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	5262122	13928045	45200938	170	31751										
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17992829	17992829	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gtagaagacctcatcaaaccTcggctgcggagcctggcacc	11	14	2	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr19:17992829T>C	ENST00000222248.3	+	9	1466	c.1119T>C	c.(1117-1119)ccT>ccC	p.P373P		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	373					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						TCATCAAACCTCGGCTGCGGA	0.602																																					Melanoma(65;1008 1708 7910 46650)											0			19											90	86	87					19																	17992829		2203	4300	6503	17853829	SO:0001819	synonymous_variant	6528				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.1119T>C	19.37:g.17992829T>C			17853829	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																				0.602	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			C	17992829	T	C	17992829	2	2	120	1	0	0	0	0	0	0	0	1	14705	1538	54	4		4	SLC5A5	19	17992829	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	4064784	17992829	41136154	171	31752										
LSR	51599	hgsc.bcm.edu	37	chr19	35758362	35758362	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cgagggacttcccacgctccCgggacccccactacgacgac	10	19	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr19:35758362C>T	ENST00000361790.3	+	9	1798	c.1639C>T	c.(1639-1641)Cgg>Tgg	p.R547W	LSR_ENST00000360798.3_Missense_Mutation_p.R479W|USF2_ENST00000595068.1_5'Flank|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000427250.1_Missense_Mutation_p.R391W|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000347609.4_Missense_Mutation_p.R489W|LSR_ENST00000354900.3_Missense_Mutation_p.R528W|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000379134.3_5'Flank|LSR_ENST00000602122.1_Missense_Mutation_p.R527W	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	547					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)			CCCACGCTCCCGGGACCCCCA	0.687																																																0			19											16	22	20					19																	35758362		2189	4278	6467	40450202	SO:0001583	missense	51599			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.1639C>T	19.37:g.35758362C>T	ENSP00000354575:p.Arg547Trp		40450202	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	37	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	C	9.893	1.204692	0.22205	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.69040	0.22;0.34;-0.04;0.09;-0.37	4.66	1.66	0.24008	.	0.590192	0.17367	N	0.176802	T	0.44540	0.1298	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.25486	0.006;0.01;0.01;0.127;0.006;0.006	B;B;B;B;B;B	0.15870	0.001;0.001;0.003;0.014;0.001;0.001	T	0.35475	-0.9787	10	0.59425	D	0.04	-4.7335	5.0201	0.14356	0.0:0.556:0.1942:0.2498	.	486;489;527;479;528;547	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	W	547;528;479;489;391	ENSP00000354575:R547W;ENSP00000346976:R528W;ENSP00000354034:R479W;ENSP00000262627:R489W;ENSP00000394479:R391W	ENSP00000262627:R489W	R	+	1	2	LSR	40450202	0.000000	0.05858	0.140000	0.22221	0.127000	0.20565	0.033000	0.13754	0.886000	0.36113	0.430000	0.28490	CGG		0.687	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		T	35758362	C	T	35758362	3	4	120	1	0	0	0	0	1	0	0	0	9093	643	23	1	1673	1	LSR	19	35758362	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	17765533	35758362	23370621	172	31753										
FPR1	2357	hgsc.bcm.edu	37	chr19	52249899	52249899	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcggtccagagcaatgagggCgatcaggaagacacttccga	14	10	1	3	rs547228145		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr19:52249899C>T	ENST00000595042.1	-	3	490	c.349G>A	c.(349-351)Gcc>Acc	p.A117T	FPR1_ENST00000304748.4_Missense_Mutation_p.A117T	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	117					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)	p.A117T(1)		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)	GCAATGAGGGCGATCAGGAAG	0.557													C|||	1	0.000199681	0	0	5008	,	,		21669	0.001		0	False		,,,				2504	0															1	Substitution - Missense(1)	kidney(1)	19											114	88	97					19																	52249899		2203	4300	6503	56941711	SO:0001583	missense	2357			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.349G>A	19.37:g.52249899C>T	ENSP00000471493:p.Ala117Thr		56941711	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	.	.	.	.	.	.	.	.	.	.	.	0.110	-1.140343	0.01728	.	.	ENSG00000171051	ENST00000304748	T	0.70986	-0.53	3.66	0.215	0.15253	GPCR, rhodopsin-like superfamily (1);	0.162995	0.40469	N	0.001099	T	0.35856	0.0946	N	0.05050	-0.12	0.27362	N	0.955931	B	0.11235	0.004	B	0.17722	0.019	T	0.27536	-1.0071	10	0.02654	T	1	.	2.8556	0.05571	0.4295:0.3723:0.0:0.1982	.	117	P21462	FPR1_HUMAN	T	117	ENSP00000302707:A117T	ENSP00000302707:A117T	A	-	1	0	FPR1	56941711	0.028000	0.19301	0.267000	0.24556	0.398000	0.30690	1.478000	0.35442	0.281000	0.22233	-0.152000	0.13540	GCC		0.557	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		T	52249899	C	T	52249899	3	4	120	1	0	0	0	0	1	0	0	0	6057	768	27	1	707	1	FPR1	19	52249899	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	16491537	52249899	6879084	173	31754										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13830868	13830868	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggatatcccggagcaaatgcGtagtttccagtttcatgacg	11	9	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr20:13830868G>A	ENST00000284951.5	-	19	1990	c.1916C>T	c.(1915-1917)aCg>aTg	p.T639M	SEL1L2_ENST00000378072.5_Missense_Mutation_p.T526M|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	639						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						GAGCAAATGCGTAGTTTCCAG	0.453																																																0			20											104	99	101					20																	13830868		1961	4156	6117	13778868	SO:0001583	missense	80343			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.1916C>T	20.37:g.13830868G>A	ENSP00000284951:p.Thr639Met		13778868	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	G	3.160	-0.172314	0.06421	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.21734	1.99;2.29	5.96	2.34	0.29019	.	0.402927	0.23714	N	0.045283	T	0.05777	0.0151	N	0.00926	-1.1	0.09310	N	0.999995	B;B	0.15473	0.013;0.001	B;B	0.04013	0.001;0.0	T	0.31420	-0.9944	10	0.33141	T	0.24	-0.0014	5.4149	0.16368	0.724:0.0:0.1472:0.1288	.	526;639	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	M	526;639	ENSP00000367312:T526M;ENSP00000284951:T639M	ENSP00000284951:T639M	T	-	2	0	SEL1L2	13778868	0.043000	0.20138	0.417000	0.26559	0.122000	0.20287	0.916000	0.28651	0.504000	0.28082	-0.247000	0.11927	ACG		0.453	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		A	13830868	G	A	13830868	3	1	120	1	0	0	0	0	1	0	0	0	14048	1145	40	1	158	1	SEL1L2	20	13830868	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		13830868	49194652	174	31755										
CST9	128822	hgsc.bcm.edu	37	chr20	23584222	23584222	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	caccccatgcagcatccacaGctgtggacctgaggaaagct	10	14	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr20:23584222G>T	ENST00000376971.3	-	2	416	c.405C>A	c.(403-405)agC>agA	p.S135R		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	135						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)					AGCATCCACAGCTGTGGACCT	0.527																																																0			20											164	132	143					20																	23584222		2203	4300	6503	23532222	SO:0001583	missense	128822			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.405C>A	20.37:g.23584222G>T	ENSP00000366170:p.Ser135Arg		23532222	B2RP76|Q8TD53	Missense_Mutation	SNP	ENST00000376971.3	37	CCDS33450.1	.	.	.	.	.	.	.	.	.	.	G	7.798	0.713033	0.15306	.	.	ENSG00000173335	ENST00000376971	D	0.94232	-3.38	2.19	0.0809	0.14422	.	0.701100	0.11723	N	0.535658	T	0.81992	0.4940	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.71307	-0.4632	10	0.72032	D	0.01	.	2.9312	0.05800	0.1941:0.299:0.5069:0.0	.	135	Q5W186	CST9_HUMAN	R	135	ENSP00000366170:S135R	ENSP00000366170:S135R	S	-	3	2	CST9	23532222	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.255000	0.08769	0.028000	0.15324	0.561000	0.74099	AGC		0.527	CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1		T	23584222	G	T	23584222	3	4	120	1	0	0	0	0	1	0	0	0	3985	962	34	2	78	2	CST9	20	23584222	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	9753354	23584222	39441298	175	31756										
C20orf177	63939	hgsc.bcm.edu	37	chr20	58519472	58519472	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcctgggacctacgagatatGgccctgcttctgaacgcaga	11	12	1	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr20:58519472G>A	ENST00000358293.3	+	5	889	c.474G>A	c.(472-474)atG>atA	p.M158I	FAM217B_ENST00000360816.3_Missense_Mutation_p.M158I|FAM217B_ENST00000469084.1_3'UTR	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	158																	TACGAGATATGGCCCTGCTTC	0.483																																																0			20											63	61	62					20																	58519472		2203	4300	6503	57952867	SO:0001583	missense	63939			AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.474G>A	20.37:g.58519472G>A	ENSP00000351040:p.Met158Ile		57952867	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	37	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261332	0.59431	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	T;T	0.26373	1.74;1.74	5.8	5.8	0.92144	.	0.139193	0.47852	D	0.000210	T	0.33498	0.0865	L	0.56769	1.78	0.30111	N	0.806589	P	0.52316	0.952	P	0.48815	0.591	T	0.40040	-0.9584	10	0.62326	D	0.03	-20.7205	11.3472	0.49567	0.0:0.1359:0.7231:0.141	.	158	Q9NTX9	CT177_HUMAN	I	158	ENSP00000351040:M158I;ENSP00000354056:M158I	ENSP00000351040:M158I	M	+	3	0	C20orf177	57952867	1.000000	0.71417	0.990000	0.47175	0.775000	0.43874	2.751000	0.47508	2.735000	0.93741	0.655000	0.94253	ATG		0.483	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		A	58519472	G	A	58519472	3	1	120	1	0	0	0	0	1	0	0	0	2102	1348	47	3	476	3	C20orf177	20	58519472	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	34935250	58519472	4506048	176	31757										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45855046	45855046	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccgcacaggactgcgtgggcGcgggagcctcagctgcttcg	16	14	1	0	rs550041022		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr21:45855046G>A	ENST00000397928.1	+	28	4452	c.4007G>A	c.(4006-4008)cGc>cAc	p.R1336H	snoZ6_ENST00000581669.1_RNA|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Missense_Mutation_p.R1282H|TRPM2_ENST00000300482.5_Missense_Mutation_p.R1336H|TRPM2_ENST00000397932.2_Missense_Mutation_p.R1386H	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1336					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)	p.R1336H(1)		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						CTGCGTGGGCGCGGGAGCCTC	0.667													G|||	1	0.000199681	8e-04	0	5008	,	,		15646	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	large_intestine(1)	21											89	82	84					21																	45855046		2203	4300	6503	44679474	SO:0001583	missense	7226			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.4007G>A	21.37:g.45855046G>A	ENSP00000381023:p.Arg1336His		44679474	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551389	0.65311	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932;ENST00000540347	T;T;T;T	0.79033	-1.23;-1.23;2.42;-1.23	4.86	4.86	0.63082	NUDIX hydrolase domain-like (1);	0.000000	0.64402	D	0.000003	D	0.88526	0.6460	M	0.91459	3.21	0.20074	N	0.999936	D;D;D;D	0.71674	0.998;0.99;0.998;0.966	D;P;P;P	0.63703	0.917;0.72;0.751;0.635	T	0.82448	-0.0452	10	0.87932	D	0	-4.4048	11.4611	0.50211	0.0897:0.0:0.9103:0.0	.	17;1386;1122;1336	B4DVI8;E9PGK7;Q5KTC1;O94759	.;.;.;TRPM2_HUMAN	H	1336;1336;1282;1386;80	ENSP00000300482:R1336H;ENSP00000381023:R1336H;ENSP00000300481:R1282H;ENSP00000381026:R1386H	ENSP00000300481:R1282H	R	+	2	0	TRPM2	44679474	0.850000	0.29656	0.224000	0.23877	0.653000	0.38743	3.901000	0.56303	2.420000	0.82092	0.543000	0.68304	CGC		0.667	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45855046	G	A	45855046	3	1	120	1	0	0	0	0	1	0	0	0	16626	1087	38	1	4117	1	TRPM2	21	45855046	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		45855046	2274849	177	31758										
EP300	2033	hgsc.bcm.edu	37	chr22	41572510	41572510	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	caagcaccatgtggagacacGctggcactgtactgtctgtg	12	11	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chr22:41572510G>A	ENST00000263253.7	+	30	6258	c.5039G>A	c.(5038-5040)cGc>cAc	p.R1680H	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	1680	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						GTGGAGACACGCTGGCACTGT	0.577			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											78	60	66					22																	41572510		2203	4300	6503	39902456	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	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.5039G>A	22.37:g.41572510G>A	ENSP00000263253:p.Arg1680His		39902456	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	G	17.22	3.335115	0.60853	.	.	ENSG00000100393	ENST00000263253	D	0.96522	-4.04	5.23	4.2	0.49525	Zinc finger, ZZ-type (4);	0.000000	0.41605	D	0.000856	D	0.98554	0.9517	H	0.95365	3.66	0.42002	D	0.990894	D	0.89917	1.0	D	0.67231	0.95	D	0.99856	1.1077	10	0.72032	D	0.01	-6.8579	15.4677	0.75416	0.0:0.0:0.8601:0.1399	.	1680	Q09472	EP300_HUMAN	H	1680	ENSP00000263253:R1680H	ENSP00000263253:R1680H	R	+	2	0	EP300	39902456	1.000000	0.71417	0.981000	0.43875	0.946000	0.59487	9.869000	0.99810	1.319000	0.45190	-0.188000	0.12872	CGC		0.577	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41572510	G	A	41572510	3	1	120	1	0	0	0	0	1	0	0	0	5161	1087	38	1	5157	1	EP300	22	41572510	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10		41572510	9732056	178	31759										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30237394	30237394	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tcctgaatatgttgggagtcTatgatggagaggagcactca	13	6	2	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:30237394T>G	ENST00000378988.4	+	2	798	c.697T>G	c.(697-699)Tat>Gat	p.Y233D		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	233	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						GTTGGGAGTCTATGATGGAGA	0.488																																																0			X											70	63	66					X																	30237394		2202	4300	6502	30147315	SO:0001583	missense	4113			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.697T>G	X.37:g.30237394T>G	ENSP00000368273:p.Tyr233Asp		30147315	O75860	Missense_Mutation	SNP	ENST00000378988.4	37	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.544357	0.45280	.	.	ENSG00000099399	ENST00000378988	T	0.04809	3.55	3.27	2.1	0.27182	.	0.382609	0.24321	N	0.039550	T	0.16428	0.0395	M	0.82132	2.575	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.04320	-1.0960	10	0.66056	D	0.02	.	4.4278	0.11513	0.0:0.1567:0.0:0.8433	.	233	O15479	MAGB2_HUMAN	D	233	ENSP00000368273:Y233D	ENSP00000368273:Y233D	Y	+	1	0	MAGEB2	30147315	0.100000	0.21855	0.031000	0.17742	0.418000	0.31294	0.620000	0.24403	0.498000	0.27948	0.356000	0.21956	TAT		0.488	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		G	30237394	T	G	30237394	3	3	120	1	0	0	0	0	1	0	0	0	9206	1522	53	4	699	4	MAGEB2	23	30237394	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10		30237394	125033166	179	31760										
PRRG1	5638	hgsc.bcm.edu	37	chrX	37312395	37312395	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tattgtattttcagaaggagTtttggagcacctacacaaaa	8	6	1	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:37312395T>C	ENST00000542554.1	+	5	450	c.178T>C	c.(178-180)Ttt>Ctt	p.F60L	PRRG1_ENST00000378628.4_Missense_Mutation_p.F60L|PRRG1_ENST00000491253.1_3'UTR|PRRG1_ENST00000449135.2_Missense_Mutation_p.F60L|TM4SF2_ENST00000465127.1_Intron|PRRG1_ENST00000543642.1_Missense_Mutation_p.F60L	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	60	Gla. {ECO:0000255|PROSITE- ProRule:PRU00463}.		F -> I (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.F60I(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						TCAGAAGGAGTTTTGGAGCAC	0.358																																																1	Substitution - Missense(1)	breast(1)	X											86	63	70					X																	37312395		2202	4300	6502	37197316	SO:0001583	missense	5638			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.178T>C	X.37:g.37312395T>C	ENSP00000444278:p.Phe60Leu		37197316	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Missense_Mutation	SNP	ENST00000542554.1	37	CCDS14239.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120047	0.77323	.	.	ENSG00000130962	ENST00000378628;ENST00000466533;ENST00000542554;ENST00000543642;ENST00000484460;ENST00000449135	D;D;D;D;D;D	0.99563	-6.17;-6.17;-6.17;-6.17;-6.17;-6.17	5.93	5.93	0.95920	Gamma-carboxyglutamic acid-rich (GLA) domain (6);Coagulation factor, subgroup, Gla domain (1);	0.000000	0.85682	D	0.000000	D	0.99658	0.9873	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97650	1.0154	10	0.87932	D	0	-11.8778	14.0516	0.64739	0.0:0.0:0.0:1.0	.	60	O14668	TMG1_HUMAN	L	60	ENSP00000367894:F60L;ENSP00000418384:F60L;ENSP00000444278:F60L;ENSP00000443271:F60L;ENSP00000420353:F60L;ENSP00000390332:F60L	ENSP00000367894:F60L	F	+	1	0	PRRG1	37197316	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.994000	0.63901	2.000000	0.58554	0.425000	0.28330	TTT		0.358	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		C	37312395	T	C	37312395	3	2	120	1	0	0	0	0	1	0	0	0	12639	1725	60	4	270	4	PRRG1	23	37312395	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	7075001	37312395	117958165	180	31761										
AKAP4	8852	hgsc.bcm.edu	37	chrX	49957693	49957693	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	tctttgcccttagtctgctgGgtcagatggtactggatcag	12	9	4	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:49957693G>A	ENST00000376056.2	-	5	1794	c.1644C>T	c.(1642-1644)acC>acT	p.T548T	AKAP4_ENST00000376058.2_Intron|AKAP4_ENST00000358526.2_Silent_p.T557T|AKAP4_ENST00000376064.3_Silent_p.T548T|AKAP4_ENST00000481402.1_5'UTR					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)					TAGTCTGCTGGGTCAGATGGT	0.468																																																0			X											149	117	128					X																	49957693		2203	4300	6503	49844433	SO:0001819	synonymous_variant	8852			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.1644C>T	X.37:g.49957693G>A			49844433		Silent	SNP	ENST00000376056.2	37	CCDS14330.1																																																																																				0.468	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		A	49957693	G	A	49957693	2	1	120	1	0	0	0	0	0	0	0	1	453	1219	43	3		3	AKAP4	23	49957693	Silent	SNP	G	TCGA-F5-6813-01A-11D-1826-10	12645298	49957693	105312867	181	31762										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	cctcctcctcctgttgcttcINStgctgctgctgttgctgctt					rs201922875|rs553160982		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				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)					cctgttgcttctgctgctgctg	0.589																																																0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			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.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup		50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		TGCTGCTGCTGT	50350759	-	TGCTGCTGCTGT	50350758	7	5	120	1	0	1	1	0	0	0	0	0	14333	912	32	0	1113	0	SHROOM4	23	50350758	In_Frame_Ins	INS	-	TCGA-F5-6813-01A-11D-1826-10	393065	50350758	104919802	182	31763										
WNK3	65267	hgsc.bcm.edu	37	chrX	54259358	54259358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	gcaaaggaatctcagtagatTgggttttgctatctttaatt	9	5	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:54259358T>C	ENST00000375159.2	-	20	4723	c.4724A>G	c.(4723-4725)cAa>cGa	p.Q1575R	WNK3_ENST00000354646.2_Missense_Mutation_p.Q1575R|WNK3_ENST00000375169.3_Missense_Mutation_p.Q1528R			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1575					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						CTCAGTAGATTGGGTTTTGCT	0.468																																																0			X											161	144	149					X																	54259358		2203	4300	6503	54276083	SO:0001583	missense	65267			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.4724A>G	X.37:g.54259358T>C	ENSP00000364301:p.Gln1575Arg		54276083	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	T	8.980	0.975101	0.18736	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.69806	-0.4;-0.43;-0.43	5.69	4.49	0.54785	.	0.261727	0.26170	N	0.025932	T	0.52613	0.1745	L	0.36672	1.1	0.18873	N	0.999985	P;B	0.35272	0.493;0.361	B;B	0.30495	0.116;0.054	T	0.41787	-0.9489	10	0.39692	T	0.17	-1.5687	10.206	0.43114	0.1512:0.0:0.0:0.8488	.	1528;1575	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	R	1528;1575;1575	ENSP00000364312:Q1528R;ENSP00000346667:Q1575R;ENSP00000364301:Q1575R	ENSP00000346667:Q1575R	Q	-	2	0	WNK3	54276083	0.155000	0.22806	0.002000	0.10522	0.644000	0.38419	1.834000	0.39171	0.730000	0.32425	0.481000	0.45027	CAA		0.468	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		C	54259358	T	C	54259358	3	2	120	1	0	0	0	0	1	0	0	0	17419	1812	63	4	694	4	WNK3	23	54259358	Missense_Mutation	SNP	T	TCGA-F5-6813-01A-11D-1826-10	3908600	54259358	101011202	183	31764										
ASB12	142689	hgsc.bcm.edu	37	chrX	63445158	63445158	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	agaggcaccagcttccaaaaGcacacgtacacagtccagat	8	13	0	2			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:63445158G>C	ENST00000396130.2	-	1	345	c.346C>G	c.(346-348)Ctt>Gtt	p.L116V	MTMR8_ENST00000453546.1_Missense_Mutation_p.L500V|ASB12_ENST00000362002.2_Missense_Mutation_p.L125V			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12	116					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.0?(2)		endometrium(2)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14						GCTTCCAAAAGCACACGTACA	0.542																																																2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	X											108	64	79					X																	63445158		2203	4300	6503	63361883	SO:0001583	missense	142689			AF403030	CCDS14378.1, CCDS14378.2	Xq11.1	2013-01-10	2011-01-25		ENSG00000198881	ENSG00000198881		"Ankyrin repeat domain containing"	19763	protein-coding gene	gene with protein product		300891	"ankyrin repeat and SOCS box-containing 12"			12076535	Standard	NM_130388		Approved	FLJ39577		Q8WXK4	OTTHUMG00000021705	ENST00000396130.2:c.346C>G	X.37:g.63445158G>C	ENSP00000379435:p.Leu116Val		63361883	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	37		.	.	.	.	.	.	.	.	.	.	G	17.01	3.278346	0.59758	.	.	ENSG00000198881;ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000396130;ENST00000361287;ENST00000453546	T;T;T	0.80480	-1.38;-1.38;-1.38	4.0	3.13	0.36017	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.92159	0.7514	H	0.97415	4	0.25038	N	0.991222	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.995	D	0.84142	0.0418	10	0.87932	D	0	-6.509	10.2576	0.43408	0.1101:0.0:0.8899:0.0	.	500;116	B4DQL0;Q8WXK4	.;ASB12_HUMAN	V	125;116;125;500	ENSP00000355195:L125V;ENSP00000379435:L116V;ENSP00000394003:L500V	ENSP00000354626:L125V	L	-	1	0	ASB12;MTMR8	63361883	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.784000	0.68990	1.986000	0.57962	0.468000	0.43344	CTT		0.542	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				C	63445158	G	C	63445158	3	2	120	1	0	0	0	0	1	0	0	0	1017	971	34	5	591	5	ASB12	23	63445158	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	9185800	63445158	91825402	184	31765										
PCDH19	57526	hgsc.bcm.edu	37	chrX	99662056	99662056	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ggatcgcagcgcgtagatgtCgcctgagttgggattgatgg	17	7	0	3			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:99662056C>T	ENST00000373034.4	-	1	3215	c.1540G>A	c.(1540-1542)Gac>Aac	p.D514N	PCDH19_ENST00000420881.2_Missense_Mutation_p.D514N|PCDH19_ENST00000255531.7_Missense_Mutation_p.D514N	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	514	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(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GCGTAGATGTCGCCTGAGTTG	0.587																																																0			X											101	101	101					X																	99662056		2171	4259	6430	99548712	SO:0001583	missense	57575			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1540G>A	X.37:g.99662056C>T	ENSP00000362125:p.Asp514Asn		99548712	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.330317	0.24167	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.54279	0.58;0.58;0.58	5.81	5.81	0.92471	Cadherin (5);Cadherin-like (1);	0.235347	0.43260	D	0.000583	T	0.45955	0.1368	N	0.12961	0.28	0.47511	D	0.999442	D;P;P	0.55800	0.973;0.928;0.942	P;B;P	0.49597	0.616;0.348;0.479	T	0.33904	-0.9850	10	0.17832	T	0.49	.	18.9952	0.92810	0.0:1.0:0.0:0.0	.	514;514;514	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	N	514	ENSP00000400327:D514N;ENSP00000362125:D514N;ENSP00000255531:D514N	ENSP00000255531:D514N	D	-	1	0	PCDH19	99548712	1.000000	0.71417	0.768000	0.31515	0.715000	0.41141	4.989000	0.63870	2.434000	0.82447	0.513000	0.50165	GAC		0.587	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		T	99662056	C	T	99662056	3	4	120	1	0	0	0	0	1	0	0	0	11545	884	31	1	1930	1	PCDH19	23	99662056	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	36216898	99662056	55608504	185	31766										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107402853	107402853	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ctggctgacgggcatcatggGgataggggcggtagtggaga	20	6	1	2	rs201417622		TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:107402853G>T	ENST00000372216.4	-	44	4754	c.4654C>A	c.(4654-4656)Ccc>Acc	p.P1552T	COL4A6_ENST00000545689.1_Missense_Mutation_p.P1527T|COL4A6_ENST00000418180.1_Missense_Mutation_p.P86T|COL4A6_ENST00000394872.2_Missense_Mutation_p.P1552T|COL4A6_ENST00000334504.7_Missense_Mutation_p.P1551T|COL4A6_ENST00000538570.1_Missense_Mutation_p.P1494T	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	1552	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				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						GGCATCATGGGGATAGGGGCG	0.562									Alport syndrome with Diffuse Leiomyomatosis																												Melanoma(87;1895 1945 2589 7165)											0			X											135	115	122					X																	107402853		2203	4300	6503	107289509	SO:0001583	missense	1288	Familial Cancer Database		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.4654C>A	X.37:g.107402853G>T	ENSP00000361290:p.Pro1552Thr		107289509	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	37	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.457806	0.63401	.	.	ENSG00000197565	ENST00000418180;ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38;-3.38	5.06	5.06	0.68205	C-type lectin fold (1);	0.000000	0.42053	D	0.000777	D	0.96821	0.8962	M	0.83692	2.655	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;0.999;1.0;0.998	D	0.96573	0.9424	10	0.45353	T	0.12	.	18.2367	0.89951	0.0:0.0:1.0:0.0	.	1527;86;1494;1552;1551	F5H851;B4DZ39;F5H3Q5;Q14031;Q14031-2	.;.;.;CO4A6_HUMAN;.	T	86;1552;1551;1552;1539;1527;1494	ENSP00000406002:P86T;ENSP00000361290:P1552T;ENSP00000334733:P1551T;ENSP00000378340:P1552T;ENSP00000443707:P1527T;ENSP00000445236:P1494T	ENSP00000334733:P1551T	P	-	1	0	COL4A6	107289509	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.766000	0.98957	2.440000	0.82611	0.529000	0.55759	CCC		0.562	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			T	107402853	G	T	107402853	3	4	120	1	0	0	0	0	1	0	0	0	3701	1232	43	2	429	2	COL4A6	23	107402853	Missense_Mutation	SNP	G	TCGA-F5-6813-01A-11D-1826-10	7740797	107402853	47867707	186	31767										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130408647	130408647	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aggcctggaggcggtagctgCagctgtagtttccaatgcct	14	10	0	0			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:130408647C>A	ENST00000361420.3	-	18	3756	c.3677G>T	c.(3676-3678)tGc>tTc	p.C1226F	IGSF1_ENST00000370910.1_Missense_Mutation_p.C1217F|IGSF1_ENST00000370904.1_Missense_Mutation_p.C1217F|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370903.3_Missense_Mutation_p.C1231F			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	1226	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						GCGGTAGCTGCAGCTGTAGTT	0.512																																																0			X											188	173	178					X																	130408647		2203	4300	6503	130236328	SO:0001583	missense	3547			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.3677G>T	X.37:g.130408647C>A	ENSP00000355010:p.Cys1226Phe		130236328	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	37	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.208944	0.58343	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	5.62	5.62	0.85841	Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000044	D	0.83571	0.5283	H	0.96916	3.905	0.43069	D	0.994701	D;D;D	0.89917	1.0;1.0;0.996	D;D;D	0.97110	0.999;1.0;0.996	D	0.88860	0.3325	10	0.87932	D	0	.	14.1406	0.65318	0.0:1.0:0.0:0.0	.	1217;670;1226	Q8N6C5-2;C9JP68;Q8N6C5	.;.;IGSF1_HUMAN	F	1217;1226;1217;1231	ENSP00000359947:C1217F;ENSP00000355010:C1226F;ENSP00000359941:C1217F;ENSP00000359940:C1231F	ENSP00000355010:C1226F	C	-	2	0	IGSF1	130236328	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.949000	0.56668	2.501000	0.84356	0.594000	0.82650	TGC		0.512	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			A	130408647	C	A	130408647	3	1	120	1	0	0	0	0	1	0	0	0	7617	710	25	2	345	2	IGSF1	23	130408647	Missense_Mutation	SNP	C	TCGA-F5-6813-01A-11D-1826-10	23005794	130408647	24861913	187	31768										
F8	2157	hgsc.bcm.edu	37	chrX	154159623	154159623	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	ccatgtggagtaggactctgTcgcaagagcatcaacaaatc	10	10	2	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrX:154159623T>C	ENST00000360256.4	-	14	2642	c.2442A>G	c.(2440-2442)cgA>cgG	p.R814R		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	814	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)	TAGGACTCTGTCGCAAGAGCA	0.413																																																0			X											210	192	198					X																	154159623		2203	4299	6502	153812817	SO:0001819	synonymous_variant	2157			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.2442A>G	X.37:g.154159623T>C			153812817	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																				0.413	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			C	154159623	T	C	154159623	2	2	120	1	0	0	0	0	0	0	0	1	5363	1654	58	4		4	F8	23	154159623	Silent	SNP	T	TCGA-F5-6813-01A-11D-1826-10	23750976	154159623	1110937	188	31769										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16953118	16953118	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0793650793650794	15	1	1.08314285714286	3.09469387755102	0.755681063122924	0.514475543396567	1	0	aacagtacaaatttaccccaCggacattccaccactagagt	5	13	0	1			TCGA-F5-6813-01A-11D-1826-10	TCGA-F5-6813-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	a1a70ad7-3e5b-4d2a-966b-c42bbdcb200a	23581057-9765-403e-b67a-3049a0050b84	g.chrY:16953118C>T	ENST00000476359.1	+	0	2972							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						ATTTACCCCACGGACATTCCA	0.428																																																0			Y																																								15462512	SO:0001624	3_prime_UTR_variant	22829				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.*2969C>T	Y.37:g.16953118C>T			15462512	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Silent	SNP	ENST00000476359.1	37																																																																																					0.428	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		T	16953118	C	T	16953118	1	4	120	0	1	0	0	0	0	0	0	0	10496	535	19	1		1	NLGN4Y	24	16953118	3'UTR	SNP	C	TCGA-F5-6813-01A-11D-1826-10		16953118	42420448	189	31770										
IGSF21	84966	hgsc.bcm.edu	37	chr1	18704793	18704793	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cggctcaccttggtgctcgcCctgacagtgattctggagct	12	13	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:18704793C>T	ENST00000251296.1	+	10	1760	c.1377C>T	c.(1375-1377)gcC>gcT	p.A459A		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	459						extracellular region (GO:0005576)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		TGGTGCTCGCCCTGACAGTGA	0.577																																																0			1											52	47	49					1																	18704793		2203	4300	6503	18577380	SO:0001819	synonymous_variant	84966			AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.1377C>T	1.37:g.18704793C>T			18577380	Q8NBR8	Silent	SNP	ENST00000251296.1	37	CCDS184.1																																																																																				0.577	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880		T	18704793	C	T	18704793	2	4	121	1	0	0	0	0	0	0	0	1	7620	610	22	3		3	IGSF21	1	18704793	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10		18704793	230545828	1	31771										
STK40	83931	hgsc.bcm.edu	37	chr1	36820980	36820980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaggcagatgcgcttcttcaTcttcttaaccatccggctgg	10	12	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:36820980T>C	ENST00000373129.3	-	6	803	c.397A>G	c.(397-399)Atg>Gtg	p.M133V	STK40_ENST00000359297.2_Missense_Mutation_p.M133V|STK40_ENST00000482458.1_5'UTR|STK40_ENST00000373130.3_Missense_Mutation_p.M138V|STK40_ENST00000373132.3_Missense_Mutation_p.M133V	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		M -> T (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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)				CGCTTCTTCATCTTCTTAACC	0.557																																																0			1											279	245	257					1																	36820980		2203	4300	6503	36593567	SO:0001583	missense	83931			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.397A>G	1.37:g.36820980T>C	ENSP00000362221:p.Met133Val		36593567	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.156425	0.38119	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.61980	0.09;0.06;0.09;0.09	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.035482	0.85682	D	0.000000	T	0.34135	0.0887	N	0.00707	-1.245	0.45390	D	0.998377	B;B;B	0.19706	0.038;0.0;0.0	B;B;B	0.24541	0.054;0.0;0.0	T	0.36939	-0.9727	10	0.42905	T	0.14	-25.2794	15.5237	0.75885	0.0:0.0:0.0:1.0	.	133;138;133	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	V	133;133;138;133	ENSP00000362221:M133V;ENSP00000352245:M133V;ENSP00000362222:M138V;ENSP00000362224:M133V	ENSP00000352245:M133V	M	-	1	0	STK40	36593567	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.742000	0.62103	2.263000	0.75096	0.379000	0.24179	ATG		0.557	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		C	36820980	T	C	36820980	3	2	121	1	0	0	0	0	1	0	0	0	15346	1435	50	4	938	4	STK40	1	36820980	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	18116187	36820980	212429641	2	31772										
MRPS15	64960	hgsc.bcm.edu	37	chr1	36921912	36921912	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agacatcatagttggtgttaCggaggtttttgagcatcttt	11	5	2	2	rs80215530	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:36921912C>A	ENST00000373116.5	-	7	673	c.512G>T	c.(511-513)cGt>cTt	p.R171L	MRPS15_ENST00000488606.1_5'UTR	NM_031280.3	NP_112570.2	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15	171					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)	p.R171H(1)		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)				GTTGGTGTTACGGAGGTTTTT	0.453													C|||	2	0.000399361	0.0015	0	5008	,	,		19207	0		0	False		,,,				2504	0															1	Substitution - Missense(1)	ovary(1)	1						C	LEU/ARG	9,4397	16.8+/-37.8	0,9,2194	94	89	90		512	6.1	1	1	dbSNP_132	90	0,8600		0,0,4300	yes	missense	MRPS15	NM_031280.3	102	0,9,6494	AA,AC,CC		0.0,0.2043,0.0692	probably-damaging	171/258	36921912	9,12997	2203	4300	6503	36694499	SO:0001583	missense	64960			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.512G>T	1.37:g.36921912C>A	ENSP00000362208:p.Arg171Leu		36694499	B2RD82|Q9H2K1	Missense_Mutation	SNP	ENST00000373116.5	37	CCDS411.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	35	5.462032	0.96240	0.002043	0.0	ENSG00000116898	ENST00000373116	.	.	.	6.06	6.06	0.98353	S15/NS1, RNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.86176	0.5870	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.88097	0.2817	9	0.87932	D	0	-26.9014	19.1847	0.93639	0.0:1.0:0.0:0.0	.	171	P82914	RT15_HUMAN	L	171	.	ENSP00000362208:R171L	R	-	2	0	MRPS15	36694499	1.000000	0.71417	0.970000	0.41538	0.995000	0.86356	7.113000	0.77095	2.882000	0.98803	0.655000	0.94253	CGT		0.453	MRPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022052.2	NM_031280		A	36921912	C	A	36921912	3	1	121	1	0	0	0	0	1	0	0	0	9855	536	19	2	269	2	MRPS15	1	36921912	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	100932	36921912	212328709	3	31773										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43909272	43909272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atctttactctcatagcggcGccatcgccctgagtcagggt	10	13	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:43909272G>A	ENST00000562955.1	+	61	8459	c.8459G>A	c.(8458-8460)cGc>cAc	p.R2820H	SZT2_ENST00000372442.1_Missense_Mutation_p.R1978H	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2877					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						TCATAGCGGCGCCATCGCCCT	0.612																																																0			1											57	59	58					1																	43909272		2203	4300	6503	43681859	SO:0001583	missense	23334			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.8459G>A	1.37:g.43909272G>A	ENSP00000457168:p.Arg2820His		43681859	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681772	0.68042	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.36	5.36	0.76844	.	0.054620	0.64402	D	0.000001	T	0.33933	0.0880	L	0.43152	1.355	0.30131	N	0.804793	P	0.49559	0.925	B	0.38327	0.271	T	0.49011	-0.8983	9	0.66056	D	0.02	.	12.4901	0.55895	0.0765:0.0:0.9235:0.0	.	2820	Q5T011-5	.	H	1978	.	ENSP00000361519:R1978H	R	+	2	0	SZT2	43681859	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	8.195000	0.89723	2.514000	0.84764	0.650000	0.86243	CGC		0.612	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43909272	G	A	43909272	3	1	121	1	0	0	0	0	1	0	0	0	8199	1087	38	1	6111	1	KIAA0467	1	43909272	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6987360	43909272	205341349	4	31774										
TMEM53	79639	hgsc.bcm.edu	37	chr1	45120664	45120664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tggtgcccaccacacgcaggCggcagaagcgacgggtctgc	15	14	1	1	rs35524791	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:45120664C>T	ENST00000372237.3	-	3	564	c.401G>A	c.(400-402)cGc>cAc	p.R134H	TMEM53_ENST00000372235.3_Missense_Mutation_p.R104H|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000476724.1_5'UTR|TMEM53_ENST00000372243.3_Intron|TMEM53_ENST00000372242.3_Missense_Mutation_p.R134H	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	134						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					CACACGCAGGCGGCAGAAGCG	0.652													T|||	22	0.00439297	0.0159	0.0014	5008	,	,		18857	0		0	False		,,,				2504	0															0			1						T	HIS/ARG	59,4347	818.5+/-416.3	1,57,2145	39	39	39		401	3.3	1	1	dbSNP_126	39	1,8599	816.5+/-406.9	0,1,4299	no	missense	TMEM53	NM_024587.2	29	1,58,6444	TT,TC,CC		0.0116,1.3391,0.4613	benign	134/278	45120664	60,12946	2203	4300	6503	44893251	SO:0001583	missense	79639				CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.401G>A	1.37:g.45120664C>T	ENSP00000361311:p.Arg134His		44893251	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Missense_Mutation	SNP	ENST00000372237.3	37	CCDS511.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	13.57	2.275791	0.40294	0.013391	1.16E-4	ENSG00000126106	ENST00000372242;ENST00000372237;ENST00000372235;ENST00000420706	.	.	.	5.67	3.34	0.38264	.	0.326909	0.35838	N	0.002942	T	0.07818	0.0196	N	0.00742	-1.23	0.09310	N	0.999992	B	0.02656	0.0	B	0.04013	0.001	T	0.25745	-1.0123	9	0.27082	T	0.32	.	9.6013	0.39605	0.0:0.1997:0.0:0.8003	rs35524791	134	Q6P2H8	TMM53_HUMAN	H	134;134;104;103	.	ENSP00000361309:R104H	R	-	2	0	TMEM53	44893251	1.000000	0.71417	0.998000	0.56505	0.816000	0.46133	1.079000	0.30766	0.105000	0.17753	-0.360000	0.07572	CGC		0.652	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587		T	45120664	C	T	45120664	3	4	121	1	0	0	0	0	1	0	0	0	16218	768	27	1	436	1	TMEM53	1	45120664	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1211392	45120664	204129957	5	31775										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55523739	55523739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	catgatgctgtctgccgagcCggagctcaccctggccgagt	13	14	2	1	rs140072072		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:55523739C>T	ENST00000302118.5	+	8	1501	c.1211C>T	c.(1210-1212)cCg>cTg	p.P404L	PCSK9_ENST00000543384.1_Missense_Mutation_p.P204L|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	404	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.P404Q(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						TCTGCCGAGCCGGAGCTCACC	0.612																																					Pancreas(137;1454 1827 5886 22361 42375)											1	Substitution - Missense(1)	ovary(1)	1						C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	71	65	67		1211	3.5	0	1	dbSNP_134	67	0,8600		0,0,4300	no	missense	PCSK9	NM_174936.3	98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	404/693	55523739	1,13005	2203	4300	6503	55296327	SO:0001583	missense	255738			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.1211C>T	1.37:g.55523739C>T	ENSP00000303208:p.Pro404Leu		55296327	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.713436	0.68730	2.27E-4	0.0	ENSG00000169174	ENST00000302118;ENST00000543384	T;T	0.81330	-1.48;-1.48	4.39	3.48	0.39840	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.067800	0.64402	D	0.000020	D	0.88625	0.6487	M	0.80183	2.485	0.48632	D	0.999684	D	0.89917	1.0	D	0.71414	0.973	D	0.89505	0.3767	10	0.87932	D	0	-11.5511	12.6057	0.56523	0.0:0.9181:0.0:0.0819	.	404	Q8NBP7	PCSK9_HUMAN	L	404;204	ENSP00000303208:P404L;ENSP00000441859:P204L	ENSP00000303208:P404L	P	+	2	0	PCSK9	55296327	0.916000	0.31088	0.013000	0.15412	0.412000	0.31113	2.014000	0.40951	0.955000	0.37878	0.563000	0.77884	CCG		0.612	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		T	55523739	C	T	55523739	3	4	121	1	0	0	0	0	1	0	0	0	11637	652	23	1	1241	1	PCSK9	1	55523739	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	10403075	55523739	193726882	6	31776										
C1orf141	400757	hgsc.bcm.edu	37	chr1	67559074	67559074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atcttttctctgtactgtagGcatagttttttggggtttga	10	5	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:67559074G>A	ENST00000371007.2	-	8	926	c.817C>T	c.(817-819)Cct>Tct	p.P273S	C1orf141_ENST00000371006.1_Missense_Mutation_p.P273S|C1orf141_ENST00000544837.1_Missense_Mutation_p.P273S	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	273								p.P273A(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						TGTACTGTAGGCATAGTTTTT	0.313																																																1	Substitution - Missense(1)	ovary(1)	1											84	85	85					1																	67559074		2203	4298	6501	67331662	SO:0001583	missense	400757			BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.817C>T	1.37:g.67559074G>A	ENSP00000360046:p.Pro273Ser		67331662	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	.	.	.	.	.	.	.	.	.	.	G	5.405	0.259886	0.10239	.	.	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837	T;T;T	0.29397	1.57;1.57;1.57	4.66	-2.04	0.07343	.	1.016720	0.07878	N	0.969119	T	0.04092	0.0114	L	0.27053	0.805	0.09310	N	1	B	0.20550	0.046	B	0.18871	0.023	T	0.36237	-0.9756	10	0.02654	T	1	1.0971	5.2647	0.15593	0.4376:0.1429:0.4195:0.0	.	273	Q5JVX7	CA141_HUMAN	S	273	ENSP00000360046:P273S;ENSP00000360045:P273S;ENSP00000444018:P273S	ENSP00000360045:P273S	P	-	1	0	C1orf141	67331662	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.001000	0.03690	-0.504000	0.06577	0.561000	0.74099	CCT		0.313	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674		A	67559074	G	A	67559074	3	1	121	1	0	0	0	0	1	0	0	0	2007	1203	42	3	389	3	C1orf141	1	67559074	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	12035335	67559074	181691547	7	31777										
HFM1	164045	hgsc.bcm.edu	37	chr1	91781407	91781407	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	taaactacttgattatctgcGtcacctatgattaaggtaac	6	8	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:91781407G>A	ENST00000370425.3	-	28	3203	c.3105C>T	c.(3103-3105)gaC>gaT	p.D1035D	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Silent_p.D714D|HFM1_ENST00000294696.5_Silent_p.D267D	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1035	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.D1035D(1)		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)		GATTATCTGCGTCACCTATGA	0.313																																																1	Substitution - coding silent(1)	endometrium(1)	1											78	77	77					1																	91781407		2202	4297	6499	91553995	SO:0001819	synonymous_variant	164045			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.3105C>T	1.37:g.91781407G>A			91553995	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	A	5.756	0.323958	0.10900	.	.	ENSG00000162669	ENST00000430465	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	T	0.50034	0.1592	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50541	-0.8816	4	.	.	.	.	11.1417	0.48406	0.927:0.0:0.073:0.0	.	.	.	.	M	247	.	.	T	-	2	0	HFM1	91553995	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	4.029000	0.57253	0.843000	0.35070	-0.550000	0.04213	ACG		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		A	91781407	G	A	91781407	2	1	121	1	0	0	0	0	0	0	0	1	7104	1136	40	1		1	HFM1	1	91781407	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	24222333	91781407	157469214	8	31778										
NHLH2	4808	hgsc.bcm.edu	37	chr1	116380728	116380728	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccaagttgaaggcttccacgCggatgcgctcgcgggtggcg	16	12	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:116380728C>A	ENST00000369506.1	-	1	5810	c.266G>T	c.(265-267)cGc>cTc	p.R89L	NHLH2_ENST00000320238.3_Missense_Mutation_p.R89L			Q02577	HEN2_HUMAN	nescient helix loop helix 2	89	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)		GGCTTCCACGCGGATGCGCTC	0.701																																																0			1											17	21	20					1																	116380728		2202	4300	6502	116182251	SO:0001583	missense	4808				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.266G>T	1.37:g.116380728C>A	ENSP00000358519:p.Arg89Leu		116182251	Q5T1P6	Missense_Mutation	SNP	ENST00000369506.1	37	CCDS885.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719173	0.89205	.	.	ENSG00000177551	ENST00000320238;ENST00000369506;ENST00000429731	D;D;D	0.99709	-6.48;-6.48;-6.48	4.49	4.49	0.54785	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	D	0.000002	D	0.99775	0.9907	H	0.96080	3.765	0.80722	D	1	D	0.69078	0.997	P	0.59056	0.851	D	0.97060	0.9770	10	0.87932	D	0	-13.4923	16.8027	0.85618	0.0:1.0:0.0:0.0	.	89	Q02577	HEN2_HUMAN	L	89	ENSP00000322087:R89L;ENSP00000358519:R89L;ENSP00000405062:R89L	ENSP00000322087:R89L	R	-	2	0	NHLH2	116182251	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.618000	0.83043	2.053000	0.61076	0.561000	0.74099	CGC		0.701	NHLH2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033090.1	NM_005599		A	116380728	C	A	116380728	3	1	121	1	0	0	0	0	1	0	0	0	10435	768	27	2	145	2	NHLH2	1	116380728	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	24599321	116380728	132869893	9	31779										
SV2A	9900	hgsc.bcm.edu	37	chr1	149881107	149881107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	attcatcctcctgatgaatcGtcttaatgtgggttacctgg	9	9	2	2	rs145220569		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:149881107G>A	ENST00000369146.3	-	7	1686	c.1196C>T	c.(1195-1197)aCg>aTg	p.T399M	SV2A_ENST00000369145.1_Missense_Mutation_p.T399M	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	399					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)	CTGATGAATCGTCTTAATGTG	0.572																																																0			1						G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	64	63	64		1196	5.4	1	1	dbSNP_134	64	0,8600		0,0,4300	no	missense	SV2A	NM_014849.3	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	399/743	149881107	1,13005	2203	4300	6503	148147731	SO:0001583	missense	9900			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.1196C>T	1.37:g.149881107G>A	ENSP00000358142:p.Thr399Met		148147731	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Missense_Mutation	SNP	ENST00000369146.3	37	CCDS940.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.828888	0.71258	2.27E-4	0.0	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.74526	-0.85;-0.85	5.38	5.38	0.77491	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.82416	0.5032	M	0.72118	2.19	0.52501	D	0.999959	D	0.89917	1.0	D	0.71414	0.973	T	0.82045	-0.0652	10	0.51188	T	0.08	-16.2921	16.6795	0.85288	0.0:0.0:1.0:0.0	.	399	Q7L0J3	SV2A_HUMAN	M	399	ENSP00000358142:T399M;ENSP00000358141:T399M	ENSP00000358141:T399M	T	-	2	0	SV2A	148147731	1.000000	0.71417	0.997000	0.53966	0.934000	0.57294	7.792000	0.85828	2.813000	0.96785	0.655000	0.94253	ACG		0.572	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1			A	149881107	G	A	149881107	3	1	121	1	0	0	0	0	1	0	0	0	15456	1145	40	1	1060	1	SV2A	1	149881107	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	33500379	149881107	99369514	10	31780										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096275	167096275	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gctggagagaagccggcagaCgctggaggagagccagtcta	17	9	1	3	rs202017285	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:167096275C>T	ENST00000361200.2	+	6	2073	c.1907C>T	c.(1906-1908)aCg>aTg	p.T636M	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.T636M|DUSP27_ENST00000443333.1_Missense_Mutation_p.T636M			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	636					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						AGCCGGCAGACGCTGGAGGAG	0.632													C|||	5	0.000998403	0	0	5008	,	,		14183	0.005		0	False		,,,				2504	0															0			1											37	34	35					1																	167096275		2202	4299	6501	165362899	SO:0001583	missense	338599			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.1907C>T	1.37:g.167096275C>T	ENSP00000354483:p.Thr636Met		165362899	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	16.28	3.078802	0.55753	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03689	3.84;3.84;3.84	5.1	5.1	0.69264	.	0.087500	0.43579	D	0.000551	T	0.03520	0.0101	M	0.65975	2.015	0.33061	D	0.534058	D	0.65815	0.995	P	0.49502	0.613	T	0.16719	-1.0393	10	0.87932	D	0	-13.8238	5.1441	0.14975	0.2009:0.6729:0.0:0.1261	.	636	Q5VZP5	DUS27_HUMAN	M	636	ENSP00000354483:T636M;ENSP00000271385:T636M;ENSP00000404874:T636M	ENSP00000271385:T636M	T	+	2	0	DUSP27	165362899	0.959000	0.32827	0.990000	0.47175	0.987000	0.75469	2.092000	0.41700	2.360000	0.80028	0.643000	0.83706	ACG		0.632	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167096275	C	T	167096275	3	4	121	1	0	0	0	0	1	0	0	0	4835	536	19	1	1925	1	DUSP27	1	167096275	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	17215168	167096275	82154346	11	31781										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176668549	176668549	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gatgggaaggtgtcgggggtGaaagtctacacctttgatga	16	5	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:176668549G>T	ENST00000367662.3	+	8	4224	c.3060G>T	c.(3058-3060)gtG>gtT	p.V1020V		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1020					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						TGTCGGGGGTGAAAGTCTACA	0.542																																																0			1											137	143	141					1																	176668549		2109	4241	6350	174935172	SO:0001819	synonymous_variant	60676			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.3060G>T	1.37:g.176668549G>T			174935172	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																				0.542	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176668549	G	T	176668549	2	4	121	1	0	0	0	0	0	0	0	1	11464	1277	45	2		2	PAPPA2	1	176668549	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	9572274	176668549	72582072	12	31782										
CEP350	9857	hgsc.bcm.edu	37	chr1	180063690	180063690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagtatttcaggttgcttctTaagttctgaattggaagatg	10	4	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:180063690T>C	ENST00000367607.3	+	34	8868	c.8450T>C	c.(8449-8451)tTa>tCa	p.L2817S	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2817					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						GGTTGCTTCTTAAGTTCTGAA	0.403																																																0			1											78	82	81					1																	180063690		2202	4300	6502	178330313	SO:0001583	missense	9857			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.8450T>C	1.37:g.180063690T>C	ENSP00000356579:p.Leu2817Ser		178330313	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379575	0.61845	.	.	ENSG00000135837	ENST00000367607;ENST00000417046	T	0.68331	-0.32	5.61	5.61	0.85477	.	0.210963	0.23760	N	0.044833	T	0.73289	0.3568	L	0.57536	1.79	0.42671	D	0.993514	D;D	0.59357	0.981;0.985	P;P	0.54590	0.69;0.756	T	0.73729	-0.3891	9	.	.	.	.	14.3537	0.66722	0.0:0.0:0.0:1.0	.	2817;2817	E7EU22;Q5VT06	.;CE350_HUMAN	S	2817;281	ENSP00000356579:L2817S	.	L	+	2	0	CEP350	178330313	0.997000	0.39634	0.794000	0.32065	0.649000	0.38597	4.992000	0.63889	2.126000	0.65437	0.482000	0.46254	TTA		0.403	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	180063690	T	C	180063690	3	2	121	1	0	0	0	0	1	0	0	0	3260	1764	61	4	8580	4	CEP350	1	180063690	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	3395141	180063690	69186931	13	31783										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183079749	183079749	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cctttcttcaatgaccggccGtggaggagggcaactgcgga	14	11	2	1	rs111388231		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:183079749G>A	ENST00000258341.4	+	4	1238	c.981G>A	c.(979-981)ccG>ccA	p.P327P		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	327	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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						ATGACCGGCCGTGGAGGAGGG	0.473													G|||	1	0.000199681	0	0	5008	,	,		19941	0.001		0	False		,,,				2504	0															0			1											181	178	179					1																	183079749		2203	4300	6503	181346372	SO:0001819	synonymous_variant	3915			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.981G>A	1.37:g.183079749G>A			181346372	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																				0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183079749	G	A	183079749	2	1	121	1	0	0	0	0	0	0	0	1	8636	1132	40	1		1	LAMC1	1	183079749	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	3016059	183079749	66170872	14	31784										
RGS21	431704	hgsc.bcm.edu	37	chr1	192316514	192316514	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tatggacacgcttttagccaAccaaggtaagatttaactaa	7	8	0	1	rs142678159	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:192316514A>G	ENST00000417209.2	+	3	257	c.83A>G	c.(82-84)aAc>aGc	p.N28S		NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	28	RGS. {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)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						CTTTTAGCCAACCAAGGTAAG	0.303													A|||	13	0.00259585	0	0	5008	,	,		15184	0.0119		0	False		,,,				2504	0.001															0			1						A	SER/ASN	1,3639		0,1,1819	122	114	117		83	5	0.9	1	dbSNP_134	117	0,8158		0,0,4079	yes	missense	RGS21	NM_001039152.3	46	0,1,5898	GG,GA,AA		0.0,0.0275,0.0085	benign	28/153	192316514	1,11797	1820	4079	5899	190583137	SO:0001583	missense	431704			AY643711	CCDS41448.1	1q31.2	2013-09-24	2007-08-14		ENSG00000253148	ENSG00000253148		"Regulators of G-protein signaling"	26839	protein-coding gene	gene with protein product		612407	"regulator of G-protein signalling 21"			15066150	Standard	NM_001039152		Approved		uc001gsh.3	Q2M5E4	OTTHUMG00000035594	ENST00000417209.2:c.83A>G	1.37:g.192316514A>G	ENSP00000428343:p.Asn28Ser		190583137		Missense_Mutation	SNP	ENST00000417209.2	37	CCDS41448.1	8	0.003663003663003663	0	0.0	0	0.0	8	0.013986013986013986	0	0.0	A	1.889	-0.455997	0.04540	2.75E-4	0.0	ENSG00000253148	ENST00000417209	T	0.29917	1.55	6.08	4.96	0.65561	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.36234	U	0.002715	T	0.07683	0.0193	N	0.02751	-0.505	0.28042	N	0.933701	B	0.16396	0.017	B	0.08055	0.003	T	0.25779	-1.0122	10	0.05833	T	0.94	.	9.9088	0.41392	0.9229:0.0:0.0771:0.0	.	28	Q2M5E4	RGS21_HUMAN	S	28	ENSP00000428343:N28S	ENSP00000428343:N28S	N	+	2	0	RGS21	190583137	0.805000	0.28982	0.892000	0.35008	0.476000	0.33039	2.099000	0.41767	1.128000	0.42052	0.482000	0.46254	AAC		0.303	RGS21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086387.2			G	192316514	A	G	192316514	3	3	121	1	0	0	0	0	1	0	0	0	13341	43	2	4	89	4	RGS21	1	192316514	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	9236765	192316514	56934107	15	31785										
ASPM	259266	hgsc.bcm.edu	37	chr1	197072050	197072050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtgcatgtgttgaatatgtcTtctaactctaatacctctat	6	8	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:197072050T>C	ENST00000367409.4	-	18	6587	c.6331A>G	c.(6331-6333)Aga>Gga	p.R2111G	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2111	IQ 16. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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						TGAATATGTCTTCTAACTCTA	0.328																																																0			1											110	117	114					1																	197072050		2203	4297	6500	195338673	SO:0001583	missense	259266			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.6331A>G	1.37:g.197072050T>C	ENSP00000356379:p.Arg2111Gly		195338673	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	t	12.01	1.810845	0.32053	.	.	ENSG00000066279	ENST00000367409	T	0.72942	-0.7	5.59	4.44	0.53790	.	0.134493	0.51477	D	0.000099	D	0.86871	0.6037	H	0.94582	3.555	0.09310	N	0.999993	D	0.60160	0.987	D	0.67231	0.95	T	0.81165	-0.1057	10	0.87932	D	0	.	12.0466	0.53483	0.0:0.0:0.3364:0.6636	.	2111	Q8IZT6	ASPM_HUMAN	G	2111	ENSP00000356379:R2111G	ENSP00000356379:R2111G	R	-	1	2	ASPM	195338673	0.017000	0.18338	0.362000	0.25862	0.421000	0.31385	0.304000	0.19228	0.916000	0.36871	0.520000	0.50463	AGA		0.328	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		C	197072050	T	C	197072050	3	2	121	1	0	0	0	0	1	0	0	0	1057	1617	56	4	4146	4	ASPM	1	197072050	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	4755536	197072050	52178571	16	31786										
C1orf186	440712	hgsc.bcm.edu	37	chr1	206241533	206241533	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccctccaaccccttactcacGcctgtaaagggaatcagaca	6	16	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:206241533G>A	ENST00000331555.5	-	4	894	c.256C>T	c.(256-258)Cat>Tat	p.H86Y		NM_001007544.1	NP_001007545.1	Q6ZWK4	CA186_HUMAN	chromosome 1 open reading frame 186	86						integral component of membrane (GO:0016021)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.0754)			CCTTACTCACGCCTGTAAAGG	0.552																																																0			1											150	153	152					1																	206241533		2203	4300	6503	204408156	SO:0001630	splice_region_variant	440712			AK122631	CCDS73014.1	1q32.1	2014-05-06			ENSG00000196533	ENSG00000263961			25341	protein-coding gene	gene with protein product							Standard	XM_005272738		Approved	FLJ16052	uc001hdt.2	Q6ZWK4	OTTHUMG00000184376	ENST00000331555.5:c.256+1C>T	1.37:g.206241533G>A			204408156		Missense_Mutation	SNP	ENST00000331555.5	37	CCDS30995.1	.	.	.	.	.	.	.	.	.	.	G	8.780	0.927952	0.18056	.	.	ENSG00000196533	ENST00000331555	.	.	.	3.05	-2.69	0.06022	.	.	.	.	.	T	0.23688	0.0573	L	0.32530	0.975	0.09310	N	1	B	0.15473	0.013	B	0.06405	0.002	T	0.19386	-1.0307	7	.	.	.	-26.9714	2.6739	0.05076	0.0952:0.2622:0.3715:0.2711	.	86	Q6ZWK4	CA186_HUMAN	Y	86	.	.	H	-	1	0	C1orf186	204408156	0.023000	0.18921	0.006000	0.13384	0.017000	0.09413	-0.221000	0.09202	-1.054000	0.03214	-1.357000	0.01221	CAT		0.552	C1orf186-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088002.1	NM_001007544	Missense_Mutation	A	206241533	G	A	206241533	5	1	121	1	0	0	0	0	0	0	1	0	2026	1101	38	1	274	1	C1orf186	1	206241533	Splice_Site	SNP	G	TCGA-G5-6235-01A-11D-1733-10	9169483	206241533	43009088	17	31787										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209800259	209800259	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aggtccggtctggacactggCggatggctgcagcgctgcac	16	12	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:209800259C>T	ENST00000356082.4	-	13	1684	c.1550G>A	c.(1549-1551)cGc>cAc	p.R517H	LAMB3_ENST00000367030.3_Missense_Mutation_p.R517H|LAMB3_ENST00000391911.1_Missense_Mutation_p.R517H	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	517	Laminin EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)	p.R517H(1)		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)		TGGACACTGGCGGATGGCTGC	0.672																																																1	Substitution - Missense(1)	central_nervous_system(1)	1											57	46	50					1																	209800259		2203	4300	6503	207866882	SO:0001583	missense	3914			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.1550G>A	1.37:g.209800259C>T	ENSP00000348384:p.Arg517His		207866882	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.160965	0.38119	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.38240	1.15;1.15;1.15	5.7	4.78	0.61160	EGF-like, laminin (3);	0.218554	0.33346	N	0.005011	T	0.32224	0.0822	L	0.60455	1.87	0.34284	D	0.682502	B	0.21688	0.059	B	0.22386	0.039	T	0.38824	-0.9643	10	0.15499	T	0.54	.	10.5105	0.44860	0.0:0.8458:0.0:0.1542	.	517	Q13751	LAMB3_HUMAN	H	517	ENSP00000375778:R517H;ENSP00000348384:R517H;ENSP00000355997:R517H	ENSP00000348384:R517H	R	-	2	0	LAMB3	207866882	0.254000	0.23992	1.000000	0.80357	0.384000	0.30261	0.484000	0.22308	1.423000	0.47198	0.650000	0.86243	CGC		0.672	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209800259	C	T	209800259	3	4	121	1	0	0	0	0	1	0	0	0	8634	768	27	1	2012	1	LAMB3	1	209800259	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3558726	209800259	39450362	18	31788										
USH2A	7399	hgsc.bcm.edu	37	chr1	215807955	215807955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acaagatcaagcccagcatcGccattaacactatgaaccac	5	14	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:215807955G>A	ENST00000307340.3	-	70	15529	c.15143C>T	c.(15142-15144)gCg>gTg	p.A5048V	USH2A_ENST00000366943.2_Missense_Mutation_p.A5048V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5048					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.A5048V(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)		GCCCAGCATCGCCATTAACAC	0.463										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	large_intestine(1)	1											133	124	127					1																	215807955		2203	4300	6503	213874578	SO:0001583	missense	7399			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.15143C>T	1.37:g.215807955G>A	ENSP00000305941:p.Ala5048Val		213874578	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915574	0.52546	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.16457	2.34;2.36	5.88	5.88	0.94601	.	0.348186	0.20392	N	0.093230	T	0.12347	0.0300	L	0.41824	1.3	0.35959	D	0.834492	P	0.46952	0.887	B	0.30495	0.116	T	0.20773	-1.0265	10	0.34782	T	0.22	.	13.85	0.63489	0.0785:0.0:0.9215:0.0	.	5048	O75445	USH2A_HUMAN	V	5048	ENSP00000305941:A5048V;ENSP00000355910:A5048V	ENSP00000305941:A5048V	A	-	2	0	USH2A	213874578	1.000000	0.71417	0.960000	0.40013	0.618000	0.37518	5.806000	0.69150	2.785000	0.95823	0.655000	0.94253	GCG		0.463	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215807955	G	A	215807955	3	1	121	1	0	0	0	0	1	0	0	0	17076	1087	38	1	477	1	USH2A	1	215807955	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6007696	215807955	33442666	19	31789										
USH2A	7399	hgsc.bcm.edu	37	chr1	215963506	215963506	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tttggaataagttcagtctcAcagcattttactggcaccgg	9	9	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:215963506A>G	ENST00000307340.3	-	51	10463	c.10077T>C	c.(10075-10077)tgT>tgC	p.C3359C	USH2A_ENST00000366943.2_Silent_p.C3359C	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3359					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.C3359*(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)		GTTCAGTCTCACAGCATTTTA	0.383										HNSCC(13;0.011)																																						1	Substitution - Nonsense(1)	ovary(1)	1											133	127	129					1																	215963506		2203	4300	6503	214030129	SO:0001819	synonymous_variant	7399			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.10077T>C	1.37:g.215963506A>G			214030129	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	215963506	A	G	215963506	2	3	121	1	0	0	0	0	0	0	0	1	17076	157	6	4		4	USH2A	1	215963506	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	155551	215963506	33287115	20	31790										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228494787	228494787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagctgcagagctgctggtaCgcggagtggagcaggaggat	18	8	0	1	rs373344634		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:228494787C>T	ENST00000422127.1	+	45	12156	c.12112C>T	c.(12112-12114)Cgc>Tgc	p.R4038C	OBSCN_ENST00000570156.2_Missense_Mutation_p.R4995C|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1157C|OBSCN_ENST00000284548.11_Missense_Mutation_p.R4038C|OBSCN_ENST00000366707.4_Missense_Mutation_p.R1672C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4038	Ig-like 41.				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)				GCTGCTGGTACGCGGAGTGGA	0.647													C|||	1	0.000199681	0	0	5008	,	,		19091	0		0	False		,,,				2504	0.001															0			1						C	CYS/ARG,CYS/ARG	0,4386		0,0,2193	62	75	71		12112,12112	-3.9	0	1		71	1,8565	1.2+/-3.3	0,1,4282	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	180,180	0,1,6475	TT,TC,CC		0.0117,0.0,0.0077	benign,benign	4038/7969,4038/6621	228494787	1,12951	2193	4283	6476	226561410	SO:0001583	missense	84033			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.12112C>T	1.37:g.228494787C>T	ENSP00000409493:p.Arg4038Cys		226561410	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	9.941	1.217487	0.22373	0.0	1.17E-4	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	5.81	-3.87	0.04218	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.082060	0.07071	N	0.835483	T	0.64227	0.2579	M	0.83774	2.66	0.09310	N	1	B;B	0.17268	0.007;0.021	B;B	0.15052	0.008;0.012	T	0.54794	-0.8240	10	0.38643	T	0.18	.	7.469	0.27338	0.1101:0.3651:0.0:0.5248	.	4038;4038	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	C	4038;4038;1672;1157	ENSP00000284548:R4038C;ENSP00000409493:R4038C;ENSP00000355668:R1672C;ENSP00000355670:R1157C	ENSP00000284548:R4038C	R	+	1	0	OBSCN	226561410	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.228000	0.09114	-0.692000	0.05128	-1.281000	0.01382	CGC		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228494787	C	T	228494787	3	4	121	1	0	0	0	0	1	0	0	0	10843	536	19	1	12286	1	OBSCN	1	228494787	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	12531281	228494787	20755834	21	31791										
OR2AK2	391191	hgsc.bcm.edu	37	chr1	248129081	248129081	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	accctttacattatcctatgCttatgagcaagaagatctgc	6	10	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr1:248129081C>A	ENST00000366480.3	+	1	547	c.448C>A	c.(448-450)Ctt>Att	p.L150I	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	150						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(1)|kidney(1)|large_intestine(2)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36	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;0.0152)			TTATCCTATGCTTATGAGCAA	0.428																																					Melanoma(45;390 1181 23848 28461 41504)											0			1											278	251	260					1																	248129081		2203	4300	6503	246195704	SO:0001583	missense	391191			BK004457	CCDS31102.1	1q44	2012-08-09			ENSG00000187080	ENSG00000187080		"GPCR / Class A : Olfactory receptors"	19569	protein-coding gene	gene with protein product				OR2AK1P			Standard	NM_001004491		Approved		uc010pzd.2	Q8NG84	OTTHUMG00000040201	ENST00000366480.3:c.448C>A	1.37:g.248129081C>A	ENSP00000355436:p.Leu150Ile		246195704	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	.	.	.	.	.	.	.	.	.	.	.	13.42	2.231286	0.39399	.	.	ENSG00000187080	ENST00000366480	T	0.00902	5.56	3.03	1.98	0.26296	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01029	0.0034	N	0.21097	0.63	0.09310	N	1	D	0.54772	0.968	P	0.47744	0.556	T	0.57027	-0.7881	9	0.46703	T	0.11	.	5.1182	0.14847	0.3656:0.4449:0.1895:0.0	.	150	Q8NG84	O2AK2_HUMAN	I	150	ENSP00000355436:L150I	ENSP00000355436:L150I	L	+	1	0	OR2AK2	246195704	0.000000	0.05858	0.002000	0.10522	0.056000	0.15407	-1.954000	0.01525	1.679000	0.50963	0.455000	0.32223	CTT		0.428	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491		A	248129081	C	A	248129081	3	1	121	1	0	0	0	0	1	0	0	0	11017	797	28	2	450	2	OR2AK2	1	248129081	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	19634294	248129081	1121540	22	31792										
TTC15	51112	hgsc.bcm.edu	37	chr2	3483174	3483174	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaagaaacaggccctgctggAggctgtcgccggcaaggagg	17	10	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:3483174A>G	ENST00000324266.5	+	12	2345	c.2150A>G	c.(2149-2151)gAg>gGg	p.E717G	TRAPPC12-AS1_ENST00000453806.1_RNA|TRAPPC12_ENST00000382110.2_Missense_Mutation_p.E717G	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	717			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		vesicle-mediated transport (GO:0016192)												GCCCTGCTGGAGGCTGTCGCC	0.597																																																0			2											76	78	77					2																	3483174		2203	4300	6503	3462181	SO:0001583	missense	51112			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.2150A>G	2.37:g.3483174A>G	ENSP00000324318:p.Glu717Gly		3462181	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.584766	0.46110	.	.	ENSG00000171853	ENST00000382110;ENST00000324266;ENST00000415624	T;T	0.50548	0.74;0.74	4.91	3.64	0.41730	.	0.249014	0.46758	N	0.000270	T	0.50650	0.1628	L	0.56340	1.77	0.58432	D	0.999997	D	0.56287	0.975	P	0.52424	0.698	T	0.49579	-0.8925	10	0.54805	T	0.06	.	8.3757	0.32442	0.8836:0.0:0.1164:0.0	.	717	Q8WVT3	TPC12_HUMAN	G	717;717;216	ENSP00000371544:E717G;ENSP00000324318:E717G	ENSP00000324318:E717G	E	+	2	0	TTC15	3462181	1.000000	0.71417	0.993000	0.49108	0.816000	0.46133	5.449000	0.66619	0.866000	0.35629	0.533000	0.62120	GAG		0.597	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		G	3483174	A	G	3483174	3	3	121	1	0	0	0	0	1	0	0	0	16722	304	11	4	2192	4	TTC15	2	3483174	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10		3483174	239716199	23	31793										
DDX1	1653	hgsc.bcm.edu	37	chr2	15742718	15742718	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	caaagcagagaagtaaaggaAtggcatgggtgtagagctac	14	5	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:15742718A>G	ENST00000381341.2	+	8	743	c.354A>G	c.(352-354)gaA>gaG	p.E118E	DDX1_ENST00000233084.3_Silent_p.E118E			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	118	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|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)		AAGTAAAGGAATGGCATGGGT	0.373																																																0			2											154	145	148					2																	15742718		2203	4300	6503	15660169	SO:0001819	synonymous_variant	1653			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.354A>G	2.37:g.15742718A>G			15660169	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	37	CCDS1686.1																																																																																				0.373	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		G	15742718	A	G	15742718	2	3	121	1	0	0	0	0	0	0	0	1	4347	98	4	4		4	DDX1	2	15742718	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	12259544	15742718	227456655	24	31794										
HADHA	3030	hgsc.bcm.edu	37	chr2	26424110	26424110	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttttcaaaaccttggtaatCaagctgcccagtcaagttgc	7	11	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:26424110C>T	ENST00000380649.3	-	13	1429	c.1300G>A	c.(1300-1302)Gat>Aat	p.D434N		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	434					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)	p.D434H(1)		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)					CCTTGGTAATCAAGCTGCCCA	0.408																																																1	Substitution - Missense(1)	ovary(1)	2											99	91	94					2																	26424110		2203	4300	6503	26277614	SO:0001583	missense	3030			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.1300G>A	2.37:g.26424110C>T	ENSP00000370023:p.Asp434Asn		26277614	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	37	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377952	0.61735	.	.	ENSG00000084754	ENST00000380649	T	0.78003	-1.14	5.43	4.56	0.56223	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.042848	0.85682	N	0.000000	T	0.73621	0.3610	L	0.45698	1.435	0.80722	D	1	B;B	0.26672	0.156;0.156	B;B	0.33121	0.158;0.158	T	0.71358	-0.4617	10	0.46703	T	0.11	.	12.9488	0.58388	0.0:0.9214:0.0:0.0786	.	434;434	E9KL44;P40939	.;ECHA_HUMAN	N	434	ENSP00000370023:D434N	ENSP00000370023:D434N	D	-	1	0	HADHA	26277614	1.000000	0.71417	0.847000	0.33407	0.963000	0.63663	6.031000	0.70911	1.305000	0.44909	-0.140000	0.14226	GAT		0.408	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		T	26424110	C	T	26424110	3	4	121	1	0	0	0	0	1	0	0	0	6964	826	29	3	1023	3	HADHA	2	26424110	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	10681392	26424110	216775263	25	31795										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32820106	32820106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aatattaaataacagaaaaaAaactgggtgaatactccaag	6	5	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:32820106A>G	ENST00000421745.2	+	68	13641	c.13507A>G	c.(13507-13509)Aaa>Gaa	p.K4503E		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4503					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)					aaCAGAAAAAAAACTGGGTGA	0.264																																					Pancreas(94;175 1509 16028 18060 45422)											0			2											24	26	25					2																	32820106		2195	4295	6490	32673610	SO:0001583	missense	57448			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.13507A>G	2.37:g.32820106A>G	ENSP00000393596:p.Lys4503Glu		32673610	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	13.42	2.230424	0.39399	.	.	ENSG00000115760	ENST00000421745	T	0.73789	-0.78	5.3	5.3	0.74995	.	0.048129	0.85682	D	0.000000	T	0.65821	0.2728	L	0.44542	1.39	0.58432	D	0.999995	B	0.20261	0.043	B	0.22601	0.04	T	0.60949	-0.7161	10	0.09338	T	0.73	.	15.2508	0.73545	1.0:0.0:0.0:0.0	.	4503	Q9NR09	BIRC6_HUMAN	E	4503	ENSP00000393596:K4503E	ENSP00000393596:K4503E	K	+	1	0	BIRC6	32673610	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.200000	0.77838	2.001000	0.58596	0.528000	0.53228	AAA		0.264	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32820106	A	G	32820106	3	3	121	1	0	0	0	0	1	0	0	0	1439	15	1	4	13777	4	BIRC6	2	32820106	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	6395996	32820106	210379267	26	31796										
FBXO41	150726	hgsc.bcm.edu	37	chr2	73490914	73490914	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gcaggatcagcaggttccccCcagctgccttcagcagggac	12	15	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:73490914C>T	ENST00000521871.1	-	8	2382	c.1967G>A	c.(1966-1968)gGg>gAg	p.G656E	FBXO41_ENST00000295133.5_Missense_Mutation_p.G717E|FBXO41_ENST00000520530.2_Missense_Mutation_p.G656E			Q8TF61	FBX41_HUMAN	F-box protein 41	656										breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						CAGGTTCCCCCCAGCTGCCTT	0.627																																																0			2											69	84	79					2																	73490914		2077	4220	6297	73344422	SO:0001583	missense	150726			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.1967G>A	2.37:g.73490914C>T	ENSP00000428646:p.Gly656Glu		73344422	G3V0Z7|Q2M1V8	Missense_Mutation	SNP	ENST00000521871.1	37	CCDS46337.2	.	.	.	.	.	.	.	.	.	.	C	19.62	3.861916	0.71949	.	.	ENSG00000163013	ENST00000295133;ENST00000521871	T;T	0.52754	0.65;0.65	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.55305	0.1912	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.41556	-0.9502	10	0.02654	T	1	-25.1158	17.897	0.88891	0.0:1.0:0.0:0.0	.	656	Q8TF61	FBX41_HUMAN	E	717;656	ENSP00000295133:G717E;ENSP00000428646:G656E	ENSP00000295133:G717E	G	-	2	0	FBXO41	73344422	1.000000	0.71417	0.946000	0.38457	0.994000	0.84299	5.684000	0.68197	2.813000	0.96785	0.561000	0.74099	GGG		0.627	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377381.1			T	73490914	C	T	73490914	3	4	121	1	0	0	0	0	1	0	0	0	5769	623	22	3	684	3	FBXO41	2	73490914	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	40670808	73490914	169708459	27	31797										
ADRA2B	151	hgsc.bcm.edu	37	chr2	96781429	96781429	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cccgcgcggctgggggccctGgtcgcccttgtagatgaggg	18	13	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:96781429G>A	ENST00000409345.3	-	1	555	c.460C>T	c.(460-462)Cag>Tag	p.Q154*		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	154					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)	TGGGGGCCCTGGTCGCCCTTG	0.647																																																0			2											25	32	30					2																	96781429		2136	4247	6383	96145156	SO:0001587	stop_gained	151			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.460C>T	2.37:g.96781429G>A	ENSP00000387281:p.Gln154*		96145156	Q4TUH9|Q53RF2|Q9BZK0	Nonsense_Mutation	SNP	ENST00000409345.3	37	CCDS56129.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201939	0.79127	.	.	ENSG00000222040	ENST00000409345	.	.	.	4.65	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	11.7755	0.51983	0.0:0.0:0.8135:0.1865	.	.	.	.	X	154	.	ENSP00000387281:Q154X	Q	-	1	0	ADRA2B	96145156	0.983000	0.35010	1.000000	0.80357	0.921000	0.55340	1.757000	0.38400	2.420000	0.82092	0.456000	0.33151	CAG		0.647	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			A	96781429	G	A	96781429	4	1	121	1	0	0	0	0	0	1	0	0	338	1357	47	3	887	3	ADRA2B	2	96781429	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	23290515	96781429	146417944	28	31798										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122216511	122216511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agttggcataatggcttcagCtccatggtcaaacttattcc	8	10	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:122216511C>T	ENST00000263710.4	-	13	1608	c.1219G>A	c.(1219-1221)Gct>Act	p.A407T	CLASP1_ENST00000409078.3_Missense_Mutation_p.A407T|CLASP1_ENST00000455322.2_Missense_Mutation_p.A407T|CLASP1_ENST00000541377.1_Missense_Mutation_p.A407T|CLASP1_ENST00000430234.1_5'UTR|CLASP1_ENST00000397587.3_Missense_Mutation_p.A407T|CLASP1_ENST00000545861.1_Missense_Mutation_p.A175T|CLASP1_ENST00000541859.1_Missense_Mutation_p.A176T	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	407					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)					ATGGCTTCAGCTCCATGGTCA	0.368																																																0			2											142	139	140					2																	122216511		1849	4096	5945	121932981	SO:0001583	missense	23332			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.1219G>A	2.37:g.122216511C>T	ENSP00000263710:p.Ala407Thr		121932981	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	C	23.1	4.374930	0.82573	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.66638	-0.22;0.81;0.81;0.81;-0.2;0.81;-0.2	5.45	5.45	0.79879	Armadillo-type fold (1);CLASP N-terminal domain (1);	0.046545	0.85682	N	0.000000	T	0.65565	0.2703	L	0.50333	1.59	0.80722	D	1	B;B;B;B	0.13145	0.006;0.005;0.007;0.002	B;B;B;B	0.18561	0.01;0.006;0.014;0.022	T	0.62609	-0.6818	10	0.72032	D	0.01	-10.7122	19.6233	0.95669	0.0:1.0:0.0:0.0	.	407;407;407;407	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	T	407;407;407;407;176;407;175	ENSP00000263710:A407T;ENSP00000389372:A407T;ENSP00000380717:A407T;ENSP00000441625:A407T;ENSP00000441770:A176T;ENSP00000386442:A407T;ENSP00000438620:A175T	ENSP00000263710:A407T	A	-	1	0	CLASP1	121932981	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.782000	0.85680	2.714000	0.92807	0.655000	0.94253	GCT		0.368	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		T	122216511	C	T	122216511	3	4	121	1	0	0	0	0	1	0	0	0	3460	797	28	3	3561	3	CLASP1	2	122216511	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	25435082	122216511	120982862	29	31799										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160289481	160289481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gctaactgctttttccttccCttgactatgcaggatgggag	10	10	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:160289481C>A	ENST00000392783.2	-	9	2182	c.1687G>T	c.(1687-1689)Ggg>Tgg	p.G563W	BAZ2B_ENST00000355831.2_Missense_Mutation_p.G563W|BAZ2B_ENST00000392782.1_Missense_Mutation_p.G561W|BAZ2B_ENST00000343439.5_Missense_Mutation_p.G561W	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G563R(1)		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						TTTTCCTTCCCTTGACTATGC	0.448																																																1	Substitution - Missense(1)	ovary(1)	2											196	182	187					2																	160289481		1909	4126	6035	159997727	SO:0001583	missense	29994			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.1687G>T	2.37:g.160289481C>A	ENSP00000376534:p.Gly563Trp		159997727	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	13.30	2.196863	0.38806	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.92	5.92	0.95590	.	0.000000	0.37669	U	0.001981	T	0.71247	0.3317	L	0.51422	1.61	0.45390	D	0.998376	D;D;D;D;D	0.89917	1.0;0.997;0.993;0.993;0.988	D;D;P;P;P	0.87578	0.998;0.924;0.724;0.852;0.715	T	0.72265	-0.4344	10	0.87932	D	0	-8.9802	15.0866	0.72158	0.1417:0.8583:0.0:0.0	.	563;367;561;561;563	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;BAZ2B_HUMAN	W	561;563;563;561;500	ENSP00000376533:G561W;ENSP00000376534:G563W;ENSP00000348087:G563W;ENSP00000339670:G561W	ENSP00000339670:G561W	G	-	1	0	BAZ2B	159997727	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.112000	0.50368	2.818000	0.97014	0.655000	0.94253	GGG		0.448	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160289481	C	A	160289481	3	1	121	1	0	0	0	0	1	0	0	0	1333	681	24	2	4935	2	BAZ2B	2	160289481	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	38072970	160289481	82909892	30	31800										
LRP2	4036	hgsc.bcm.edu	37	chr2	170137024	170137024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggagaagataatggaggcctCgccaactaaatgcgaagaag	13	7	0	3	rs548624353		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:170137024C>T	ENST00000263816.3	-	11	1462	c.1177G>A	c.(1177-1179)Gag>Aag	p.E393K	LRP2_ENST00000443831.1_Missense_Mutation_p.E393K	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	393					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)"	ATGGAGGCCTCGCCAACTAAA	0.453																																																0			2											43	42	43					2																	170137024		2203	4300	6503	169845270	SO:0001583	missense	4036				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.1177G>A	2.37:g.170137024C>T	ENSP00000263816:p.Glu393Lys		169845270	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.767037	0.00645	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.94723	-2.55;-3.5	5.54	0.163	0.14986	.	0.642841	0.15574	N	0.255295	D	0.85873	0.5798	L	0.31371	0.925	0.09310	N	1	P;P	0.40794	0.729;0.552	B;B	0.27796	0.083;0.06	T	0.75303	-0.3365	9	.	.	.	.	9.3925	0.38381	0.0:0.462:0.4093:0.1287	.	393;393	E9PC35;P98164	.;LRP2_HUMAN	K	393	ENSP00000263816:E393K;ENSP00000409813:E393K	.	E	-	1	0	LRP2	169845270	0.004000	0.15560	0.000000	0.03702	0.039000	0.13416	0.882000	0.28186	-0.282000	0.09128	-0.176000	0.13171	GAG		0.453	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170137024	C	T	170137024	3	4	121	1	0	0	0	0	1	0	0	0	8985	893	31	1	13066	1	LRP2	2	170137024	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	9847543	170137024	73062349	31	31801										
TTN	7273	hgsc.bcm.edu	37	chr2	179452773	179452773	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gcgtacaagctgtgctgcagCattacaccgtttccagcctt	9	13	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:179452773C>T	ENST00000591111.1	-	255	58662	c.58438G>A	c.(58438-58440)Gct>Act	p.A19480T	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A21121T|TTN_ENST00000342175.6_Missense_Mutation_p.A12248T|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A12056T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A12181T|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A18553T			Q8WZ42	TITIN_HUMAN	titin	19480	Fibronectin type-III 41. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> S (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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.A12056S(1)		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)			TGTGCTGCAGCATTACACCGT	0.463																																																1	Substitution - Missense(1)	stomach(1)	2											99	95	96					2																	179452773		1974	4168	6142	179161019	SO:0001583	missense	7273			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.58438G>A	2.37:g.179452773C>T	ENSP00000465570:p.Ala19480Thr		179161019	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	37		.	.	.	.	.	.	.	.	.	.	C	11.49	1.655221	0.29425	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.78	5.78	0.91487	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.27278	0.0669	N	0.00473	-1.45	0.37235	D	0.905862	B;B;B;B	0.17465	0.022;0.022;0.022;0.022	B;B;B;B	0.16289	0.008;0.008;0.008;0.015	T	0.40308	-0.9570	9	0.87932	D	0	.	20.0204	0.97499	0.0:1.0:0.0:0.0	.	12056;12181;12248;19480	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	18553;12056;12248;12181;12054	ENSP00000343764:A18553T;ENSP00000434586:A12056T;ENSP00000340554:A12248T;ENSP00000352154:A12181T	ENSP00000340554:A12248T	A	-	1	0	TTN	179161019	1.000000	0.71417	0.994000	0.49952	0.534000	0.34807	5.893000	0.69798	2.729000	0.93468	0.650000	0.86243	GCT		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179452773	C	T	179452773	3	4	121	1	0	0	0	0	1	0	0	0	16775	710	25	3	44850	3	TTN	2	179452773	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	9315749	179452773	63746600	32	31802										
TTN	7273	hgsc.bcm.edu	37	chr2	179476518	179476518	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aatggataggatttctgtggGttcacttgggtggccaactc	13	7	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:179476518G>C	ENST00000591111.1	-	218	45819	c.45595C>G	c.(45595-45597)Ccc>Gcc	p.P15199A	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P16840A|TTN_ENST00000342175.6_Missense_Mutation_p.P7967A|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P7775A|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P7900A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P14272A|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15199	Fibronectin type-III 10. {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)			ATTTCTGTGGGTTCACTTGGG	0.418																																																0			2											138	134	135					2																	179476518		1943	4145	6088	179184763	SO:0001583	missense	7273			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.45595C>G	2.37:g.179476518G>C	ENSP00000465570:p.Pro15199Ala		179184763	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	37		.	.	.	.	.	.	.	.	.	.	G	12.59	1.984911	0.35036	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	6.06	5.17	0.71159	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.41143	0.1146	L	0.31804	0.96	0.58432	D	0.999995	P;P;P;P	0.36144	0.539;0.539;0.539;0.539	B;B;B;B	0.31101	0.124;0.124;0.124;0.124	T	0.46871	-0.9160	9	0.87932	D	0	.	15.6525	0.77108	0.0662:0.0:0.9338:0.0	.	7775;7900;7967;15199	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	14272;7775;7967;7900;7775	ENSP00000343764:P14272A;ENSP00000434586:P7775A;ENSP00000340554:P7967A;ENSP00000352154:P7900A	ENSP00000340554:P7967A	P	-	1	0	TTN	179184763	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.952000	0.87827	2.879000	0.98667	0.650000	0.86243	CCC		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179476518	G	C	179476518	3	2	121	1	0	0	0	0	1	0	0	0	16775	1261	44	5	57555	5	TTN	2	179476518	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	23745	179476518	63722855	33	31803										
TTN	7273	hgsc.bcm.edu	37	chr2	179486328	179486328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttcagtcagtatttcatatcTtcctgtttcaatgatctcct	4	10	6	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:179486328T>C	ENST00000591111.1	-	195	40524	c.40300A>G	c.(40300-40302)Aga>Gga	p.R13434G	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R15075G|TTN_ENST00000342175.6_Missense_Mutation_p.R6202G|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R6010G|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R6135G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R12507G|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13434	Ig-like 90.		R -> K (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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)			ATTTCATATCTTCCTGTTTCA	0.448																																																0			2											143	138	139					2																	179486328		1966	4153	6119	179194573	SO:0001583	missense	7273			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.40300A>G	2.37:g.179486328T>C	ENSP00000465570:p.Arg13434Gly		179194573	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	37		.	.	.	.	.	.	.	.	.	.	T	12.70	2.016736	0.35606	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38	6.17	4.96	0.65561	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);	.	.	.	.	D	0.86912	0.6047	M	0.76938	2.355	0.40106	D	0.976425	P;P;P;P	0.50819	0.939;0.939;0.939;0.939	P;P;P;P	0.56278	0.739;0.739;0.739;0.795	D	0.89065	0.3465	9	0.87932	D	0	.	13.2634	0.60120	0.0:0.0:0.132:0.868	.	6010;6135;6202;13434	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	12507;6010;6202;6135;6010	ENSP00000343764:R12507G;ENSP00000434586:R6010G;ENSP00000340554:R6202G;ENSP00000352154:R6135G	ENSP00000340554:R6202G	R	-	1	2	TTN	179194573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.449000	0.52950	2.371000	0.80710	0.533000	0.62120	AGA		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179486328	T	C	179486328	3	2	121	1	0	0	0	0	1	0	0	0	16775	1617	56	4	62942	4	TTN	2	179486328	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	9810	179486328	63713045	34	31804										
TTN	7273	hgsc.bcm.edu	37	chr2	179585663	179585663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctaacctttcactgtcaacgCtgtgctgcagctggcgtcac	9	14	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:179585663C>T	ENST00000591111.1	-	77	22356	c.22132G>A	c.(22132-22134)Gcg>Acg	p.A7378T	TTN_ENST00000589042.1_Missense_Mutation_p.A7695T|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A6451T			Q8WZ42	TITIN_HUMAN	titin	12938	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)			ACTGTCAACGCTGTGCTGCAG	0.433																																																0			2											59	59	59					2																	179585663		2024	4202	6226	179293908	SO:0001583	missense	7273			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.22132G>A	2.37:g.179585663C>T	ENSP00000465570:p.Ala7378Thr		179293908	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	37		.	.	.	.	.	.	.	.	.	.	C	11.97	1.797535	0.31777	.	.	ENSG00000155657	ENST00000342992	T	0.65364	-0.15	6.02	4.18	0.49190	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.38241	0.1033	N	0.03268	-0.37	0.80722	D	1	B	0.13145	0.007	B	0.15052	0.012	T	0.22173	-1.0224	9	0.87932	D	0	.	9.9241	0.41481	0.2593:0.6744:0.0:0.0663	.	7378	Q8WZ42	TITIN_HUMAN	T	6451	ENSP00000343764:A6451T	ENSP00000343764:A6451T	A	-	1	0	TTN	179293908	0.002000	0.14202	0.969000	0.41365	0.953000	0.61014	0.688000	0.25422	0.829000	0.34733	0.650000	0.86243	GCG		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179585663	C	T	179585663	3	4	121	1	0	0	0	0	1	0	0	0	16775	797	28	3	81582	3	TTN	2	179585663	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	99335	179585663	63613710	35	31805										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187627354	187627354	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgaggacccagctttaaggcAcatcctagatggagggagtg	14	8	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:187627354A>G	ENST00000304698.5	+	8	2488	c.2285A>G	c.(2284-2286)cAc>cGc	p.H762R		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	762						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.H762P(1)		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						GCTTTAAGGCACATCCTAGAT	0.498																																																1	Substitution - Missense(1)	ovary(1)	2											75	77	77					2																	187627354		2203	4300	6503	187335599	SO:0001583	missense	165215			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.2285A>G	2.37:g.187627354A>G	ENSP00000304108:p.His762Arg		187335599	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.915613	0.52546	.	.	ENSG00000144369	ENST00000304698	T	0.29655	1.56	6.02	4.81	0.61882	.	0.143965	0.64402	D	0.000006	T	0.34308	0.0893	L	0.36672	1.1	0.44500	D	0.99744	P;P	0.52692	0.955;0.955	P;P	0.51701	0.677;0.677	T	0.03000	-1.1084	10	0.38643	T	0.18	-18.4059	13.0247	0.58808	0.8658:0.1342:0.0:0.0	.	762;763	Q6P995;A8K122	F171B_HUMAN;.	R	762	ENSP00000304108:H762R	ENSP00000304108:H762R	H	+	2	0	FAM171B	187335599	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	4.628000	0.61282	2.299000	0.77371	0.528000	0.53228	CAC		0.498	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		G	187627354	A	G	187627354	3	3	121	1	0	0	0	0	1	0	0	0	5507	159	6	4	2315	4	FAM171B	2	187627354	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	8041691	187627354	55572019	36	31806										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207175290	207175290	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agccttagtctgtgttctttCttctttaaatattaaactga	5	7	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:207175290C>A	ENST00000374423.3	+	5	6424	c.6038C>A	c.(6037-6039)tCt>tAt	p.S2013Y		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2013							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						TGTGTTCTTTCTTCTTTAAAT	0.348																																																0			2											31	31	31					2																	207175290		1825	4078	5903	206883535	SO:0001583	missense	57683			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.6038C>A	2.37:g.207175290C>A	ENSP00000363545:p.Ser2013Tyr		206883535	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.886096	0.51908	.	.	ENSG00000204186	ENST00000374423	T	0.64618	-0.11	5.46	5.46	0.80206	.	.	.	.	.	T	0.76183	0.3952	L	0.50333	1.59	0.40920	D	0.984304	D	0.89917	1.0	D	0.76575	0.988	T	0.78481	-0.2187	9	0.87932	D	0	.	19.292	0.94103	0.0:1.0:0.0:0.0	.	2013	Q9HCK1	ZDBF2_HUMAN	Y	2013	ENSP00000363545:S2013Y	ENSP00000363545:S2013Y	S	+	2	0	ZDBF2	206883535	0.835000	0.29415	0.264000	0.24511	0.061000	0.15899	1.905000	0.39878	2.559000	0.86315	0.563000	0.77884	TCT		0.348	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207175290	C	A	207175290	3	1	121	1	0	0	0	0	1	0	0	0	17638	913	32	2	6048	2	ZDBF2	2	207175290	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	19547936	207175290	36024083	37	31807										
MAP2	4133	hgsc.bcm.edu	37	chr2	210559008	210559008	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagcatgtcaatcaatttgcCgatgtcttgcctagattcca	7	10	3	1	rs146432517		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:210559008C>T	ENST00000360351.4	+	7	2620	c.2114C>T	c.(2113-2115)cCg>cTg	p.P705L	MAP2_ENST00000447185.1_Missense_Mutation_p.P701L|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	705			P -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.P705L(1)		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)	ATCAATTTGCCGATGTCTTGC	0.438																																					Pancreas(27;423 979 28787 29963)											1	Substitution - Missense(1)	large_intestine(1)	2						C	,LEU/PRO,,	0,4406		0,0,2203	241	231	234		,2114,,	6.1	1	2	dbSNP_134	234	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense,intron,intron	MAP2	NM_001039538.1,NM_002374.3,NM_031845.2,NM_031847.2	,98,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,probably-damaging,,	,705/1828,,	210559008	1,13005	2203	4300	6503	210267253	SO:0001583	missense	10988				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.2114C>T	2.37:g.210559008C>T	ENSP00000353508:p.Pro705Leu		210267253	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342024	0.81911	0.0	1.16E-4	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.28666	1.6;1.6	6.06	6.06	0.98353	MAP2/Tau projection (1);	0.000000	0.64402	D	0.000006	T	0.55832	0.1945	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.977;0.987	T	0.52682	-0.8543	10	0.87932	D	0	-13.3508	20.6244	0.99512	0.0:1.0:0.0:0.0	.	701;705	P11137-3;P11137	.;MAP2_HUMAN	L	705;701	ENSP00000353508:P705L;ENSP00000392164:P701L	ENSP00000353508:P705L	P	+	2	0	MAP2	210267253	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.238000	0.78173	2.879000	0.98667	0.650000	0.86243	CCG		0.438	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210559008	C	T	210559008	3	4	121	1	0	0	0	0	1	0	0	0	9265	652	23	1	2128	1	MAP2	2	210559008	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3383718	210559008	32640365	38	31808										
CPS1	1373	hgsc.bcm.edu	37	chr2	211521298	211521298	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgaagatgcaggtgtccactCgggagatgccactctgatgc	13	10	1	4	rs149518280		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:211521298C>T	ENST00000233072.5	+	30	3804	c.3608C>T	c.(3607-3609)tCg>tTg	p.S1203L	CPS1_ENST00000451903.2_Missense_Mutation_p.S752L|CPS1_ENST00000430249.2_Missense_Mutation_p.S1209L	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1203	ATP-grasp 2.		S -> L (in CPS1D). {ECO:0000269|PubMed:21120950}.|S -> P (in CPS1D). {ECO:0000269|PubMed:16737834}.		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)	GGTGTCCACTCGGGAGATGCC	0.418																																																0			2						C	LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	72	73	73		3626,2255,3608	5.9	1	2	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	145,145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	1209/1507,752/1050,1203/1501	211521298	1,13005	2203	4300	6503	211229543	SO:0001583	missense	1589			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.3608C>T	2.37:g.211521298C>T	ENSP00000233072:p.Ser1203Leu		211229543	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	33	5.233778	0.95207	0.0	1.16E-4	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.98264	-4.83;-4.83;-4.83	5.87	5.87	0.94306	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.99507	0.9824	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	0.97998	1.0358	10	0.87932	D	0	-6.1836	20.206	0.98277	0.0:1.0:0.0:0.0	.	1213;1203	Q59HF8;P31327	.;CPSM_HUMAN	L	1209;1211;1203;752	ENSP00000402608:S1209L;ENSP00000233072:S1203L;ENSP00000406136:S752L	ENSP00000233072:S1203L	S	+	2	0	CPS1	211229543	1.000000	0.71417	0.970000	0.41538	0.978000	0.69477	7.340000	0.79292	2.785000	0.95823	0.655000	0.94253	TCG		0.418	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211521298	C	T	211521298	3	4	121	1	0	0	0	0	1	0	0	0	3829	893	31	1	3748	1	CPS1	2	211521298	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	962290	211521298	31678075	39	31809										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215890452	215890452	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aatcttcataggaaccattgCgaagaaaagattttttaaat	6	5	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:215890452C>G	ENST00000272895.7	-	11	1451	c.1232G>C	c.(1231-1233)cGc>cCc	p.R411P	AC072062.3_ENST00000595058.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.R93P|AC072062.3_ENST00000419251.1_RNA|AC072062.3_ENST00000602182.1_RNA|AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	411					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)		GGAACCATTGCGAAGAAAAGA	0.318																																					Ovarian(66;664 1488 5121 34295)											0			2											81	85	84					2																	215890452		2203	4300	6503	215598697	SO:0001583	missense	26154			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.1232G>C	2.37:g.215890452C>G	ENSP00000272895:p.Arg411Pro		215598697	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444963	0.43429	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.58797	0.31;0.31	5.96	-1.02	0.10135	.	1.014940	0.07896	N	0.971950	T	0.37293	0.0998	N	0.14661	0.345	0.80722	D	1	B;B	0.33000	0.393;0.236	B;B	0.31290	0.06;0.127	T	0.09058	-1.0692	10	0.29301	T	0.29	.	10.0453	0.42184	0.0:0.4926:0.0:0.5074	.	411;93	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	411;93	ENSP00000272895:R411P;ENSP00000374312:R93P	ENSP00000272895:R411P	R	-	2	0	ABCA12	215598697	0.961000	0.32948	0.996000	0.52242	0.825000	0.46686	-0.285000	0.08410	-0.056000	0.13221	0.655000	0.94253	CGC		0.318	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215890452	C	G	215890452	3	3	121	1	0	0	0	0	1	0	0	0	30	768	27	5	6727	5	ABCA12	2	215890452	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	4369154	215890452	27308921	40	31810										
PTPRN	5798	hgsc.bcm.edu	37	chr2	220162096	220162096	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctgctcacccgtgaaggctcCggtggaccctctgcccggtt	12	16	2	1	rs560429997		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:220162096C>T	ENST00000295718.2	-	14	2187	c.1947G>A	c.(1945-1947)ccG>ccA	p.P649P	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Silent_p.P559P|PTPRN_ENST00000409251.3_Silent_p.P620P|PTPRN_ENST00000497977.1_5'Flank	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	649					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GTGAAGGCTCCGGTGGACCCT	0.652																																																0			2											66	68	68					2																	220162096		2203	4300	6503	219870340	SO:0001819	synonymous_variant	5798				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1947G>A	2.37:g.220162096C>T			219870340	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	37	CCDS2440.1																																																																																				0.652	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			T	220162096	C	T	220162096	2	4	121	1	0	0	0	0	0	0	0	1	12844	639	23	1		1	PTPRN	2	220162096	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	4271644	220162096	23037277	41	31811										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225695293	225695293	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtcaatcaagtgctgtgccaTcgattttaggataattgcaa	9	7	2	0	rs199559649		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:225695293T>A	ENST00000258390.7	-	27	3068	c.3001A>T	c.(3001-3003)Atg>Ttg	p.M1001L	DOCK10_ENST00000409592.3_Missense_Mutation_p.M995L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1001					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)		TGCTGTGCCATCGATTTTAGG	0.284																																																0			2											41	38	39					2																	225695293		1800	4062	5862	225403537	SO:0001583	missense	55619			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.3001A>T	2.37:g.225695293T>A	ENSP00000258390:p.Met1001Leu		225403537	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.156282	0.57259	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.03413	3.97;3.94	5.78	4.64	0.57946	.	0.035122	0.85682	D	0.000000	T	0.08935	0.0221	M	0.87617	2.895	0.37959	D	0.932926	B;B	0.26258	0.058;0.145	B;B	0.25759	0.012;0.063	T	0.01739	-1.1284	10	0.87932	D	0	.	11.2311	0.48912	0.0:0.0711:0.0:0.9289	.	1001;995	Q96BY6;B3FL70	DOC10_HUMAN;.	L	995;1001	ENSP00000386694:M995L;ENSP00000258390:M1001L	ENSP00000258390:M1001L	M	-	1	0	DOCK10	225403537	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.995000	0.57001	2.211000	0.71520	0.459000	0.35465	ATG		0.284	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225695293	T	A	225695293	3	1	121	1	0	0	0	0	1	0	0	0	4696	1435	50	5	3679	5	DOCK10	2	225695293	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	5533197	225695293	17504080	42	31812										
DGKD	8527	hgsc.bcm.edu	37	chr2	234346055	234346055	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgtaaagaatccttgctgacCaagtgcccacttggcctgtg	10	11	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:234346055C>A	ENST00000264057.2	+	8	864	c.852C>A	c.(850-852)acC>acA	p.T284T	DGKD_ENST00000409813.3_Silent_p.T240T	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	284					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)	CCTTGCTGACCAAGTGCCCAC	0.532																																																0			2											177	147	157					2																	234346055		2203	4300	6503	234010794	SO:0001819	synonymous_variant	8527			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.852C>A	2.37:g.234346055C>A			234010794	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	37	CCDS2504.1																																																																																				0.532	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		A	234346055	C	A	234346055	2	1	121	1	0	0	0	0	0	0	0	1	4478	581	21	2		2	DGKD	2	234346055	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	8650762	234346055	8853318	43	31813										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242179360	242179360	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctccttctgtgcctctcggaCggcgtcctcctttccaatga	8	16	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr2:242179360C>T	ENST00000391975.1	-	18	2574	c.2347G>A	c.(2347-2349)Gtc>Atc	p.V783I	HDLBP_ENST00000391976.2_Missense_Mutation_p.V783I|HDLBP_ENST00000427183.2_Missense_Mutation_p.V750I|HDLBP_ENST00000310931.4_Missense_Mutation_p.V783I	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	783	KH 9. {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)			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)		GCCTCTCGGACGGCGTCCTCC	0.617																																																0			2											95	92	93					2																	242179360		2203	4300	6503	241828033	SO:0001583	missense	3069				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.2347G>A	2.37:g.242179360C>T	ENSP00000375836:p.Val783Ile		241828033	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	37	CCDS2547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.34|16.34	3.097034|3.097034	0.56075|0.56075	.|.	.|.	ENSG00000115677|ENSG00000115677	ENST00000373292|ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183	.|T;T;T;T	.|0.38401	.|1.14;1.14;1.14;1.14	5.38|5.38	4.5|4.5	0.54988|0.54988	.|K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.51568|0.51568	0.1682|0.1682	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.995	.|P;D	.|0.66602	.|0.895;0.945	T|T	0.51671|0.51671	-0.8676|-0.8676	5|10	.|0.51188	.|T	.|0.08	-53.9113|-53.9113	14.0666|14.0666	0.64834|0.64834	0.0:0.9274:0.0:0.0726|0.0:0.9274:0.0:0.0726	.|.	.|750;783	.|E7EM71;Q00341	.|.;VIGLN_HUMAN	H|I	591|783;783;783;750	.|ENSP00000375836:V783I;ENSP00000375837:V783I;ENSP00000312042:V783I;ENSP00000399139:V750I	.|ENSP00000312042:V783I	R|V	-|-	2|1	0|0	HDLBP|HDLBP	241828033|241828033	1.000000|1.000000	0.71417|0.71417	0.016000|0.016000	0.15963|0.15963	0.046000|0.046000	0.14306|0.14306	6.010000|6.010000	0.70753|0.70753	1.284000|1.284000	0.44531|0.44531	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.617	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		T	242179360	C	T	242179360	3	4	121	1	0	0	0	0	1	0	0	0	7046	536	19	1	1503	1	HDLBP	2	242179360	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	7833305	242179360	1020013	44	31814										
RAD18	56852	hgsc.bcm.edu	37	chr3	8983368	8983368	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaattatccattaacctgctCccctgctttaaagactgtct	4	12	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:8983368C>A	ENST00000264926.2	-	5	503	c.387G>T	c.(385-387)ggG>ggT	p.G129G	RAD18_ENST00000495087.1_5'UTR	NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	129					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		TTAACCTGCTCCCCTGCTTTA	0.393								Rad6 pathway																																								0			3											124	128	127					3																	8983368		2203	4300	6503	8958368	SO:0001819	synonymous_variant	56852				CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.387G>T	3.37:g.8983368C>A			8958368	Q58F55|Q9NRT6	Silent	SNP	ENST00000264926.2	37	CCDS2571.1																																																																																				0.393	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165		A	8983368	C	A	8983368	2	1	121	1	0	0	0	0	0	0	0	1	13017	842	30	2		2	RAD18	3	8983368	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10		8983368	189039062	45	31815										
VHL	7428	hgsc.bcm.edu	37	chr3	10191571	10191571	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aggtcgctctacgaagatctGgaagaccacccaaatgtgca	10	11	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:10191571G>A	ENST00000256474.2	+	3	1404	c.564G>A	c.(562-564)ctG>ctA	p.L188L	VHL_ENST00000345392.2_Silent_p.L147L|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	188			L -> P (in VHLD; type I-II). {ECO:0000269|PubMed:9829912}.|L -> Q (in VHLD; type I). {ECO:0000269|PubMed:8956040}.|L -> V (in ECYT2, pheochromocytoma and VHLD; type IIA; dbSNP:rs5030824). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:12844285}.		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.D187fs*14(1)|p.E189fs*27(1)|p.E189fs*25(1)|p.Y185fs*11(1)|p.L188L(1)|p.L188>?(1)|p.D187_N193del(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)		ACGAAGATCTGGAAGACCACC	0.502		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	7	Deletion - Frameshift(3)|Substitution - coding silent(1)|Deletion - In frame(1)|Insertion - Frameshift(1)|Complex(1)	kidney(7)	3											77	70	72					3																	10191571		2203	4300	6503	10166571	SO:0001819	synonymous_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	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.564G>A	3.37:g.10191571G>A			10166571	B2RE45|Q13599|Q6PDA9	Silent	SNP	ENST00000256474.2	37	CCDS2597.1																																																																																				0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10191571	G	A	10191571	2	1	121	1	0	0	0	0	0	0	0	1	17202	1335	47	3		3	VHL	3	10191571	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1208203	10191571	187830859	46	31816										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37125235	37125235	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atcaaattgttcttctcattGtctaactgtgcattggaaac	6	8	4	0	rs576073289		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:37125235G>A	ENST00000336686.4	-	19	1250	c.1170C>T	c.(1168-1170)gaC>gaT	p.D390D	LRRFIP2_ENST00000421276.2_Silent_p.D158D|LRRFIP2_ENST00000354379.4_Silent_p.D134D|LRRFIP2_ENST00000396428.2_Silent_p.D206D|LRRFIP2_ENST00000421307.1_Silent_p.D390D|LRRFIP2_ENST00000440230.1_Silent_p.D158D			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	390					Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.D390D(1)|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						TCTTCTCATTGTCTAACTGTG	0.348													G|||	1	0.000199681	0	0	5008	,	,		18328	0.001		0	False		,,,				2504	0															2	Whole gene deletion(1)|Substitution - coding silent(1)	ovary(2)	3											198	187	191					3																	37125235		2203	4300	6503	37100239	SO:0001819	synonymous_variant	9209			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.1170C>T	3.37:g.37125235G>A			37100239	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Silent	SNP	ENST00000336686.4	37	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	G	9.805	1.181639	0.21787	.	.	ENSG00000093167	ENST00000440742	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.0785	14.1881	0.65620	0.0712:0.0:0.9288:0.0	.	.	.	.	X	3	.	.	Q	-	1	0	LRRFIP2	37100239	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.978000	0.49305	2.733000	0.93635	0.561000	0.74099	CAA		0.348	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37125235	G	A	37125235	2	1	121	1	0	0	0	0	0	0	0	1	9057	1368	48	3		3	LRRFIP2	3	37125235	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	26933664	37125235	160897195	47	31817										
OXSR1	9943	hgsc.bcm.edu	37	chr3	38292940	38292940	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctcatttctgctggcctggtCgacggaagggatttagtaat	12	8	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:38292940C>T	ENST00000311806.3	+	16	1794	c.1422C>T	c.(1420-1422)gtC>gtT	p.V474V		NM_005109.2	NP_005100.1			oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CTGGCCTGGTCGACGGAAGGG	0.448																																																0			3											311	280	291					3																	38292940		2203	4300	6503	38267944	SO:0001819	synonymous_variant	9943			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	ENST00000311806.3:c.1422C>T	3.37:g.38292940C>T			38267944		Silent	SNP	ENST00000311806.3	37	CCDS2675.1																																																																																				0.448	OXSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253744.1	NM_005109		T	38292940	C	T	38292940	2	4	121	1	0	0	0	0	0	0	0	1	11367	871	31	1		1	OXSR1	3	38292940	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1167705	38292940	159729490	48	31818										
CCR9	10803	hgsc.bcm.edu	37	chr3	45943063	45943063	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtgaccatcactgtcctgacCgtctttgtcttgtctcagtt	8	12	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:45943063C>T	ENST00000357632.2	+	3	963	c.783C>T	c.(781-783)acC>acT	p.T261T	LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000395963.2_Silent_p.T249T|CCR9_ENST00000355983.2_Silent_p.T249T|CCR9_ENST00000422395.1_3'UTR|Y_RNA_ENST00000364765.1_RNA|LZTFL1_ENST00000536047.1_Intron	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	261					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)	p.T261T(1)		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)		CTGTCCTGACCGTCTTTGTCT	0.473																																																1	Substitution - coding silent(1)	ovary(1)	3											216	176	189					3																	45943063		2203	4300	6503	45918067	SO:0001819	synonymous_variant	10803			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.783C>T	3.37:g.45943063C>T			45918067	Q4VBM3|Q549E0|Q9UQQ6	Silent	SNP	ENST00000357632.2	37	CCDS2732.1																																																																																				0.473	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			T	45943063	C	T	45943063	2	4	121	1	0	0	0	0	0	0	0	1	2954	639	23	1		1	CCR9	3	45943063	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	7650123	45943063	152079367	49	31819										
P4HTM	54681	hgsc.bcm.edu	37	chr3	49044280	49044280	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttgcccgagaagggggcacCgactcacagcccgagtgggc	15	14	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:49044280C>A	ENST00000383729.4	+	9	1820	c.1449C>A	c.(1447-1449)acC>acA	p.T483T	WDR6_ENST00000415265.2_5'Flank|WDR6_ENST00000448293.1_5'Flank|P4HTM_ENST00000343546.4_Silent_p.T544T|WDR6_ENST00000395474.3_5'Flank|WDR6_ENST00000608424.1_5'Flank	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	483						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)	AAGGGGGCACCGACTCACAGC	0.657																																																0			3											28	31	30					3																	49044280		2203	4300	6503	49019284	SO:0001819	synonymous_variant	54681				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.1449C>A	3.37:g.49044280C>A			49019284	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Silent	SNP	ENST00000383729.4	37	CCDS43089.1																																																																																				0.657	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938		A	49044280	C	A	49044280	2	1	121	1	0	0	0	0	0	0	0	1	11391	639	23	2		2	P4HTM	3	49044280	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3101217	49044280	148978150	50	31820										
WDR6	11180	hgsc.bcm.edu	37	chr3	49052280	49052280	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttggcaccccctccctgacTctccaggcccacagctgtgg	9	19	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:49052280T>C	ENST00000608424.1	+	6	2964	c.2925T>C	c.(2923-2925)acT>acC	p.T975T	WDR6_ENST00000415265.2_Silent_p.T423T|WDR6_ENST00000448293.1_Silent_p.T924T|WDR6_ENST00000395474.3_Silent_p.T1005T|DALRD3_ENST00000496568.1_5'Flank			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	975					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)		CCTCCCTGACTCTCCAGGCCC	0.622																																																0			3											79	85	83					3																	49052280		2203	4300	6503	49027284	SO:0001819	synonymous_variant	11180			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.2925T>C	3.37:g.49052280T>C			49027284	B4DHK2|Q3MIT1|Q9UF63	Silent	SNP	ENST00000608424.1	37																																																																																					0.622	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			C	49052280	T	C	49052280	2	2	121	1	0	0	0	0	0	0	0	1	17350	1538	54	4		4	WDR6	3	49052280	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	8000	49052280	148970150	51	31821										
UBA7	7318	hgsc.bcm.edu	37	chr3	49848739	49848739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgggcagctactgcacccagCatggccaccatagggctcaa	11	14	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:49848739C>T	ENST00000333486.3	-	9	1247	c.1089G>A	c.(1087-1089)atG>atA	p.M363I	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	363	2 approximate repeats.			GVLSPMVAMLGAVAAQEVLKAISR -> RCLEPMVACWVSS CPGSAEGNLQ (in Ref. 1; AAA75388 and 2; AAG49557). {ECO:0000305}.	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)	p.M363I(1)		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)		CTGCACCCAGCATGGCCACCA	0.597																																																1	Substitution - Missense(1)	large_intestine(1)	3											121	102	109					3																	49848739		2203	4300	6503	49823743	SO:0001583	missense	7318			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.1089G>A	3.37:g.49848739C>T	ENSP00000333266:p.Met363Ile		49823743	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	9.101	1.004172	0.19199	.	.	ENSG00000182179	ENST00000333486	T	0.32023	1.47	5.76	-2.74	0.05932	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	1.010520	0.07901	N	0.972595	T	0.09379	0.0231	N	0.02379	-0.575	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24083	-1.0170	10	0.34782	T	0.22	0.3312	0.5062	0.00588	0.2301:0.326:0.1577:0.2862	.	363	P41226	UBA7_HUMAN	I	363	ENSP00000333266:M363I	ENSP00000333266:M363I	M	-	3	0	UBA7	49823743	0.000000	0.05858	0.021000	0.16686	0.373000	0.29922	-0.334000	0.07883	-0.192000	0.10432	0.462000	0.41574	ATG		0.597	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		T	49848739	C	T	49848739	3	4	121	1	0	0	0	0	1	0	0	0	16873	710	25	3	2013	3	UBA7	3	49848739	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	796459	49848739	148173691	52	31822										
NISCH	11188	hgsc.bcm.edu	37	chr3	52522565	52522565	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atcgccaagacccccgggacGggaggcagcccccagggctc	14	17	0	1	rs374429650		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:52522565G>T	ENST00000479054.1	+	17	3129	c.3057G>T	c.(3055-3057)acG>acT	p.T1019T	NISCH_ENST00000345716.4_Silent_p.T1019T			Q9Y2I1	NISCH_HUMAN	nischarin	1019					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)	CCCCCGGGACGGGAGGCAGCC	0.677																																																0			3											27	30	29					3																	52522565		2203	4299	6502	52497605	SO:0001819	synonymous_variant	11188			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.3057G>T	3.37:g.52522565G>T			52497605	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	37	CCDS33767.1																																																																																				0.677	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52522565	G	T	52522565	2	4	121	1	0	0	0	0	0	0	0	1	10463	1103	39	2		2	NISCH	3	52522565	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	2673826	52522565	145499865	53	31823										
PRKCD	5580	hgsc.bcm.edu	37	chr3	53212456	53212456	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	accatggcgccgttcctgcgCatcgccttcaactcctatga	8	16	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:53212456C>T	ENST00000394729.2	+	2	346	c.18C>T	c.(16-18)cgC>cgT	p.R6R	PRKCD_ENST00000477794.2_3'UTR|PRKCD_ENST00000330452.3_Silent_p.R6R	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	6	C2.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|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)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	CGTTCCTGCGCATCGCCTTCA	0.677																																																0			3											45	42	43					3																	53212456		2203	4300	6503	53187496	SO:0001819	synonymous_variant	5580				CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.18C>T	3.37:g.53212456C>T			53187496	B0KZ81|B2R834|Q15144|Q86XJ6	Silent	SNP	ENST00000394729.2	37	CCDS2870.1																																																																																				0.677	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1			T	53212456	C	T	53212456	2	4	121	1	0	0	0	0	0	0	0	1	12543	697	25	3		3	PRKCD	3	53212456	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	689891	53212456	144809974	54	31824										
OR5K2	402135	hgsc.bcm.edu	37	chr3	98216960	98216960	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aactctgcattcagatgaccAcaggcgccttcatagctgga	9	12	3	2	rs150442894		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:98216960A>G	ENST00000427338.1	+	1	513	c.436A>G	c.(436-438)Aca>Gca	p.T146A	CLDND1_ENST00000502288.1_3'UTR	NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	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)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCAGATGACCACAGGCGCCTT	0.458																																																0			3											141	143	142					3																	98216960		2203	4300	6503	99699650	SO:0001583	missense	402135			AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"GPCR / Class A : Olfactory receptors"	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.436A>G	3.37:g.98216960A>G	ENSP00000393889:p.Thr146Ala		99699650	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	.	.	.	.	.	.	.	.	.	.	A	0.035	-1.314158	0.01331	.	.	ENSG00000231861	ENST00000427338	T	0.33438	1.41	2.87	1.67	0.24075	GPCR, rhodopsin-like superfamily (1);	0.527844	0.15802	N	0.243912	T	0.10252	0.0251	N	0.03209	-0.39	0.09310	N	0.999995	B	0.09022	0.002	B	0.17979	0.02	T	0.37126	-0.9719	10	0.02654	T	1	-2.8453	6.8357	0.23935	0.7924:0.0:0.0:0.2076	.	146	Q8NHB8	OR5K2_HUMAN	A	146	ENSP00000393889:T146A	ENSP00000393889:T146A	T	+	1	0	OR5K2	99699650	0.017000	0.18338	0.581000	0.28614	0.604000	0.37047	-0.260000	0.08708	0.485000	0.27652	0.248000	0.18094	ACA		0.458	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2			G	98216960	A	G	98216960	3	3	121	1	0	0	0	0	1	0	0	0	11198	159	6	4	438	4	OR5K2	3	98216960	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	45004504	98216960	99805470	55	31825										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135722029	135722029	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaatctaaagtctcttcaccCatagaaaaagtctcaccttc	3	12	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:135722029C>T	ENST00000264977.3	+	2	2306	c.1689C>T	c.(1687-1689)ccC>ccT	p.P563P	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	563					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						TCTCTTCACCCATAGAAAAAG	0.408																																																0			3											58	59	59					3																	135722029		2203	4299	6502	137204719	SO:0001819	synonymous_variant	5523			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.1689C>T	3.37:g.135722029C>T			137204719	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																				0.408	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		T	135722029	C	T	135722029	2	4	121	1	0	0	0	0	0	0	0	1	12422	581	21	3		3	PPP2R3A	3	135722029	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	37505069	135722029	62300401	56	31826										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916891	178916891	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagacgactttgtgaccttcGgctttttcaaccctttttaa	6	10	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:178916891G>A	ENST00000263967.3	+	2	435	c.278G>A	c.(277-279)cGg>cAg	p.R93Q		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	93	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)	p.R93Q(11)		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)	TGTGACCTTCGGCTTTTTCAA	0.343		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	11	Substitution - Missense(11)	endometrium(11)	3											102	98	99					3																	178916891		1821	4076	5897	180399585	SO:0001583	missense	5290				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.278G>A	3.37:g.178916891G>A	ENSP00000263967:p.Arg93Gln		180399585	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.278752	0.80692	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.73681	-0.77;-0.77	5.52	5.52	0.82312	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	T	0.82153	0.4975	L	0.54323	1.7	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.80636	-0.1294	9	.	.	.	-9.1625	19.4271	0.94746	0.0:0.0:1.0:0.0	.	93	P42336	PK3CA_HUMAN	Q	93	ENSP00000263967:R93Q;ENSP00000417479:R93Q	.	R	+	2	0	PIK3CA	180399585	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.471000	0.97696	2.584000	0.87258	0.555000	0.69702	CGG		0.343	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178916891	G	A	178916891	3	1	121	1	0	0	0	0	1	0	0	0	11944	1116	39	1	280	1	PIK3CA	3	178916891	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	43194862	178916891	19105539	57	31827										
CHRD	8646	hgsc.bcm.edu	37	chr3	184104655	184104655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acgaacggtgatctgtgaccCggtggtgtgcccaccgccca	13	14	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:184104655C>T	ENST00000204604.1	+	17	2465	c.2219C>T	c.(2218-2220)cCg>cTg	p.P740L	CHRD_ENST00000545352.1_Missense_Mutation_p.P282L|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000348986.3_Missense_Mutation_p.P700L|CHRD_ENST00000450923.1_Missense_Mutation_p.P740L	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	740	VWFC 2. {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)			ATCTGTGACCCGGTGGTGTGC	0.662																																																0			3											56	45	49					3																	184104655		2203	4300	6503	185587349	SO:0001583	missense	8646			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.2219C>T	3.37:g.184104655C>T	ENSP00000204604:p.Pro740Leu		185587349	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.109587	0.77096	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.14	4.44	4.44	0.53790	von Willebrand factor, type C (4);	0.000000	0.85682	D	0.000000	T	0.81880	0.4916	M	0.69823	2.125	0.44946	D	0.997966	D;D;D;D	0.89917	0.996;1.0;0.997;1.0	P;D;D;D	0.78314	0.843;0.985;0.931;0.991	T	0.81289	-0.1000	10	0.35671	T	0.21	-14.8595	14.9202	0.70832	0.0:1.0:0.0:0.0	.	282;700;740;740	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	L	740;740;700;282;453	ENSP00000204604:P740L;ENSP00000408972:P740L;ENSP00000334036:P700L;ENSP00000442948:P282L	ENSP00000204604:P740L	P	+	2	0	CHRD	185587349	1.000000	0.71417	0.914000	0.36105	0.638000	0.38207	7.075000	0.76798	2.181000	0.69327	0.462000	0.41574	CCG		0.662	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184104655	C	T	184104655	3	4	121	1	0	0	0	0	1	0	0	0	3378	652	23	1	2285	1	CHRD	3	184104655	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	5187764	184104655	13917775	58	31828										
IQCG	84223	hgsc.bcm.edu	37	chr3	197659160	197659160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aatggtatctgcaatcacatCgctgaaaaactgcctgtaag	8	9	2	1	rs67877771	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr3:197659160C>T	ENST00000265239.6	-	6	953	c.529G>A	c.(529-531)Gat>Aat	p.D177N	IQCG_ENST00000455191.1_Missense_Mutation_p.D177N|IQCG_ENST00000453254.1_Missense_Mutation_p.D177N	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	177				D -> H (in Ref. 4; AAH04816). {ECO:0000305}.		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)		GCAATCACATCGCTGAAAAAC	0.428																																																0			3											107	101	103					3																	197659160		2203	4300	6503	199143557	SO:0001583	missense	84223			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.529G>A	3.37:g.197659160C>T	ENSP00000265239:p.Asp177Asn		199143557	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.630917	0.28978	.	.	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.55052	0.83;0.83;0.81;0.54	4.81	2.88	0.33553	.	0.205977	0.38837	N	0.001547	T	0.42698	0.1214	M	0.75264	2.295	0.35713	D	0.816549	P;P	0.45474	0.859;0.648	B;B	0.33568	0.166;0.091	T	0.53265	-0.8463	10	0.30078	T	0.28	-14.1493	7.1513	0.25612	0.0:0.7581:0.0:0.2419	.	177;177	C9JKX8;Q9H095	.;IQCG_HUMAN	N	177;177;177;158	ENSP00000265239:D177N;ENSP00000407736:D177N;ENSP00000389897:D177N;ENSP00000406411:D158N	ENSP00000265239:D177N	D	-	1	0	IQCG	199143557	0.961000	0.32948	0.987000	0.45799	0.493000	0.33554	1.099000	0.31013	1.073000	0.40885	0.460000	0.39030	GAT		0.428	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263		T	197659160	C	T	197659160	3	4	121	1	0	0	0	0	1	0	0	0	7831	884	31	1	830	1	IQCG	3	197659160	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	13554505	197659160	363270	59	31829										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25671402	25671402	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agagcttccacttcaagaatGgagaagatgccccagatctt	9	10	2	5			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:25671402G>T	ENST00000382051.3	+	7	819	c.769G>T	c.(769-771)Gga>Tga	p.G257*	SLC34A2_ENST00000504570.1_Nonsense_Mutation_p.G256*|SLC34A2_ENST00000503434.1_Nonsense_Mutation_p.G256*	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	257					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)				CTTCAAGAATGGAGAAGATGC	0.493			T	ROS1	NSCLC																																		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	0			4											201	196	198					4																	25671402		2203	4300	6503	25280500	SO:0001587	stop_gained	10568			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.769G>T	4.37:g.25671402G>T	ENSP00000371483:p.Gly257*		25280500	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Nonsense_Mutation	SNP	ENST00000382051.3	37	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423040	0.83559	.	.	ENSG00000157765	ENST00000504570;ENST00000382051;ENST00000503434	.	.	.	5.39	5.39	0.77823	.	0.048173	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-5.1239	19.5216	0.95187	0.0:0.0:1.0:0.0	.	.	.	.	X	256;257;256	.	ENSP00000371483:G257X	G	+	1	0	SLC34A2	25280500	1.000000	0.71417	0.962000	0.40283	0.190000	0.23558	9.491000	0.97954	2.700000	0.92200	0.561000	0.74099	GGA		0.493	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		T	25671402	G	T	25671402	4	4	121	1	0	0	0	0	0	1	0	0	14605	1349	47	2	791	2	SLC34A2	4	25671402	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10		25671402	165482874	60	31830										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55141120	55141120	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgactcaagatgggagtttcCaagagatggactagtgcttg	13	6	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:55141120C>A	ENST00000257290.5	+	12	2097	c.1766C>A	c.(1765-1767)cCa>cAa	p.P589Q	FIP1L1_ENST00000507166.1_Missense_Mutation_p.P349Q	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	589					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)	TGGGAGTTTCCAAGAGATGGA	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)																											Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	0			4											92	91	92					4																	55141120		2203	4300	6503	54835877	SO:0001583	missense	5156	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	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.1766C>A	4.37:g.55141120C>A	ENSP00000257290:p.Pro589Gln		54835877	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.594965	0.66219	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	D;D	0.89343	-2.5;-2.5	6.03	6.03	0.97812	Protein kinase-like domain (1);	0.000000	0.31936	U	0.006834	D	0.93245	0.7848	M	0.81802	2.56	0.80722	D	1	D;P	0.59357	0.985;0.904	P;B	0.57152	0.814;0.227	D	0.93608	0.6936	10	0.87932	D	0	.	15.2928	0.73879	0.14:0.86:0.0:0.0	.	589;589	P16234-3;P16234	.;PGFRA_HUMAN	Q	349;589	ENSP00000423325:P349Q;ENSP00000257290:P589Q	ENSP00000423325:P349Q	P	+	2	0	FIP1L1;PDGFRA	54835877	1.000000	0.71417	0.998000	0.56505	0.284000	0.27059	4.641000	0.61375	2.861000	0.98227	0.655000	0.94253	CCA		0.453	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55141120	C	A	55141120	3	1	121	1	0	0	0	0	1	0	0	0	11692	594	21	2	1808	2	PDGFRA	4	55141120	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	29469718	55141120	136013156	61	31831										
KIT	3815	hgsc.bcm.edu	37	chr4	55564500	55564500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccttgtatgggaaagaagacAacgacacgctggtccgctgt	12	10	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:55564500A>G	ENST00000288135.5	+	3	485	c.388A>G	c.(388-390)Aac>Gac	p.N130D		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	130	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)	GAAAGAAGACAACGACACGCT	0.498		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																													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"	0			4											45	42	43					4																	55564500		2203	4300	6503	55259257	SO:0001583	missense	3815	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.388A>G	4.37:g.55564500A>G	ENSP00000288135:p.Asn130Asp		55259257	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	2.143	-0.396442	0.04899	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	T;T	0.76186	-1.0;-1.0	5.59	1.67	0.24075	Immunoglobulin-like fold (1);	1.478020	0.04233	N	0.335594	T	0.57257	0.2041	N	0.22421	0.69	0.09310	N	1	B;B	0.14805	0.0;0.011	B;B	0.19946	0.001;0.027	T	0.36065	-0.9763	10	0.09338	T	0.73	.	3.4772	0.07589	0.6519:0.1411:0.0722:0.1347	.	130;130	P10721-2;P10721	.;KIT_HUMAN	D	130	ENSP00000288135:N130D;ENSP00000390987:N130D	ENSP00000288135:N130D	N	+	1	0	KIT	55259257	0.117000	0.22190	0.001000	0.08648	0.249000	0.25844	1.839000	0.39220	0.061000	0.16311	0.459000	0.35465	AAC		0.498	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55564500	A	G	55564500	3	3	121	1	0	0	0	0	1	0	0	0	8350	130	5	4	398	4	KIT	4	55564500	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	423380	55564500	135589776	62	31832										
KIT	3815	hgsc.bcm.edu	37	chr4	55594177	55594177	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atgcatgtttccaattttagCgagtgcccatttgacagaac	8	9	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:55594177C>T	ENST00000288135.5	+	13	1977	c.1880C>T	c.(1879-1881)cCg>cTg	p.P627L		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	627	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)	p.P627L(1)		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)	CCAATTTTAGCGAGTGCCCAT	0.433		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																													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"	1	Substitution - Missense(1)	soft_tissue(1)	4											145	134	137					4																	55594177		2203	4300	6503	55288934	SO:0001630	splice_region_variant	3815	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.1880-1C>T	4.37:g.55594177C>T			55288934	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903525	0.72754	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.82711	-1.64;-1.64	6.06	5.22	0.72569	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	0.000013	D	0.82314	0.5010	N	0.13327	0.33	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.999	P;P;D	0.66084	0.818;0.898;0.941	T	0.81947	-0.0700	9	.	.	.	.	15.2169	0.73274	0.0:0.933:0.0:0.067	.	134;623;627	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	L	627;623	ENSP00000288135:P627L;ENSP00000390987:P623L	.	P	+	2	0	KIT	55288934	1.000000	0.71417	0.997000	0.53966	0.170000	0.22686	7.743000	0.85020	1.576000	0.49790	0.655000	0.94253	CCG		0.433	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		Missense_Mutation	T	55594177	C	T	55594177	5	4	121	1	0	0	0	0	0	0	1	0	8350	782	27	1	1930	1	KIT	4	55594177	Splice_Site	SNP	C	TCGA-G5-6235-01A-11D-1733-10	29677	55594177	135560099	63	31833										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83778206	83778206	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tataatggcatcggccatgcGgttatcatgtaaacaaaggt	10	7	1	0	rs140582072		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:83778206G>A	ENST00000395310.2	-	16	1962	c.1780C>T	c.(1780-1782)Cgc>Tgc	p.R594C	SEC31A_ENST00000509142.1_Missense_Mutation_p.R594C|SEC31A_ENST00000505984.1_Missense_Mutation_p.R555C|SEC31A_ENST00000508502.1_Missense_Mutation_p.R594C|SEC31A_ENST00000348405.4_Missense_Mutation_p.R555C|SEC31A_ENST00000500777.2_Missense_Mutation_p.R555C|SEC31A_ENST00000443462.2_Missense_Mutation_p.R589C|SEC31A_ENST00000432794.1_Missense_Mutation_p.R594C|SEC31A_ENST00000355196.2_Missense_Mutation_p.R594C|SEC31A_ENST00000448323.1_Missense_Mutation_p.R594C|SEC31A_ENST00000264405.5_Missense_Mutation_p.R327C|SEC31A_ENST00000513858.1_Missense_Mutation_p.R555C|SEC31A_ENST00000326950.5_Missense_Mutation_p.R555C|SEC31A_ENST00000505472.1_Missense_Mutation_p.R594C|SEC31A_ENST00000311785.7_Missense_Mutation_p.R594C|SEC31A_ENST00000508479.1_Missense_Mutation_p.R594C	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)	594					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)	p.R555C(1)	SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TCGGCCATGCGGTTATCATGT	0.413																																																1	Substitution - Missense(1)	breast(1)	4											83	78	80					4																	83778206		2203	4300	6503	83997230	SO:0001583	missense	22872			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.1780C>T	4.37:g.83778206G>A	ENSP00000378721:p.Arg594Cys		83997230	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Missense_Mutation	SNP	ENST00000395310.2	37	CCDS3596.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.299224|5.299224	0.95574|0.95574	.|.	.|.	ENSG00000138674|ENSG00000138674	ENST00000507828;ENST00000512664|ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984;ENST00000508479;ENST00000510167	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.54279	.|0.62;0.58;1.83;1.8;0.77;1.71;1.83;0.62;0.77;0.58;0.58;1.83;1.83;2.6;1.63;1.83;1.83	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80681|0.80681	0.4669|0.4669	M|M	0.92169|0.92169	3.28|3.28	0.80722|0.80722	D|D	1|1	.|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	.|D;D;D;D;D;D;D;D;D	.|0.97110	.|0.999;0.999;1.0;1.0;0.989;1.0;0.999;0.998;0.999	D|D	0.84659|0.84659	0.0705|0.0705	5|10	.|0.87932	.|D	.|0	-10.908|-10.908	19.949|19.949	0.97192|0.97192	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|589;555;594;555;555;594;594;594;327	.|B4DIW6;B7ZL00;D6RHZ5;O94979-6;O94979-4;O94979-3;O94979-2;O94979;O94979-7	.|.;.;.;.;.;.;.;SC31A_HUMAN;.	L|C	210;108|555;555;594;589;594;594;594;555;594;594;555;594;594;327;555;594;182	.|ENSP00000337602:R555C;ENSP00000426886:R555C;ENSP00000378721:R594C;ENSP00000408027:R589C;ENSP00000426569:R594C;ENSP00000407944:R594C;ENSP00000400926:R594C;ENSP00000325087:R555C;ENSP00000309070:R594C;ENSP00000421633:R594C;ENSP00000421464:R555C;ENSP00000424635:R594C;ENSP00000347329:R594C;ENSP00000264405:R327C;ENSP00000424451:R555C;ENSP00000425999:R594C;ENSP00000422267:R182C	.|ENSP00000264405:R327C	P|R	-|-	2|1	0|0	SEC31A|SEC31A	83997230|83997230	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.869000|9.869000	0.99810|0.99810	2.706000|2.706000	0.92434|0.92434	0.655000|0.655000	0.94253|0.94253	CCG|CGC		0.413	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		A	83778206	G	A	83778206	3	1	121	1	0	0	0	0	1	0	0	0	14035	1116	39	1	1930	1	SEC31A	4	83778206	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	28184029	83778206	107376070	64	31834										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535012	88535012	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggaaaggcaacgaaggtaaaGaggataaaggacaacatgga	14	4	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:88535012G>T	ENST00000282478.7	+	4	1231	c.1198G>T	c.(1198-1200)Gag>Tag	p.E400*	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Nonsense_Mutation_p.E400*			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	400					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)		CGAAGGTAAAGAGGATAAAGG	0.443																																																0			4											129	120	123					4																	88535012		1941	4139	6080	88754036	SO:0001587	stop_gained	1834			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.1198G>T	4.37:g.88535012G>T	ENSP00000282478:p.Glu400*		88754036	A8MUI0|O95815	Nonsense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783870	0.70222	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	.	.	.	4.2	-0.0492	0.13836	.	0.811716	0.10029	N	0.725009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-3.9603	3.3817	0.07257	0.3719:0.2042:0.4239:0.0	.	.	.	.	X	400	.	ENSP00000282478:E400X	E	+	1	0	DSPP	88754036	0.000000	0.05858	0.004000	0.12327	0.023000	0.10783	0.494000	0.22467	0.059000	0.16252	0.446000	0.29264	GAG		0.443	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88535012	G	T	88535012	4	4	121	1	0	0	0	0	0	1	0	0	4793	943	33	2	1212	2	DSPP	4	88535012	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	4756806	88535012	102619264	65	31835										
HERC5	51191	hgsc.bcm.edu	37	chr4	89425454	89425454	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggcggtttatgaagaatttcGgagaggattttataaaatgt	12	2	0	3	rs375430185		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:89425454G>T	ENST00000264350.3	+	21	2807	c.2654G>T	c.(2653-2655)cGg>cTg	p.R885L	HERC5_ENST00000508159.1_Missense_Mutation_p.R523L	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	885	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)		GAAGAATTTCGGAGAGGATTT	0.323																																					Esophageal Squamous(39;887 1012 34045 50514)											0			4											78	82	81					4																	89425454		2203	4299	6502	89644477	SO:0001583	missense	51191			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.2654G>T	4.37:g.89425454G>T	ENSP00000264350:p.Arg885Leu		89644477	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.459796	0.43736	.	.	ENSG00000138646	ENST00000264350;ENST00000508159	T;T	0.45276	0.9;0.9	4.62	3.45	0.39498	HECT (4);	0.316302	0.21246	N	0.077721	T	0.27559	0.0677	N	0.16066	0.365	0.24863	N	0.99234	B	0.22746	0.074	B	0.34038	0.174	T	0.23868	-1.0176	10	0.36615	T	0.2	.	7.6934	0.28581	0.896:0.0:0.104:0.0	.	885	Q9UII4	HERC5_HUMAN	L	885;523	ENSP00000264350:R885L;ENSP00000424129:R523L	ENSP00000264350:R885L	R	+	2	0	HERC5	89644477	0.988000	0.35896	1.000000	0.80357	0.745000	0.42441	4.021000	0.57196	0.819000	0.34492	-0.302000	0.09304	CGG		0.323	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		T	89425454	G	T	89425454	3	4	121	1	0	0	0	0	1	0	0	0	7082	1116	39	2	2736	2	HERC5	4	89425454	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	890442	89425454	101728822	66	31836										
GRID2	2895	hgsc.bcm.edu	37	chr4	94006419	94006419	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaaattcattatattctatgAtagtgaatacggtaagtgtt	8	3	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:94006419A>G	ENST00000282020.4	+	3	776	c.518A>G	c.(517-519)gAt>gGt	p.D173G	GRID2_ENST00000510992.1_Intron|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	173					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)		ATATTCTATGATAGTGAATAC	0.358																																																0			4											88	92	91					4																	94006419		2203	4300	6503	94225442	SO:0001583	missense	2895			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.518A>G	4.37:g.94006419A>G	ENSP00000282020:p.Asp173Gly		94225442	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.187776	0.78789	.	.	ENSG00000152208	ENST00000282020	D	0.89681	-2.55	5.23	5.23	0.72850	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.92348	0.7572	L	0.46157	1.445	0.80722	D	1	D;D	0.69078	0.997;0.972	D;P	0.83275	0.996;0.86	D	0.93246	0.6630	10	0.87932	D	0	.	15.4223	0.75022	1.0:0.0:0.0:0.0	.	173;114	O43424;B4DYB9	GRID2_HUMAN;.	G	173	ENSP00000282020:D173G	ENSP00000282020:D173G	D	+	2	0	GRID2	94225442	1.000000	0.71417	0.886000	0.34754	0.861000	0.49209	9.279000	0.95777	2.112000	0.64535	0.533000	0.62120	GAT		0.358	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			G	94006419	A	G	94006419	3	3	121	1	0	0	0	0	1	0	0	0	6793	333	12	4	528	4	GRID2	4	94006419	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	4580965	94006419	97147857	67	31837										
TACR3	6870	hgsc.bcm.edu	37	chr4	104511134	104511134	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gacaccagcgaaatgctctcTtgaagccagctcgaaatctg	9	12	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:104511134T>C	ENST00000304883.2	-	5	1243	c.1103A>G	c.(1102-1104)aAg>aGg	p.K368R	RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	368					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)		AAATGCTCTCTTGAAGCCAGC	0.428																																																0			4											66	66	66					4																	104511134		2203	4300	6503	104730583	SO:0001583	missense	6870			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.1103A>G	4.37:g.104511134T>C	ENSP00000303325:p.Lys368Arg		104730583	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029177	0.54790	.	.	ENSG00000169836	ENST00000304883	T	0.38077	1.16	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.33206	0.0855	L	0.50847	1.595	0.58432	D	0.999995	B	0.31040	0.305	B	0.27796	0.083	T	0.07790	-1.0754	10	0.23891	T	0.37	.	15.3584	0.74448	0.0:0.0:0.0:1.0	.	368	P29371	NK3R_HUMAN	R	368	ENSP00000303325:K368R	ENSP00000303325:K368R	K	-	2	0	TACR3	104730583	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.565000	0.82337	2.217000	0.71921	0.482000	0.46254	AAG		0.428	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		C	104511134	T	C	104511134	3	2	121	1	0	0	0	0	1	0	0	0	15546	1609	56	4	298	4	TACR3	4	104511134	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	10504715	104511134	86643142	68	31838										
DKK2	27123	hgsc.bcm.edu	37	chr4	107846994	107846994	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tggggcagcacatgccatctCggtggcagcgcttctttttt	12	11	2	0	rs370095806		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:107846994C>T	ENST00000285311.3	-	2	1040	c.335G>A	c.(334-336)cGa>cAa	p.R112Q	DKK2_ENST00000510463.1_Missense_Mutation_p.R66Q|DKK2_ENST00000513208.1_Missense_Mutation_p.R12Q	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	112	DKK-type Cys-1.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		CATGCCATCTCGGTGGCAGCG	0.498																																																0			4						C	GLN/ARG	0,4406		0,0,2203	173	159	164		335	5.4	0.9	4		164	1,8599	1.2+/-3.3	0,1,4299	no	missense	DKK2	NM_014421.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	112/260	107846994	1,13005	2203	4300	6503	108066443	SO:0001583	missense	27123			AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"dickkopf (Xenopus laevis) homolog 2", "dickkopf 2 homolog (Xenopus laevis)"			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.335G>A	4.37:g.107846994C>T	ENSP00000285311:p.Arg112Gln		108066443	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	37	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	C	36	5.743262	0.96873	0.0	1.16E-4	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.60424	0.19;0.44;0.34	5.42	5.42	0.78866	Dickkopf, N-terminal cysteine-rich (1);	0.000000	0.85682	D	0.000000	T	0.78194	0.4245	M	0.79011	2.435	0.58432	D	0.999996	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.988	T	0.79992	-0.1569	10	0.72032	D	0.01	-15.7364	19.5778	0.95452	0.0:1.0:0.0:0.0	.	112;112	Q9H3R7;Q9UBU2	.;DKK2_HUMAN	Q	112;12;66	ENSP00000285311:R112Q;ENSP00000421255:R12Q;ENSP00000423797:R66Q	ENSP00000285311:R112Q	R	-	2	0	DKK2	108066443	1.000000	0.71417	0.917000	0.36280	0.983000	0.72400	7.410000	0.80065	2.704000	0.92352	0.467000	0.42956	CGA		0.498	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			T	107846994	C	T	107846994	3	4	121	1	0	0	0	0	1	0	0	0	4556	884	31	1	456	1	DKK2	4	107846994	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3335860	107846994	83307282	69	31839										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153247183	153247183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atgaatagactctattagtaTgcccctgcaacgtgtgtaga	9	8	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:153247183T>C	ENST00000281708.4	-	10	2848	c.1619A>G	c.(1618-1620)cAt>cGt	p.H540R	FBXW7_ENST00000296555.5_Missense_Mutation_p.H422R|FBXW7_ENST00000263981.5_Missense_Mutation_p.H460R|FBXW7_ENST00000603548.1_Missense_Mutation_p.H540R|FBXW7_ENST00000393956.3_Missense_Mutation_p.H364R|FBXW7_ENST00000603841.1_Missense_Mutation_p.H540R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	540					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.?(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)				TCTATTAGTATGCCCCTGCAA	0.403			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											170	166	167					4																	153247183		2203	4300	6503	153466633	SO:0001583	missense	55294			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.1619A>G	4.37:g.153247183T>C	ENSP00000281708:p.His540Arg		153466633	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.328066	0.81690	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46	5.72	5.72	0.89469	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	0.93022	0.7779	H	0.96518	3.835	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.94748	0.7925	10	0.59425	D	0.04	-19.0933	16.2962	0.82776	0.0:0.0:0.0:1.0	.	364;540;422;460	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	R	540;422;460;364	ENSP00000281708:H540R;ENSP00000296555:H422R;ENSP00000263981:H460R;ENSP00000377528:H364R	ENSP00000263981:H460R	H	-	2	0	FBXW7	153466633	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.304000	0.77564	0.528000	0.53228	CAT		0.403	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153247183	T	C	153247183	3	2	121	1	0	0	0	0	1	0	0	0	5788	1464	51	4	516	4	FBXW7	4	153247183	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	45400189	153247183	37907093	70	31840										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153253824	153253824	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tagcgacatgtctgagctgcTtgtagcaggtctttgggttc	13	8	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:153253824T>C	ENST00000281708.4	-	6	2138	c.909A>G	c.(907-909)caA>caG	p.Q303Q	FBXW7_ENST00000296555.5_Silent_p.Q185Q|FBXW7_ENST00000263981.5_Silent_p.Q223Q|FBXW7_ENST00000603548.1_Silent_p.Q303Q|FBXW7_ENST00000393956.3_Silent_p.Q127Q|FBXW7_ENST00000603841.1_Silent_p.Q303Q	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	303	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.?(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)				TCTGAGCTGCTTGTAGCAGGT	0.368			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											68	69	68					4																	153253824		2203	4300	6503	153473274	SO:0001819	synonymous_variant	55294			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.909A>G	4.37:g.153253824T>C			153473274	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				0.368	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			C	153253824	T	C	153253824	2	2	121	1	0	0	0	0	0	0	0	1	5788	1606	56	4		4	FBXW7	4	153253824	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	6641	153253824	37900452	71	31841										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153332919	153332919	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagagagcctccagttcgtcGtcttttgctgcccacagaga	10	13	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:153332919G>A	ENST00000281708.4	-	2	1266	c.37C>T	c.(37-39)Cga>Tga	p.R13*	FBXW7_ENST00000604872.1_Nonsense_Mutation_p.R13*|FBXW7_ENST00000603548.1_Nonsense_Mutation_p.R13*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.R13*	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	13					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.R13*(3)		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)				CCAGTTCGTCGTCTTTTGCTG	0.483			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	3	Substitution - Nonsense(3)	large_intestine(2)|kidney(1)	4											75	66	69					4																	153332919		2203	4300	6503	153552369	SO:0001587	stop_gained	55294			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.37C>T	4.37:g.153332919G>A	ENSP00000281708:p.Arg13*		153552369	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875991	0.91664	.	.	ENSG00000109670	ENST00000281708	.	.	.	5.67	4.75	0.60458	.	0.098967	0.39475	N	0.001355	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.8831	17.3378	0.87287	0.0:0.0:0.8664:0.1336	.	.	.	.	X	13	.	ENSP00000281708:R13X	R	-	1	2	FBXW7	153552369	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.689000	0.68234	2.668000	0.90789	0.650000	0.86243	CGA		0.483	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153332919	G	A	153332919	4	1	121	1	0	0	0	0	0	1	0	0	5788	1153	40	1	2546	1	FBXW7	4	153332919	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	79095	153332919	37821357	72	31842										
FGA	2243	hgsc.bcm.edu	37	chr4	155506888	155506888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agggaattcagctatcccagGgtgatgagaactggattcct	12	8	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:155506888G>A	ENST00000302053.3	-	5	1771	c.1693C>T	c.(1693-1695)Cct>Tct	p.P565S	FGA_ENST00000403106.3_Missense_Mutation_p.P565S	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	565					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)	GCTATCCCAGGGTGATGAGAA	0.428																																					NSCLC(143;340 1922 20892 22370 48145)											0			4											94	90	92					4																	155506888		2203	4300	6503	155726338	SO:0001583	missense	2243				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.1693C>T	4.37:g.155506888G>A	ENSP00000306361:p.Pro565Ser		155726338	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	2.661	-0.279853	0.05642	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.54675	0.56;3.02	4.46	-8.91	0.00778	.	20.600900	0.00166	N	0.000000	T	0.22589	0.0545	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.36866	-0.9730	10	0.05525	T	0.97	.	0.964	0.01401	0.2304:0.1814:0.3265:0.2617	.	565;565	P02671-2;P02671	.;FIBA_HUMAN	S	565	ENSP00000306361:P565S;ENSP00000385981:P565S	ENSP00000306361:P565S	P	-	1	0	FGA	155726338	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.166000	0.09954	-1.538000	0.01734	-1.052000	0.02337	CCT		0.428	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		A	155506888	G	A	155506888	3	1	121	1	0	0	0	0	1	0	0	0	5849	1232	43	3	959	3	FGA	4	155506888	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	2173969	155506888	35647388	73	31843										
NAF1	92345	hgsc.bcm.edu	37	chr4	164061373	164061373	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aacatgccggtaaagtacttActgttttagtttttctgtga	8	6	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:164061373A>C	ENST00000274054.2	-	5	1072		c.e5+1		NAF1_ENST00000509434.1_Splice_Site|NAF1_ENST00000422287.2_Splice_Site	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein						pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				TAAAGTACTTACTGTTTTAGT	0.289																																																0			4											90	95	93					4																	164061373		2202	4293	6495	164280823	SO:0001630	splice_region_variant	92345				CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.878+1T>G	4.37:g.164061373A>C			164280823	D3DP28|E9PAZ2	Splice_Site	SNP	ENST00000274054.2	37	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.863511	0.51482	.	.	ENSG00000145414	ENST00000509434;ENST00000422287;ENST00000274054	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1134	0.72380	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NAF1	164280823	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	7.991000	0.88244	2.175000	0.68902	0.533000	0.62120	.		0.289	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	Intron	C	164061373	A	C	164061373	5	2	121	1	0	0	0	0	0	0	1	0	10170	405	14	4	761	4	NAF1	4	164061373	Splice_Site	SNP	A	TCGA-G5-6235-01A-11D-1733-10	8554485	164061373	27092903	74	31844										
WWC2	80014	hgsc.bcm.edu	37	chr4	184190299	184190299	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tttgctctgtcagtaaacacCgaagggaagaatgcctggta	11	8	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr4:184190299C>A	ENST00000403733.3	+	15	2582	c.2383C>A	c.(2383-2385)Cga>Aga	p.R795R	WWC2_ENST00000513834.1_Silent_p.R746R|WWC2_ENST00000448232.2_Silent_p.R795R|WWC2_ENST00000378925.3_Intron|WWC2_ENST00000506225.1_3'UTR|WWC2_ENST00000504005.1_Silent_p.R477R	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	795	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)	p.R795*(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CAGTAAACACCGAAGGGAAGA	0.413																																																1	Substitution - Nonsense(1)	ovary(1)	4											78	76	76					4																	184190299		2203	4300	6503	184427293	SO:0001819	synonymous_variant	80014			BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2383C>A	4.37:g.184190299C>A			184427293	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Silent	SNP	ENST00000403733.3	37	CCDS34109.2																																																																																				0.413	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		A	184190299	C	A	184190299	2	1	121	1	0	0	0	0	0	0	0	1	17452	644	23	2		2	WWC2	4	184190299	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	20128926	184190299	6963977	75	31845										
TERT	7015	hgsc.bcm.edu	37	chr5	1264569	1264569	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cgggtatccagcagcaggccGcaccaggggaataggccgtg	16	12	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:1264569G>A	ENST00000310581.5	-	11	2850	c.2793C>T	c.(2791-2793)tgC>tgT	p.C931C	TERT_ENST00000334602.6_Intron|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	931	Primer grip sequence.|Reverse transcriptase. {ECO:0000255|PROSITE-ProRule:PRU00405}.				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)	GCAGCAGGCCGCACCAGGGGA	0.647									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																																							0			5											34	42	39					5																	1264569		2037	4190	6227	1317569	SO:0001819	synonymous_variant	7015	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	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.2793C>T	5.37:g.1264569G>A			1317569	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																				0.647	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			A	1264569	G	A	1264569	2	1	121	1	0	0	0	0	0	0	0	1	15803	1079	38	1		1	TERT	5	1264569	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10		1264569	179650691	76	31846										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15936756	15936756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gccgctgcgtccgcctgaccGacgaaggcctgcgctacctg	13	17	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:15936756G>A	ENST00000504595.1	+	4	1418	c.937G>A	c.(937-939)Gac>Aac	p.D313N	FBXL7_ENST00000510662.1_Missense_Mutation_p.D266N|FBXL7_ENST00000329673.7_Missense_Mutation_p.D301N|MIR887_ENST00000401258.1_RNA	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	313					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						CCGCCTGACCGACGAAGGCCT	0.667																																																0			5											35	39	37					5																	15936756		2187	4282	6469	15989756	SO:0001583	missense	23194			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.937G>A	5.37:g.15936756G>A	ENSP00000423630:p.Asp313Asn		15989756	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	37	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	G	33	5.231581	0.95207	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.11063	2.81;4.37;2.81	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	L	0.41710	1.295	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00664	-1.1620	10	0.56958	D	0.05	.	19.109	0.93309	0.0:0.0:1.0:0.0	.	313	Q9UJT9	FBXL7_HUMAN	N	313;266;301	ENSP00000423630:D313N;ENSP00000425184:D266N;ENSP00000329632:D301N	ENSP00000329632:D301N	D	+	1	0	FBXL7	15989756	1.000000	0.71417	0.988000	0.46212	0.944000	0.59088	9.869000	0.99810	2.525000	0.85131	0.655000	0.94253	GAC		0.667	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15936756	G	A	15936756	3	1	121	1	0	0	0	0	1	0	0	0	5743	1058	37	1	951	1	FBXL7	5	15936756	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	14672187	15936756	164978504	77	31847										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32089484	32089484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaaaccctcagtgtctgacaCgagcatcaggacatttgtct	9	11	4	1	rs200449834		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:32089484C>T	ENST00000438447.1	+	20	6318	c.5930C>T	c.(5929-5931)aCg>aTg	p.T1977M	PDZD2_ENST00000282493.3_Missense_Mutation_p.T1977M			O15018	PDZD2_HUMAN	PDZ domain containing 2	1977					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						GTGTCTGACACGAGCATCAGG	0.592													C|||	1	0.000199681	0	0	5008	,	,		16643	0.001		0	False		,,,				2504	0															0			5						C	MET/THR	0,4406		0,0,2203	104	99	101		5930	4.2	0	5		101	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PDZD2	NM_178140.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1977/2840	32089484	1,13005	2203	4300	6503	32125241	SO:0001583	missense	23037			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.5930C>T	5.37:g.32089484C>T	ENSP00000402033:p.Thr1977Met		32125241	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116334	0.56505	0.0	1.16E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.10005	2.92;2.92	4.2	4.2	0.49525	.	0.433550	0.19832	N	0.105069	T	0.18467	0.0443	L	0.46157	1.445	0.09310	N	1	D	0.69078	0.997	P	0.54210	0.745	T	0.02208	-1.1195	10	0.72032	D	0.01	.	12.339	0.55083	0.0:1.0:0.0:0.0	.	1977	O15018	PDZD2_HUMAN	M	1977;1778;1977	ENSP00000402033:T1977M;ENSP00000282493:T1977M	ENSP00000282493:T1977M	T	+	2	0	PDZD2	32125241	0.021000	0.18746	0.021000	0.16686	0.032000	0.12392	1.019000	0.30014	2.630000	0.89119	0.650000	0.86243	ACG		0.592	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32089484	C	T	32089484	3	4	121	1	0	0	0	0	1	0	0	0	11732	536	19	1	6004	1	PDZD2	5	32089484	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	16152728	32089484	148825776	78	31848										
DAB2	1601	hgsc.bcm.edu	37	chr5	39382915	39382915	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagccgttctgttctctttcAgataccccattttgagttct	6	11	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:39382915A>G	ENST00000320816.6	-	10	1613	c.1146T>C	c.(1144-1146)tcT>tcC	p.S382S	DAB2_ENST00000509337.1_Silent_p.S361S|DAB2_ENST00000545653.1_Silent_p.S361S|DAB2_ENST00000339788.6_Intron|DAB2_ENST00000512525.1_5'Flank	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	382	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)			GTTCTCTTTCAGATACCCCAT	0.517																																																0			5											91	95	94					5																	39382915		2203	4300	6503	39418672	SO:0001819	synonymous_variant	1601			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.1146T>C	5.37:g.39382915A>G			39418672	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	CCDS34149.1																																																																																				0.517	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		G	39382915	A	G	39382915	2	3	121	1	0	0	0	0	0	0	0	1	4224	175	7	4		4	DAB2	5	39382915	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	7293431	39382915	141532345	79	31849										
CARD6	84674	hgsc.bcm.edu	37	chr5	40853347	40853347	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agtgatgttctcttcttgccTcagatgtgtgtctgtggagg	13	7	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:40853347T>A	ENST00000254691.5	+	3	2112	c.1913T>A	c.(1912-1914)cTc>cAc	p.L638H	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	638					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						TCTTCTTGCCTCAGATGTGTG	0.517																																																0			5											141	143	143					5																	40853347		2203	4300	6503	40889104	SO:0001583	missense	84674			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.1913T>A	5.37:g.40853347T>A	ENSP00000254691:p.Leu638His		40889104	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.903234	0.52333	.	.	ENSG00000132357	ENST00000254691	T	0.14144	2.53	5.0	5.0	0.66597	.	0.000000	0.47852	D	0.000218	T	0.32645	0.0836	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.01993	-1.1233	10	0.39692	T	0.17	-15.3616	11.0274	0.47753	0.0:0.0:0.0:1.0	.	638	Q9BX69	CARD6_HUMAN	H	638	ENSP00000254691:L638H	ENSP00000254691:L638H	L	+	2	0	CARD6	40889104	0.011000	0.17503	0.981000	0.43875	0.776000	0.43924	0.626000	0.24492	2.107000	0.64212	0.459000	0.35465	CTC		0.517	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			A	40853347	T	A	40853347	3	1	121	1	0	0	0	0	1	0	0	0	2656	1551	54	5	1923	5	CARD6	5	40853347	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	1470432	40853347	140061913	80	31850										
VCAN	1462	hgsc.bcm.edu	37	chr5	82834548	82834548	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atccagggaaatagtgatttCagagcgattaggagaaccaa	11	6	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:82834548C>A	ENST00000265077.3	+	8	6291	c.5726C>A	c.(5725-5727)tCa>tAa	p.S1909*	VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Nonsense_Mutation_p.S922*|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1909	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)	ATAGTGATTTCAGAGCGATTA	0.413																																																0			5											102	108	106					5																	82834548		2201	4300	6501	82870304	SO:0001587	stop_gained	1462			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.5726C>A	5.37:g.82834548C>A	ENSP00000265077:p.Ser1909*		82870304	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Nonsense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	47	13.054789	0.99716	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	.	.	.	5.9	5.04	0.67666	.	0.381500	0.22050	N	0.065336	.	.	.	.	.	.	0.36652	D	0.877432	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2845	0.54786	0.0:0.9211:0.0:0.0789	.	.	.	.	X	1909;922;922	.	ENSP00000265077:S1909X	S	+	2	0	VCAN	82870304	0.091000	0.21658	0.006000	0.13384	0.023000	0.10783	2.292000	0.43549	1.510000	0.48803	0.655000	0.94253	TCA		0.413	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82834548	C	A	82834548	4	1	121	1	0	0	0	0	0	1	0	0	17178	838	29	2	5752	2	VCAN	5	82834548	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	41981201	82834548	98080712	81	31851										
GPR98	84059	hgsc.bcm.edu	37	chr5	89940600	89940600	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tggttagtccagactttacaCaagatgtatttcctgtacaa	7	8	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:89940600C>T	ENST00000405460.2	+	15	2908	c.2812C>T	c.(2812-2814)Caa>Taa	p.Q938*		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	938	Calx-beta 7. {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)		AGACTTTACACAAGATGTATT	0.363																																																0			5											247	230	235					5																	89940600		1861	4099	5960	89976356	SO:0001587	stop_gained	84059			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.2812C>T	5.37:g.89940600C>T	ENSP00000384582:p.Gln938*		89976356	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.619269|6.619269	0.97709|0.97709	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043|ENST00000504142	.|T	.|0.28255	.|1.62	5.51|5.51	-0.0341|-0.0341	0.13898|0.13898	.|.	0.666605|.	0.16552|.	N|.	0.209454|.	.|T	.|0.27313	.|0.0670	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999998|0.999998	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.30592	.|-0.9973	.|6	0.12430|0.66056	T|D	0.62|0.02	.|.	4.3199|4.3199	0.11011|0.11011	0.3163:0.2049:0.4028:0.0761|0.3163:0.2049:0.4028:0.0761	.|.	.|.	.|.	.|.	X|I	938|526	.|ENSP00000424736:T526I	ENSP00000296619:Q938X|ENSP00000424736:T526I	Q|T	+|+	1|2	0|0	GPR98|GPR98	89976356|89976356	0.012000|0.012000	0.17670|0.17670	0.924000|0.924000	0.36721|0.36721	0.663000|0.663000	0.39108|0.39108	0.170000|0.170000	0.16663|0.16663	0.242000|0.242000	0.21303|0.21303	-0.531000|-0.531000	0.04308|0.04308	CAA|ACA		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89940600	C	T	89940600	4	4	121	1	0	0	0	0	0	1	0	0	6742	479	17	3	2870	3	GPR98	5	89940600	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	7106052	89940600	90974660	82	31852										
APC	324	hgsc.bcm.edu	37	chr5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccaatggttcagaaacaaatCgagtgggttctaatcatgga	10	7	3	1	rs121913331		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1114	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.R1114*(30)|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)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	31	Substitution - Nonsense(30)|Unknown(1)	large_intestine(29)|ovary(1)|skin(1)	5	GRCh37	CM920048	APC	M	rs121913331						90	82	85					5																	112174631		2202	4300	6502	112202530	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*		112202530	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174631	C	T	112174631	4	4	121	1	0	0	0	0	0	1	0	0	763	876	31	1	3398	1	APC	5	112174631	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	22234031	112174631	68740629	83	31853			1	41		5	5	718	N	T_G_C_A	6.103757e-11
APC	324	hgsc.bcm.edu	37	chr5	112175148	112175148	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tttgtcatcagctgaagatgAaataggatgtaatcagacga	10	5	3	4			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:112175148A>T	ENST00000457016.1	+	16	4237	c.3857A>T	c.(3856-3858)gAa>gTa	p.E1286V	APC_ENST00000257430.4_Missense_Mutation_p.E1286V|APC_ENST00000508376.2_Missense_Mutation_p.E1286V|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1286	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.I1287fs*1(1)|p.K1192fs*3(1)|p.?(1)|p.E1286G(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)		GCTGAAGATGAAATAGGATGT	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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)	ovary(1)|large_intestine(1)|soft_tissue(1)|skin(1)	5											55	57	56					5																	112175148		2202	4300	6502	112203047	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.3857A>T	5.37:g.112175148A>T	ENSP00000413133:p.Glu1286Val		112203047	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.178993	0.38511	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.91792	-2.64;-2.64;-2.64;-2.91	6.03	6.03	0.97812	.	0.179817	0.47455	D	0.000223	D	0.93096	0.7802	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.66716	0.946;0.946	D	0.92340	0.5881	9	.	.	.	-25.935	16.2316	0.82347	1.0:0.0:0.0:0.0	.	1288;1286	Q4LE70;P25054	.;APC_HUMAN	V	1286	ENSP00000413133:E1286V;ENSP00000257430:E1286V;ENSP00000427089:E1286V;ENSP00000423828:E1286V	.	E	+	2	0	APC	112203047	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.472000	0.66768	2.308000	0.77769	0.533000	0.62120	GAA		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175148	A	T	112175148	3	4	121	1	0	0	0	0	1	0	0	0	763	246	9	5	3915	5	APC	5	112175148	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	517	112175148	68740112	84	31854			1	41		5	5	718	N	T_G_C_A	6.103757e-11
APC	324	hgsc.bcm.edu	37	chr5	112175308	112175308	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaatccagcagactgcagggTtctagtttatcttcagaatc	8	9	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:112175308T>C	ENST00000457016.1	+	16	4397	c.4017T>C	c.(4015-4017)ggT>ggC	p.G1339G	APC_ENST00000257430.4_Silent_p.G1339G|APC_ENST00000508376.2_Silent_p.G1339G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1339	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.S1335fs*70(1)|p.K1192fs*3(1)|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)		GACTGCAGGGTTCTAGTTTAT	0.458		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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											56	60	59					5																	112175308		2202	4300	6502	112203207	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.4017T>C	5.37:g.112175308T>C			112203207	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.458	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175308	T	C	112175308	2	2	121	1	0	0	0	0	0	0	0	1	763	1712	60	4		4	APC	5	112175308	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	160	112175308	68739952	85	31855			1	41		5	5	718	N	T_G_C_A	6.103757e-11
APC	324	hgsc.bcm.edu	37	chr5	112175325	112175325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gggttctagtttatcttcagAatcagccaggcacaaagctg	10	9	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:112175325A>G	ENST00000457016.1	+	16	4414	c.4034A>G	c.(4033-4035)gAa>gGa	p.E1345G	APC_ENST00000257430.4_Missense_Mutation_p.E1345G|APC_ENST00000508376.2_Missense_Mutation_p.E1345G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1345	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.E1345fs*8(1)|p.S1335fs*70(1)|p.K1192fs*3(1)|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)		TTATCTTCAGAATCAGCCAGG	0.483		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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											58	62	61					5																	112175325		2202	4300	6502	112203224	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.4034A>G	5.37:g.112175325A>G	ENSP00000413133:p.Glu1345Gly		112203224	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.724161	0.30593	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89552	-2.53;-2.53;-2.53	6.03	6.03	0.97812	.	0.216974	0.45867	D	0.000337	T	0.81645	0.4866	N	0.19112	0.55	0.35676	D	0.813722	B;B	0.23937	0.094;0.094	B;B	0.22386	0.039;0.024	T	0.80412	-0.1393	9	.	.	.	-25.7885	16.2316	0.82347	1.0:0.0:0.0:0.0	.	1347;1345	Q4LE70;P25054	.;APC_HUMAN	G	1345	ENSP00000413133:E1345G;ENSP00000257430:E1345G;ENSP00000427089:E1345G	.	E	+	2	0	APC	112203224	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	4.023000	0.57211	2.308000	0.77769	0.533000	0.62120	GAA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112175325	A	G	112175325	3	3	121	1	0	0	0	0	1	0	0	0	763	246	9	4	4092	4	APC	5	112175325	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	17	112175325	68739935	86	31856			1	41		5	5	718	N	T_G_C_A	6.103757e-11
APC	324	hgsc.bcm.edu	37	chr5	112175348	112175348	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagccaggcacaaagctgttGaattttcttcaggagcgaaa	10	9	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:112175348G>T	ENST00000457016.1	+	16	4437	c.4057G>T	c.(4057-4059)Gaa>Taa	p.E1353*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1353*|APC_ENST00000508376.2_Nonsense_Mutation_p.E1353*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1353	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.E1353*(12)|p.E1353fs*19(1)|p.K1192fs*3(1)|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)		CAAAGCTGTTGAATTTTCTTC	0.483		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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	15	Substitution - Nonsense(12)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5	GRCh37	CD972008	APC	D							62	65	64					5																	112175348		2202	4300	6502	112203247	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.4057G>T	5.37:g.112175348G>T	ENSP00000413133:p.Glu1353*		112203247	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.431314	0.98808	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.111916	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8759	20.1672	0.98154	0.0:0.0:1.0:0.0	.	.	.	.	X	1353	.	.	E	+	1	0	APC	112203247	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	5.308000	0.65768	2.861000	0.98227	0.655000	0.94253	GAA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112175348	G	T	112175348	4	4	121	1	0	0	0	0	0	1	0	0	763	1291	45	2	4115	2	APC	5	112175348	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	23	112175348	68739912	87	31857			1	41		5	5	718	N	T_G_C_A	6.103757e-11
TRIM36	55521	hgsc.bcm.edu	37	chr5	114469751	114469751	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tccgatattcaagaacatagCtatcagctttatccttttct	4	10	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:114469751C>A	ENST00000282369.3	-	8	1461	c.1340G>T	c.(1339-1341)aGc>aTc	p.S447I	TRIM36_ENST00000514154.1_Missense_Mutation_p.S292I|TRIM36_ENST00000513154.1_Missense_Mutation_p.S435I	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	447	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AAGAACATAGCTATCAGCTTT	0.363																																																0			5											123	114	117					5																	114469751		2202	4300	6502	114497650	SO:0001583	missense	55521			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.1340G>T	5.37:g.114469751C>A	ENSP00000282369:p.Ser447Ile		114497650	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905590	0.52333	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.58652	0.32;0.32;0.32	5.63	4.76	0.60689	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.472746	0.24681	N	0.036478	T	0.53948	0.1828	L	0.44542	1.39	0.80722	D	1	P;P	0.37276	0.533;0.589	B;P	0.45610	0.317;0.487	T	0.55010	-0.8207	10	0.49607	T	0.09	.	6.3583	0.21414	0.1214:0.6198:0.1863:0.0724	.	435;447	E9PFI8;Q9NQ86	.;TRI36_HUMAN	I	447;435;292	ENSP00000282369:S447I;ENSP00000423934:S435I;ENSP00000424259:S292I	ENSP00000282369:S447I	S	-	2	0	TRIM36	114497650	0.995000	0.38212	1.000000	0.80357	0.971000	0.66376	0.768000	0.26590	1.375000	0.46248	0.655000	0.94253	AGC		0.363	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		A	114469751	C	A	114469751	3	1	121	1	0	0	0	0	1	0	0	0	16550	797	28	2	858	2	TRIM36	5	114469751	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	2294403	114469751	66445509	88	31858										
FSTL4	23105	hgsc.bcm.edu	37	chr5	132534902	132534902	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	actctcgggctggtgtgaggAggtactgtccaaacagccca	13	11	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:132534902A>T	ENST00000265342.7	-	16	2663	c.2414T>A	c.(2413-2415)cTc>cAc	p.L805H	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	805						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L805H(1)		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)			TGGTGTGAGGAGGTACTGTCC	0.582																																																1	Substitution - Missense(1)	central_nervous_system(1)	5											69	66	67					5																	132534902		2203	4300	6503	132562801	SO:0001583	missense	23105			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.2414T>A	5.37:g.132534902A>T	ENSP00000265342:p.Leu805His		132562801	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	37	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.123389	0.77436	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.38077	1.16	5.04	5.04	0.67666	.	0.068048	0.64402	D	0.000012	T	0.62405	0.2425	M	0.82323	2.585	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.80764	0.966;0.994	T	0.68857	-0.5298	10	0.87932	D	0	-23.9565	13.6113	0.62080	1.0:0.0:0.0:0.0	.	805;454	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	H	805;636	ENSP00000265342:L805H	ENSP00000265342:L805H	L	-	2	0	FSTL4	132562801	1.000000	0.71417	0.998000	0.56505	0.936000	0.57629	8.962000	0.93254	1.897000	0.54924	0.477000	0.44152	CTC		0.582	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		T	132534902	A	T	132534902	3	4	121	1	0	0	0	0	1	0	0	0	6098	304	11	5	118	5	FSTL4	5	132534902	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	18065151	132534902	48380358	89	31859										
PSD2	84249	hgsc.bcm.edu	37	chr5	139202353	139202353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgccctgatgctgctcaacaCggacctgcacggccacgtga	11	15	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:139202353C>T	ENST00000274710.3	+	7	1458	c.1253C>T	c.(1252-1254)aCg>aTg	p.T418M		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	418	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)|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)			CTGCTCAACACGGACCTGCAC	0.607																																																0			5											97	65	76					5																	139202353		2203	4300	6503	139182537	SO:0001583	missense	84249			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.1253C>T	5.37:g.139202353C>T	ENSP00000274710:p.Thr418Met		139182537	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	37	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553149	0.86127	.	.	ENSG00000146005	ENST00000274710	T	0.67171	-0.25	4.91	4.91	0.64330	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.91041	0.4871	10	0.87932	D	0	.	16.6356	0.85058	0.0:1.0:0.0:0.0	.	418	Q9BQI7	PSD2_HUMAN	M	418	ENSP00000274710:T418M	ENSP00000274710:T418M	T	+	2	0	PSD2	139182537	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.990000	0.76225	2.428000	0.82296	0.455000	0.32223	ACG		0.607	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139202353	C	T	139202353	3	4	121	1	0	0	0	0	1	0	0	0	12681	536	19	1	1275	1	PSD2	5	139202353	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	6667451	139202353	41712907	90	31860										
ZMAT2	153527	hgsc.bcm.edu	37	chr5	140084144	140084144	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tttgaggaaaggatgaaggaGctcagagaagaggtaagggt	17	2	1	4			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:140084144G>A	ENST00000274712.3	+	5	571	c.444G>A	c.(442-444)gaG>gaA	p.E148E		NM_144723.1	NP_653324.1	Q96NC0	ZMAT2_HUMAN	zinc finger, matrin-type 2	148						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(1)|liver(1)|lung(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGATGAAGGAGCTCAGAGAAG	0.458																																																0			5											141	142	142					5																	140084144		2203	4300	6503	140064328	SO:0001819	synonymous_variant	153527			AK055683	CCDS4239.1	5q31	2012-10-05	2010-09-15		ENSG00000146007	ENSG00000146007		"Zinc fingers, matrin-type"	26433	protein-coding gene	gene with protein product						12477932	Standard	NM_144723		Approved	FLJ31121, hSNU23, Snu23	uc003lgy.1	Q96NC0	OTTHUMG00000129503	ENST00000274712.3:c.444G>A	5.37:g.140084144G>A			140064328		Silent	SNP	ENST00000274712.3	37	CCDS4239.1																																																																																				0.458	ZMAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468143.1	NM_144723		A	140084144	G	A	140084144	2	1	121	1	0	0	0	0	0	0	0	1	17731	962	34	3		3	ZMAT2	5	140084144	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	881791	140084144	40831116	91	31861										
PCDHGA7	56108	hgsc.bcm.edu	37	chr5	140762692	140762692	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaggtaggacgcagcttttcGccctgaaccagcgcagcggc	14	13	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:140762692G>A	ENST00000518325.1	+	1	226	c.226G>A	c.(226-228)Gcc>Acc	p.A76T	PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	76	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)			GCAGCTTTTCGCCCTGAACCA	0.622																																																0			5											52	61	58					5																	140762692		2191	4297	6488	140742876	SO:0001583	missense	56108			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.226G>A	5.37:g.140762692G>A	ENSP00000430024:p.Ala76Thr		140742876	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	8.635	0.894608	0.17613	.	.	ENSG00000253537	ENST00000518325	T	0.27557	1.66	4.86	-0.687	0.11320	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.28830	0.0715	M	0.70842	2.15	0.09310	N	1	B;B	0.27853	0.063;0.191	B;B	0.31337	0.119;0.128	T	0.34750	-0.9816	9	0.19590	T	0.45	.	6.5182	0.22260	0.1479:0.0:0.2897:0.5624	.	76;76	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	T	76	ENSP00000430024:A76T	ENSP00000430024:A76T	A	+	1	0	PCDHGA7	140742876	0.000000	0.05858	0.288000	0.24862	0.766000	0.43426	0.150000	0.16263	-0.408000	0.07565	-0.182000	0.12963	GCC		0.622	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		A	140762692	G	A	140762692	3	1	121	1	0	0	0	0	1	0	0	0	11590	1087	38	1	228	1	PCDHGA7	5	140762692	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	678548	140762692	40152568	92	31862										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147510894	147510894	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtccaaaggatttaaagcctGtctgtggtgacgatggccaa	12	8	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:147510894G>A	ENST00000256084.7	+	31	3079	c.3037G>A	c.(3037-3039)Gtc>Atc	p.V1013I	SPINK5_ENST00000359874.3_Missense_Mutation_p.V1043I	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	1013	Kazal-like 15. {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)	p.V1013L(1)		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)			TTTAAAGCCTGTCTGTGGTGA	0.413																																																1	Substitution - Missense(1)	ovary(1)	5											246	234	238					5																	147510894		1970	4164	6134	147491087	SO:0001583	missense	11005			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.3037G>A	5.37:g.147510894G>A	ENSP00000256084:p.Val1013Ile		147491087	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.320355	0.60634	.	.	ENSG00000133710	ENST00000359874;ENST00000256084	T;T	0.80304	-1.36;-1.36	4.69	4.69	0.59074	Proteinase inhibitor I1, Kazal (3);	0.000000	0.64402	D	0.000006	D	0.87736	0.6252	M	0.72118	2.19	0.33339	D	0.569639	D;D	0.89917	1.0;0.999	D;D	0.91635	0.998;0.999	D	0.89203	0.3559	10	0.33940	T	0.23	-15.7605	13.8363	0.63410	0.0:0.0:1.0:0.0	.	1043;1013	Q9NQ38-3;Q9NQ38	.;ISK5_HUMAN	I	1043;1013	ENSP00000352936:V1043I;ENSP00000256084:V1013I	ENSP00000256084:V1013I	V	+	1	0	SPINK5	147491087	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	4.484000	0.60271	2.514000	0.84764	0.655000	0.94253	GTC		0.413	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		A	147510894	G	A	147510894	3	1	121	1	0	0	0	0	1	0	0	0	15101	1377	48	3	3265	3	SPINK5	5	147510894	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6748202	147510894	33404366	93	31863										
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149495377	149495377	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggcgcagggcaccccgaatcCggcaactgttccagctctgg	13	15	1	0	rs183852315	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:149495377C>T	ENST00000261799.4	-	23	3739	c.3270G>A	c.(3268-3270)ccG>ccA	p.P1090P	CSF1R_ENST00000286301.3_5'Flank	NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	1090					adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|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)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|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 chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|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 metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|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 phosphoprotein phosphatase activity (GO:0032516)|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)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)	p.P1090P(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACCCCGAATCCGGCAACTGTT	0.682			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"								C|||	3	0.000599042	8e-04	0.0029	5008	,	,		18020	0		0	False		,,,				2504	0						Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	1	Substitution - coding silent(1)	large_intestine(1)	5						C		0,4406		0,0,2203	30	33	32		3270	1.9	0	5		32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDGFRB	NM_002609.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1090/1107	149495377	1,13005	2203	4300	6503	149475570	SO:0001819	synonymous_variant	5159			M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.3270G>A	5.37:g.149495377C>T			149475570	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																				0.682	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		T	149495377	C	T	149495377	2	4	121	1	0	0	0	0	0	0	0	1	11693	639	23	1		1	PDGFRB	5	149495377	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1984483	149495377	31419883	94	31864										
FAT2	2196	hgsc.bcm.edu	37	chr5	150923090	150923090	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gagtggcaatctggccattgGggtttatggagaacttctca	13	7	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:150923090G>T	ENST00000261800.5	-	9	7610	c.7598C>A	c.(7597-7599)cCc>cAc	p.P2533H		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2533	Cadherin 22. {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)	p.P2533R(1)		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)			CTGGCCATTGGGGTTTATGGA	0.428																																																1	Substitution - Missense(1)	ovary(1)	5											146	149	148					5																	150923090		2203	4300	6503	150903283	SO:0001583	missense	2196			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.7598C>A	5.37:g.150923090G>T	ENSP00000261800:p.Pro2533His		150903283	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859779	0.32884	.	.	ENSG00000086570	ENST00000261800	T	0.55234	0.53	5.34	5.34	0.76211	Cadherin (4);Cadherin-like (1);	0.398004	0.24443	N	0.038491	T	0.56659	0.2000	L	0.52573	1.65	0.22342	N	0.999189	P	0.48089	0.905	P	0.51016	0.656	T	0.54186	-0.8331	10	0.51188	T	0.08	.	12.2297	0.54480	0.0:0.0:0.7116:0.2884	.	2533	Q9NYQ8	FAT2_HUMAN	H	2533	ENSP00000261800:P2533H	ENSP00000261800:P2533H	P	-	2	0	FAT2	150903283	0.876000	0.30132	0.984000	0.44739	0.960000	0.62799	2.692000	0.47018	2.498000	0.84270	0.462000	0.41574	CCC		0.428	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150923090	G	T	150923090	3	4	121	1	0	0	0	0	1	0	0	0	5709	1232	43	2	5511	2	FAT2	5	150923090	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1427713	150923090	29992170	95	31865										
ITK	3702	hgsc.bcm.edu	37	chr5	156671390	156671390	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagattatctacgcacccagCggggactttttgctgcagag	11	11	1	2	rs200331133		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:156671390C>T	ENST00000422843.3	+	13	1503	c.1351C>T	c.(1351-1353)Cgg>Tgg	p.R451W	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	451	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	ACGCACCCAGCGGGGACTTTT	0.577			T	SYK	peripheral T-cell lymphoma								C|||	1	0.000199681	0	0.0014	5008	,	,		17969	0		0	False		,,,				2504	0				Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	0			5						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	91	90	90		1351	3.3	1	5		90	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ITK	NM_005546.3	101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	451/621	156671390	2,13004	2203	4300	6503	156603968	SO:0001583	missense	3702			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1351C>T	5.37:g.156671390C>T	ENSP00000398655:p.Arg451Trp		156603968	B2R752|Q32ML7	Missense_Mutation	SNP	ENST00000422843.3	37	CCDS4336.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	20.4	3.985241	0.74474	2.27E-4	1.16E-4	ENSG00000113263	ENST00000422843	T	0.64438	-0.1	6.08	3.32	0.38043	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.102510	0.64402	D	0.000004	T	0.81772	0.4893	M	0.88377	2.95	0.42913	D	0.994263	D	0.89917	1.0	D	0.75484	0.986	D	0.85166	0.0995	10	0.66056	D	0.02	.	16.1251	0.81386	0.4551:0.5449:0.0:0.0	.	451	Q08881	ITK_HUMAN	W	451	ENSP00000398655:R451W	ENSP00000398655:R451W	R	+	1	2	ITK	156603968	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.047000	0.30367	0.435000	0.26365	-0.230000	0.12252	CGG		0.577	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			T	156671390	C	T	156671390	3	4	121	1	0	0	0	0	1	0	0	0	7930	759	27	1	1401	1	ITK	5	156671390	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	5748300	156671390	24243870	96	31866										
WWC1	23286	hgsc.bcm.edu	37	chr5	167894878	167894878	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cggagcacaagggtgagcttCagacagacaagatgatgagg	15	7	1	6			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:167894878C>T	ENST00000265293.4	+	22	3686	c.3184C>T	c.(3184-3186)Cag>Tag	p.Q1062*	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Nonsense_Mutation_p.Q1068*	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	1062	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)		GGGTGAGCTTCAGACAGACAA	0.582																																																0			5											76	73	74					5																	167894878		2203	4300	6503	167827456	SO:0001587	stop_gained	23286			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.3184C>T	5.37:g.167894878C>T	ENSP00000265293:p.Gln1062*		167827456	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Nonsense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.106421|8.106421	0.98657|0.98657	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038|ENST00000393895;ENST00000524228	.|.	.|.	.|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.424159|.	0.24396|.	N|.	0.038885|.	.|T	.|0.61961	.|0.2389	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69335	.|-0.5172	.|3	0.05525|.	T|.	0.97|.	.|.	11.8777|11.8777	0.52556|0.52556	0.2213:0.7787:0.0:0.0|0.2213:0.7787:0.0:0.0	.|.	.|.	.|.	.|.	X|L	1062;1068;393|1028;837	.|.	ENSP00000265293:Q1062X|.	Q|S	+|+	1|2	0|0	WWC1|WWC1	167827456|167827456	0.986000|0.986000	0.35501|0.35501	0.625000|0.625000	0.29200|0.29200	0.967000|0.967000	0.64934|0.64934	2.791000|2.791000	0.47829|0.47829	2.479000|2.479000	0.83701|0.83701	0.591000|0.591000	0.81541|0.81541	CAG|TCA		0.582	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		T	167894878	C	T	167894878	4	4	121	1	0	0	0	0	0	1	0	0	17451	827	29	3	3288	3	WWC1	5	167894878	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	11223488	167894878	13020382	97	31867										
NSD1	64324	hgsc.bcm.edu	37	chr5	176721629	176721629	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttgtcccagagactcccaccTcctgagaaagtactatcagc	7	14	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:176721629T>C	ENST00000439151.2	+	23	7305	c.7260T>C	c.(7258-7260)ccT>ccC	p.P2420P	NSD1_ENST00000354179.4_Silent_p.P2151P|NSD1_ENST00000361032.4_Silent_p.P2317P|NSD1_ENST00000347982.4_Silent_p.P2151P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2420	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)		GACTCCCACCTCCTGAGAAAG	0.507			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																													Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	0			5											72	82	79					5																	176721629		2203	4300	6503	176654235	SO:0001819	synonymous_variant	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	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.7260T>C	5.37:g.176721629T>C			176654235	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																				0.507	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176721629	T	C	176721629	2	2	121	1	0	0	0	0	0	0	0	1	10700	1538	54	4		4	NSD1	5	176721629	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	8826751	176721629	4193631	98	31868										
DBN1	1627	hgsc.bcm.edu	37	chr5	176887554	176887554	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgggcaataatagctgctgcCtcctgagggcacgaggaaaa	13	9	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr5:176887554C>A	ENST00000309007.5	-	10	1053	c.834G>T	c.(832-834)gaG>gaT	p.E278D	DBN1_ENST00000512501.1_Missense_Mutation_p.E10D|DBN1_ENST00000393563.4_Missense_Mutation_p.E10D|DBN1_ENST00000292385.5_Missense_Mutation_p.E280D|DBN1_ENST00000393565.1_Missense_Mutation_p.E278D	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	278			E -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)			TAGCTGCTGCCTCCTGAGGGC	0.617																																																0			5											158	149	152					5																	176887554		2203	4300	6503	176820160	SO:0001583	missense	1627				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.834G>T	5.37:g.176887554C>A	ENSP00000308532:p.Glu278Asp		176820160	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.855758	0.71834	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563;ENST00000477391	T;T;T;T;T	0.62788	1.06;1.06;1.55;0.0;0.47	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.74313	0.3700	M	0.68952	2.095	0.43965	D	0.996641	D;D;D;D	0.76494	0.996;0.999;0.997;0.998	D;D;D;D	0.77557	0.987;0.99;0.978;0.99	T	0.76293	-0.3012	10	0.72032	D	0.01	-12.6217	9.9236	0.41478	0.0:0.905:0.0:0.095	.	228;278;278;280	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	D	278;280;278;10;10;277	ENSP00000308532:E278D;ENSP00000292385:E280D;ENSP00000377195:E278D;ENSP00000423208:E10D;ENSP00000377193:E10D	ENSP00000292385:E280D	E	-	3	2	DBN1	176820160	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	2.998000	0.49465	2.368000	0.80403	0.561000	0.74099	GAG		0.617	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		A	176887554	C	A	176887554	3	1	121	1	0	0	0	0	1	0	0	0	4258	680	24	2	1135	2	DBN1	5	176887554	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	165925	176887554	4027706	99	31869										
GCM2	9247	hgsc.bcm.edu	37	chr6	10875152	10875152	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctgaaatgaccactgctgtcTtgattttcttctgcctagaa	7	10	3	4			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:10875152T>C	ENST00000379491.4	-	5	744	c.597A>G	c.(595-597)caA>caG	p.Q199Q	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	199					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|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 (GO:0043565)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				CACTGCTGTCTTGATTTTCTT	0.418																																																0			6											89	85	87					6																	10875152		2203	4300	6503	10983138	SO:0001819	synonymous_variant	9247			AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.597A>G	6.37:g.10875152T>C			10983138	D3GDV6|Q5THN5	Silent	SNP	ENST00000379491.4	37	CCDS4517.1																																																																																				0.418	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			C	10875152	T	C	10875152	2	2	121	1	0	0	0	0	0	0	0	1	6318	1606	56	4		4	GCM2	6	10875152	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10		10875152	160239915	100	31870										
GNL1	2794	hgsc.bcm.edu	37	chr6	30523411	30523411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gatatgatgggtcacagactCcccgtccgaggtgtcggtct	13	11	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:30523411C>T	ENST00000376621.3	-	2	1130	c.160G>A	c.(160-162)Gag>Aag	p.E54K	PRR3_ENST00000376560.3_5'Flank|PRR3_ENST00000376557.3_5'Flank	NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	54					cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GTCACAGACTCCCCGTCCGAG	0.667																																																0			6											90	84	86					6																	30523411		2203	4300	6503	30631390	SO:0001583	missense	2794				CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.160G>A	6.37:g.30523411C>T	ENSP00000365806:p.Glu54Lys		30631390	B0S838|Q96CT5	Missense_Mutation	SNP	ENST00000376621.3	37	CCDS4680.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.200724	0.58126	.	.	ENSG00000204590	ENST00000376621;ENST00000433809	T	0.46451	0.87	5.08	5.08	0.68730	.	0.113743	0.64402	D	0.000020	T	0.25419	0.0618	L	0.56769	1.78	0.52501	D	0.999951	B;B	0.12013	0.001;0.005	B;B	0.10450	0.002;0.005	T	0.06643	-1.0815	10	0.20046	T	0.44	-41.8254	15.7365	0.77849	0.0:1.0:0.0:0.0	.	52;54	B4DYK6;P36915	.;GNL1_HUMAN	K	54;52	ENSP00000365806:E54K	ENSP00000365806:E54K	E	-	1	0	GNL1	30631390	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.377000	0.52425	2.534000	0.85438	0.561000	0.74099	GAG		0.667	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2			T	30523411	C	T	30523411	3	4	121	1	0	0	0	0	1	0	0	0	6555	864	30	3	1707	3	GNL1	6	30523411	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	19648259	30523411	140591656	101	31871										
VPS52	6293	hgsc.bcm.edu	37	chr6	33232205	33232205	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgggggtcagtgcttcggacGctctgaacattcatctccag	12	11	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:33232205G>A	ENST00000445902.2	-	14	1688	c.1470C>T	c.(1468-1470)agC>agT	p.S490S	VPS52_ENST00000436044.2_Silent_p.S365S|VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	490					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						TGCTTCGGACGCTCTGAACAT	0.562																																																0			6											106	104	105					6																	33232205		2203	4300	6503	33340183	SO:0001819	synonymous_variant	6293			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.1470C>T	6.37:g.33232205G>A			33340183	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																				0.562	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		A	33232205	G	A	33232205	2	1	121	1	0	0	0	0	0	0	0	1	17254	1078	38	1		1	VPS52	6	33232205	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	2708794	33232205	137882862	102	31872										
USP49	25862	hgsc.bcm.edu	37	chr6	41774568	41774568	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaagtgtttcagggcgtggtCctcaatatagcggccgcagg	14	9	2	0	rs148441118	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:41774568C>T	ENST00000394253.3	-	3	483	c.154G>A	c.(154-156)Gac>Aac	p.D52N	USP49_ENST00000373009.3_Missense_Mutation_p.D52N|USP49_ENST00000373010.1_Missense_Mutation_p.D52N|USP49_ENST00000373006.1_Missense_Mutation_p.D52N|USP49_ENST00000297229.2_Missense_Mutation_p.D52N			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	52					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)	p.D52N(1)		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)			AGGGCGTGGTCCTCAATATAG	0.587													C|||	2	0.000399361	0	0	5008	,	,		13562	0.001		0.001	False		,,,				2504	0															1	Substitution - Missense(1)	lung(1)	6						C	ASN/ASP	0,4406		0,0,2203	97	103	101		154	5.1	1	6	dbSNP_134	101	6,8594	4.3+/-15.6	0,6,4294	yes	missense	USP49	NM_018561.3	23	0,6,6497	TT,TC,CC		0.0698,0.0,0.0461	benign	52/641	41774568	6,13000	2203	4300	6503	41882546	SO:0001583	missense	25862			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.154G>A	6.37:g.41774568C>T	ENSP00000377797:p.Asp52Asn		41882546	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	27.7	4.856125	0.91355	0.0	6.98E-4	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.05	5.05	0.67936	.	0.048851	0.85682	D	0.000000	T	0.13157	0.0319	N	0.05280	-0.08	0.47214	D	0.99935	P	0.37500	0.597	B	0.41666	0.363	T	0.16897	-1.0387	10	0.59425	D	0.04	-16.9524	18.203	0.89844	0.0:1.0:0.0:0.0	.	52	Q70CQ1-2	.	N	52	ENSP00000377797:D52N;ENSP00000362101:D52N;ENSP00000362100:D52N;ENSP00000362097:D52N;ENSP00000297229:D52N	ENSP00000297229:D52N	D	-	1	0	USP49	41882546	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	5.581000	0.67471	2.624000	0.88883	0.655000	0.94253	GAC		0.587	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561		T	41774568	C	T	41774568	3	4	121	1	0	0	0	0	1	0	0	0	17120	855	30	3	1784	3	USP49	6	41774568	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	8542363	41774568	129340499	103	31873										
GPR110	266977	hgsc.bcm.edu	37	chr6	46984471	46984471	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcagatgcactgctggagccAacaacttcatacccagcaac	7	14	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:46984471A>G	ENST00000371253.2	-	8	860	c.645T>C	c.(643-645)gtT>gtC	p.V215V	GPR110_ENST00000283297.5_Silent_p.V18V|GPR110_ENST00000449332.2_5'UTR	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	215	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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						TGCTGGAGCCAACAACTTCAT	0.458																																																0			6											104	90	95					6																	46984471		2203	4300	6503	47092430	SO:0001819	synonymous_variant	266977			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.645T>C	6.37:g.46984471A>G			47092430	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																				0.458	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		G	46984471	A	G	46984471	2	3	121	1	0	0	0	0	0	0	0	1	6647	117	5	4		4	GPR110	6	46984471	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	5209903	46984471	124130596	104	31874										
GSTA2	2939	hgsc.bcm.edu	37	chr6	52615427	52615427	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagatttctcatccatgggaGgcttccttgggctgccaggc	12	11	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:52615427G>T	ENST00000493422.1	-	7	772	c.617C>A	c.(616-618)cCt>cAt	p.P206H		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	206	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)	ATCCATGGGAGGCTTCCTTGG	0.433																																																0			6											125	128	127					6																	52615427		2203	4300	6503	52723386	SO:0001583	missense	2939			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.617C>A	6.37:g.52615427G>T	ENSP00000420168:p.Pro206His		52723386	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	37	CCDS4944.1	.	.	.	.	.	.	.	.	.	.	g	12.10	1.836529	0.32421	.	.	ENSG00000244067	ENST00000493422	T	0.11930	2.73	2.32	0.28	0.15682	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);	0.073236	0.53938	N	0.000044	T	0.16428	0.0395	M	0.86953	2.85	0.22457	N	0.999084	D	0.69078	0.997	P	0.60415	0.874	T	0.03957	-1.0989	10	0.87932	D	0	.	4.162	0.10289	0.1436:0.0:0.63:0.2263	.	206	P09210	GSTA2_HUMAN	H	206	ENSP00000420168:P206H	ENSP00000420168:P206H	P	-	2	0	GSTA2	52723386	0.997000	0.39634	0.064000	0.19789	0.184000	0.23303	3.677000	0.54619	-0.076000	0.12775	0.298000	0.19748	CCT		0.433	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846		T	52615427	G	T	52615427	3	4	121	1	0	0	0	0	1	0	0	0	6852	1000	35	2	55	2	GSTA2	6	52615427	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	5630956	52615427	118499640	105	31875										
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461682	82461682	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agcacattgcagtgcgccgtAgggctttcgcaatagtccaa	11	11	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:82461682A>C	ENST00000320172.6	-	2	491	c.177T>G	c.(175-177)ccT>ccG	p.P59P	FAM46A_ENST00000369756.3_Silent_p.P140P|FAM46A_ENST00000369754.3_Silent_p.P78P	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	59					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)		AGTGCGCCGTAGGGCTTTCGC	0.667																																																0			6											41	38	39					6																	82461682		2200	4297	6497	82518401	SO:0001819	synonymous_variant	55603			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.177T>G	6.37:g.82461682A>C			82518401	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	37	CCDS34489.1																																																																																				0.667	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			C	82461682	A	C	82461682	2	2	121	1	0	0	0	0	0	0	0	1	5584	407	15	4		4	FAM46A	6	82461682	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	29846255	82461682	88653385	106	31876										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93982020	93982020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgctcttagcacttactttcTcgtaatacttgatttcatat	4	9	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:93982020T>C	ENST00000369303.4	-	6	1629	c.1445A>G	c.(1444-1446)gAg>gGg	p.E482G		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	482	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		ACTTACTTTCTCGTAATACTT	0.418																																																0			6											304	271	282					6																	93982020		2203	4300	6503	94038741	SO:0001583	missense	2045			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.1445A>G	6.37:g.93982020T>C	ENSP00000358309:p.Glu482Gly		94038741	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936201	0.73442	.	.	ENSG00000135333	ENST00000369303	T	0.59224	0.28	5.49	5.49	0.81192	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.70798	0.3265	M	0.75264	2.295	0.80722	D	1	D;D;D	0.89917	0.989;1.0;1.0	D;D;D	0.79784	0.969;0.988;0.993	T	0.75687	-0.3231	10	0.87932	D	0	.	15.8744	0.79151	0.0:0.0:0.0:1.0	.	482;482;482	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	G	482	ENSP00000358309:E482G	ENSP00000358309:E482G	E	-	2	0	EPHA7	94038741	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	7.655000	0.83696	2.219000	0.72066	0.459000	0.35465	GAG		0.418	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			C	93982020	T	C	93982020	3	2	121	1	0	0	0	0	1	0	0	0	5185	1551	54	4	1599	4	EPHA7	6	93982020	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	11520338	93982020	77133047	107	31877										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99323420	99323420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctggtgtgccagtctggtgaAgcacccggtgctgctctgca	14	12	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:99323420A>G	ENST00000369244.2	-	9	2001	c.1573T>C	c.(1573-1575)Ttc>Ctc	p.F525L	FBXL4_ENST00000229971.1_Missense_Mutation_p.F525L	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	525					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)		AGTCTGGTGAAGCACCCGGTG	0.483																																																0			6											91	87	88					6																	99323420		2203	4300	6503	99430141	SO:0001583	missense	26235			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.1573T>C	6.37:g.99323420A>G	ENSP00000358247:p.Phe525Leu		99430141	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	37	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192762	0.38707	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.00745	5.75;5.75	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.00724	0.0024	N	0.21097	0.63	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.97	T	0.66492	-0.5910	10	0.02654	T	1	.	16.2898	0.82742	1.0:0.0:0.0:0.0	.	525;525	B2R7Q5;Q9UKA2	.;FBXL4_HUMAN	L	525	ENSP00000358247:F525L;ENSP00000229971:F525L	ENSP00000229971:F525L	F	-	1	0	FBXL4	99430141	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.000000	0.76290	2.250000	0.74265	0.482000	0.46254	TTC		0.483	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			G	99323420	A	G	99323420	3	3	121	1	0	0	0	0	1	0	0	0	5740	72	3	4	300	4	FBXL4	6	99323420	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	5341400	99323420	71791647	108	31878										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101248259	101248259	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccagcctttttttctcgtctGgcaattcttttttcttcacg	5	12	5	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:101248259G>A	ENST00000369162.2	-	6	1388	c.1044C>T	c.(1042-1044)gcC>gcT	p.A348A	ASCC3_ENST00000522650.1_Silent_p.A348A	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	348					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)		TTTCTCGTCTGGCAATTCTTT	0.368																																																0			6											161	149	153					6																	101248259		2203	4299	6502	101354980	SO:0001819	synonymous_variant	10973			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.1044C>T	6.37:g.101248259G>A			101354980	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																				0.368	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101248259	G	A	101248259	2	1	121	1	0	0	0	0	0	0	0	1	1034	1335	47	3		3	ASCC3	6	101248259	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1924839	101248259	69866808	109	31879										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119344188	119344188	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctcactttccacttctttgtGcttgcttaatagggccattt	6	11	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:119344188G>T	ENST00000338891.7	-	3	1515	c.1072C>A	c.(1072-1074)Cac>Aac	p.H358N	FAM184A_ENST00000521531.1_Missense_Mutation_p.H358N|FAM184A_ENST00000352896.5_Missense_Mutation_p.H238N|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Missense_Mutation_p.H238N|FAM184A_ENST00000522284.1_Missense_Mutation_p.H238N	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	358						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						ACTTCTTTGTGCTTGCTTAAT	0.403																																																0			6											164	156	158					6																	119344188		1941	4160	6101	119385887	SO:0001583	missense	79632			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.1072C>A	6.37:g.119344188G>T	ENSP00000342604:p.His358Asn		119385887	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107049	0.77096	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.73	5.73	0.89815	.	0.123438	0.64402	D	0.000018	T	0.28366	0.0701	L	0.57536	1.79	0.53005	D	0.999967	P;P;P	0.43352	0.763;0.763;0.804	P;B;P	0.47299	0.461;0.288;0.543	T	0.02244	-1.1189	10	0.15066	T	0.55	-13.5553	19.9133	0.97031	0.0:0.0:1.0:0.0	.	358;238;358	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	N	358;238;238;358;238	ENSP00000342604:H358N;ENSP00000326608:H238N;ENSP00000357460:H238N;ENSP00000430442:H358N;ENSP00000429826:H238N	ENSP00000342604:H358N	H	-	1	0	FAM184A	119385887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.241000	0.95402	2.721000	0.93114	0.655000	0.94253	CAC		0.403	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119344188	G	T	119344188	3	4	121	1	0	0	0	0	1	0	0	0	5527	1319	46	2	2414	2	FAM184A	6	119344188	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	18095929	119344188	51770879	110	31880										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152638118	152638118	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtattcttctaaatgtgatgCtgcctgaaaaaccagtaaca	7	8	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:152638118C>T	ENST00000367255.5	-	87	17177	c.16576G>A	c.(16576-16578)Gca>Aca	p.A5526T	SYNE1_ENST00000423061.1_Missense_Mutation_p.A5455T|SYNE1_ENST00000448038.1_Missense_Mutation_p.A5455T|SYNE1_ENST00000341594.5_Missense_Mutation_p.A5138T|SYNE1_ENST00000356820.4_Missense_Mutation_p.A50T|SYNE1_ENST00000265368.4_Missense_Mutation_p.A5526T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5526				A -> T (in Ref. 1; AAL33798). {ECO:0000305}.	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.A5526T(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)		AAATGTGATGCTGCCTGAAAA	0.353										HNSCC(10;0.0054)																																						1	Substitution - Missense(1)	central_nervous_system(1)	6											88	88	88					6																	152638118		2203	4300	6503	152679811	SO:0001583	missense	23345			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.16576G>A	6.37:g.152638118C>T	ENSP00000356224:p.Ala5526Thr		152679811	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	6.459	0.452849	0.12283	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50277	1.34;1.34;1.34;1.34;0.75;1.34	5.59	4.7	0.59300	.	0.339402	0.25186	N	0.032492	T	0.13200	0.0320	L	0.31294	0.92	0.24607	N	0.993746	B;B;B;B	0.13145	0.007;0.004;0.004;0.007	B;B;B;B	0.09377	0.004;0.002;0.002;0.004	T	0.16988	-1.0384	10	0.13470	T	0.59	.	8.4487	0.32858	0.1419:0.7409:0.0:0.1172	.	5526;5526;5526;5455	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	T	5526;5455;5526;5455;5138;50	ENSP00000356224:A5526T;ENSP00000396024:A5455T;ENSP00000265368:A5526T;ENSP00000390975:A5455T;ENSP00000341887:A5138T;ENSP00000349276:A50T	ENSP00000265368:A5526T	A	-	1	0	SYNE1	152679811	0.985000	0.35326	0.998000	0.56505	0.993000	0.82548	1.392000	0.34486	1.299000	0.44798	0.557000	0.71058	GCA		0.353	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152638118	C	T	152638118	3	4	121	1	0	0	0	0	1	0	0	0	15484	797	28	3	10130	3	SYNE1	6	152638118	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	33293930	152638118	18476949	111	31881										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654306	159654306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gagaggggccagcctgcatcGgaaggaacccatcccagaga	14	12	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr6:159654306G>A	ENST00000297267.9	+	11	2962	c.2762G>A	c.(2761-2763)cGg>cAg	p.R921Q	FNDC1_ENST00000340366.6_Missense_Mutation_p.R858Q	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	921					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)		p.R921Q(2)		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)		AGCCTGCATCGGAAGGAACCC	0.602																																																2	Substitution - Missense(2)	large_intestine(2)	6											66	76	72					6																	159654306		1971	4154	6125	159574296	SO:0001583	missense	84624			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.2762G>A	6.37:g.159654306G>A	ENSP00000297267:p.Arg921Gln		159574296	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.811076	0.32053	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.18657	2.2;2.81	5.33	-0.659	0.11424	.	0.921751	0.09236	N	0.829883	T	0.03564	0.0102	N	0.24115	0.695	0.09310	N	1	B;B	0.27117	0.168;0.105	B;B	0.19946	0.027;0.012	T	0.42361	-0.9456	10	0.36615	T	0.2	-5.173	5.1953	0.15233	0.4093:0.14:0.4507:0.0	.	858;921	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	Q	921;858	ENSP00000297267:R921Q;ENSP00000342460:R858Q	ENSP00000297267:R921Q	R	+	2	0	FNDC1	159574296	0.044000	0.20184	0.017000	0.16124	0.535000	0.34838	0.042000	0.13949	-0.500000	0.06614	-0.749000	0.03505	CGG		0.602	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159654306	G	A	159654306	3	1	121	1	0	0	0	0	1	0	0	0	5987	1116	39	1	2804	1	FNDC1	6	159654306	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	7016188	159654306	11460761	112	31882										
SDK1	221935	hgsc.bcm.edu	37	chr7	4169684	4169684	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cgttcacccgcatcgggaacGgggtccccagcacgcccctc	11	19	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:4169684G>A	ENST00000404826.2	+	27	4223	c.4084G>A	c.(4084-4086)Ggg>Agg	p.G1362R	SDK1_ENST00000389531.3_Missense_Mutation_p.G1362R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1362	Fibronectin type-III 7. {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)		CATCGGGAACGGGGTCCCCAG	0.662																																																0			7											46	47	47					7																	4169684		2203	4300	6503	4136210	SO:0001583	missense	221935			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.4084G>A	7.37:g.4169684G>A	ENSP00000385899:p.Gly1362Arg		4136210	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	35	5.465207	0.96257	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.66280	-0.2;-0.2	5.67	5.67	0.87782	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.89322	0.6682	H	0.99555	4.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93668	0.6987	10	0.87932	D	0	.	19.7534	0.96277	0.0:0.0:1.0:0.0	.	1362;1362	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	R	1362	ENSP00000385899:G1362R;ENSP00000374182:G1362R	ENSP00000374182:G1362R	G	+	1	0	SDK1	4136210	1.000000	0.71417	0.947000	0.38551	0.972000	0.66771	9.041000	0.93788	2.686000	0.91538	0.655000	0.94253	GGG		0.662	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4169684	G	A	4169684	3	1	121	1	0	0	0	0	1	0	0	0	14005	1116	39	1	4190	1	SDK1	7	4169684	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10		4169684	154968979	113	31883										
TNS3	64759	hgsc.bcm.edu	37	chr7	47467961	47467961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atgatatgaccactcctatgCgtcctttcccgccctgcagg	8	15	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:47467961C>T	ENST00000398879.1	-	9	704	c.338G>A	c.(337-339)cGc>cAc	p.R113H	TNS3_ENST00000442536.2_Missense_Mutation_p.R113H|TNS3_ENST00000355730.3_Missense_Mutation_p.R113H|TNS3_ENST00000311160.9_Missense_Mutation_p.R113H|TNS3_ENST00000458317.2_Missense_Mutation_p.R113H			Q68CZ2	TENS3_HUMAN	tensin 3	113	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				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						CACTCCTATGCGTCCTTTCCC	0.478																																																0			7											111	107	108					7																	47467961		2015	4182	6197	47434486	SO:0001583	missense	64759			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.338G>A	7.37:g.47467961C>T	ENSP00000381854:p.Arg113His		47434486	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831196	0.91036	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000457718;ENST00000450444;ENST00000442536;ENST00000458317;ENST00000415929	D;D;D;D;D;D;D;D	0.99861	-7.26;-7.26;-7.26;-7.26;-7.26;-7.26;-7.26;-7.26	5.82	5.82	0.92795	Phosphatase tensin type (1);	0.112759	0.64402	D	0.000017	D	0.99908	0.9956	H	0.96142	3.775	0.48395	D	0.999644	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.96498	0.9369	10	0.72032	D	0.01	-46.5292	17.5737	0.87942	0.0:1.0:0.0:0.0	.	113;113	Q68CZ2-4;Q68CZ2	.;TENS3_HUMAN	H	113;223;113;113;216;202;113;113;113	ENSP00000312143:R113H;ENSP00000381854:R113H;ENSP00000347968:R113H;ENSP00000414358:R216H;ENSP00000396914:R202H;ENSP00000389285:R113H;ENSP00000388318:R113H;ENSP00000409415:R113H	ENSP00000312143:R113H	R	-	2	0	TNS3	47434486	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.100000	0.64560	2.736000	0.93811	0.655000	0.94253	CGC		0.478	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47467961	C	T	47467961	3	4	121	1	0	0	0	0	1	0	0	0	16383	768	27	1	4091	1	TNS3	7	47467961	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	43298277	47467961	111670702	114	31884										
GTF2IRD2B	389524	hgsc.bcm.edu	37	chr7	74564623	74564623	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atccgggcgttcctagcaaaActgtgcctctgggagactca	11	12	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:74564623A>G	ENST00000312575.7	+	16	2545	c.2370A>G	c.(2368-2370)aaA>aaG	p.K790K	GTF2IRD2B_ENST00000418185.2_Silent_p.K337K	NM_001003795.2	NP_001003795.1	Q6EKJ0	GTD2B_HUMAN	GTF2I repeat domain containing 2B	790					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|ovary(2)|prostate(1)	4						tcctagcaaaactgtgcctct	0.483																																																0			7											23	24	23					7																	74564623		1482	3150	4632	74202559	SO:0001819	synonymous_variant	389524			AY312850	CCDS34659.1	7q11.23	2014-05-06			ENSG00000174428	ENSG00000174428			33125	protein-coding gene	gene with protein product		608900				15100712	Standard	XM_005277580		Approved		uc003ubt.3	Q6EKJ0	OTTHUMG00000181534	ENST00000312575.7:c.2370A>G	7.37:g.74564623A>G			74202559	B2RNE9|Q69GU6|Q8N979|Q9H739	Silent	SNP	ENST00000312575.7	37	CCDS34659.1																																																																																				0.483	GTF2IRD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342728.1	NM_001003795		G	74564623	A	G	74564623	2	3	121	1	0	0	0	0	0	0	0	1	6891	40	2	4		4	GTF2IRD2B	7	74564623	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	27096662	74564623	84574040	115	31885										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77885427	77885427	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgtcaagtatttgtttcaccCgctgtcctgtaggactgtcg	10	10	2	0	rs201473728		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:77885427C>A	ENST00000354212.4	-	10	2133	c.1880G>T	c.(1879-1881)cGg>cTg	p.R627L	MAGI2_ENST00000419488.1_Missense_Mutation_p.R627L|MAGI2_ENST00000535697.1_Missense_Mutation_p.R464L|MAGI2_ENST00000522391.1_Missense_Mutation_p.R627L|MAGI2_ENST00000536571.1_Missense_Mutation_p.R459L	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	627	PDZ 3. {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)				TTGTTTCACCCGCTGTCCTGT	0.512																																																0			7											71	60	64					7																	77885427		2203	4300	6503	77723363	SO:0001583	missense	9863			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.1880G>T	7.37:g.77885427C>A	ENSP00000346151:p.Arg627Leu		77723363	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529903	0.85706	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78	5.65	5.65	0.86999	PDZ/DHR/GLGF (4);	0.000000	0.33457	U	0.004881	T	0.53174	0.1780	M	0.72894	2.215	0.80722	D	1	D;P;D;D;D;D	0.89917	0.994;0.942;1.0;1.0;0.999;0.999	D;P;D;D;D;D	0.91635	0.937;0.704;0.999;0.999;0.966;0.997	T	0.54186	-0.8331	10	0.87932	D	0	.	18.6986	0.91611	0.0:1.0:0.0:0.0	.	464;459;627;627;627;627	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	L	627;627;627;627;459;464	ENSP00000405766:R627L;ENSP00000346151:R627L;ENSP00000428389:R627L;ENSP00000441584:R459L;ENSP00000441603:R464L	ENSP00000346151:R627L	R	-	2	0	MAGI2	77723363	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.814000	0.86154	2.653000	0.90120	0.561000	0.74099	CGG		0.512	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77885427	C	A	77885427	3	1	121	1	0	0	0	0	1	0	0	0	9221	652	23	2	2539	2	MAGI2	7	77885427	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3320804	77885427	81253236	116	31886										
ADAM22	53616	hgsc.bcm.edu	37	chr7	87782584	87782584	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgagaaactgaatattgaagGgacggagaagggtaactgtg	15	3	0	4			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:87782584G>A	ENST00000265727.7	+	21	1809	c.1730G>A	c.(1729-1731)gGg>gAg	p.G577E	ADAM22_ENST00000315984.7_Missense_Mutation_p.G577E|ADAM22_ENST00000398201.4_Missense_Mutation_p.G577E|ADAM22_ENST00000398204.4_Missense_Mutation_p.G577E|ADAM22_ENST00000398209.3_Missense_Mutation_p.G577E			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	577	Cys-rich.				adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			AATATTGAAGGGACGGAGAAG	0.438																																																0			7											116	115	116					7																	87782584		1939	4137	6076	87620520	SO:0001583	missense	53616			AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"ADAM metallopeptidase domain containing"	201	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"	603709	"a disintegrin and metalloproteinase domain 22"			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.1730G>A	7.37:g.87782584G>A	ENSP00000265727:p.Gly577Glu		87620520	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Missense_Mutation	SNP	ENST00000265727.7	37	CCDS47637.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.614944	0.87359	.	.	ENSG00000008277	ENST00000398204;ENST00000398201;ENST00000265727;ENST00000315984;ENST00000398209;ENST00000398203	T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72	5.45	5.45	0.79879	ADAM, cysteine-rich (2);	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	H	0.98256	4.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.81642	-0.0840	10	0.87932	D	0	.	18.0363	0.89303	0.0:0.0:1.0:0.0	.	629;577;577;577	E9PBH5;Q9P0K1-5;Q9P0K1;Q9P0K1-2	.;.;ADA22_HUMAN;.	E	577;577;577;577;577;544	ENSP00000381262:G577E;ENSP00000381260:G577E;ENSP00000265727:G577E;ENSP00000315900:G577E;ENSP00000381267:G577E;ENSP00000381261:G544E	ENSP00000265727:G577E	G	+	2	0	ADAM22	87620520	1.000000	0.71417	0.973000	0.42090	0.669000	0.39330	9.286000	0.95898	2.554000	0.86153	0.655000	0.94253	GGG		0.438	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		A	87782584	G	A	87782584	3	1	121	1	0	0	0	0	1	0	0	0	244	1232	43	3	1812	3	ADAM22	7	87782584	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	9897157	87782584	71356079	117	31887										
CYP3A4	1576	hgsc.bcm.edu	37	chr7	99381645	99381645	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gttactcacagatagaggagCaccaggctgacagccaggag	13	10	1	3	rs375059964		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:99381645C>T	ENST00000336411.2	-	1	243	c.60G>A	c.(58-60)gtG>gtA	p.V20V	CYP3A4_ENST00000354593.2_Silent_p.V20V	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	20					alkaloid catabolic process (GO:0009822)|androgen metabolic process (GO:0008209)|calcitriol biosynthetic process from calciol (GO:0036378)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|lipid metabolic process (GO:0006629)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	albendazole monooxygenase activity (GO:0047638)|caffeine oxidase activity (GO:0034875)|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, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)|quinine 3-monooxygenase activity (GO:0050591)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)|taurochenodeoxycholate 6alpha-hydroxylase activity (GO:0033780)|testosterone 6-beta-hydroxylase activity (GO:0050649)|vitamin D 24-hydroxylase activity (GO:0070576)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(3)|central_nervous_system(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Abiraterone(DB05812)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetazolamide(DB00819)|Adinazolam(DB00546)|ado-trastuzumab emtansine(DB05773)|Albendazole(DB00518)|Alclometasone(DB00240)|Aldesleukin(DB00041)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Alimemazine(DB01246)|Aliskiren(DB01258)|Allylestrenol(DB01431)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alosetron(DB00969)|Alprazolam(DB00404)|Ambroxol(DB06742)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Arsenic trioxide(DB01169)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atazanavir(DB01072)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Avanafil(DB06237)|Axitinib(DB06626)|Azatadine(DB00719)|Azelastine(DB00972)|Azithromycin(DB00207)|Bedaquiline(DB08903)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bezafibrate(DB01393)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bisoprolol(DB00612)|Boceprevir(DB08873)|Bortezomib(DB00188)|Bosentan(DB00559)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Brinzolamide(DB01194)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Brompheniramine(DB00835)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Busulfan(DB01008)|Cabazitaxel(DB06772)|Cabergoline(DB00248)|Cabozantinib(DB08875)|Caffeine(DB00201)|Calcitriol(DB00136)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Caspofungin(DB00520)|Cefradine(DB01333)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chenodeoxycholic acid(DB06777)|Chloramphenicol(DB00446)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clemastine(DB00283)|Clevidipine(DB04920)|Clindamycin(DB01190)|Clobazam(DB00349)|Clofazimine(DB00845)|Clofibrate(DB00636)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonazepam(DB01068)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Colchicine(DB01394)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cortisone acetate(DB01380)|Crizotinib(DB08865)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Cytarabine(DB00987)|Dabrafenib(DB08912)|Dalfopristin(DB01764)|Danazol(DB01406)|Dantrolene(DB01219)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Deferasirox(DB01609)|Delavirdine(DB00705)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Dicloxacillin(DB00485)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydrocodeine(DB01551)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Disopyramide(DB00280)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dofetilide(DB00204)|Dolasetron(DB00757)|Dolutegravir(DB08930)|Domperidone(DB01184)|Donepezil(DB00843)|Dorzolamide(DB00869)|Doxepin(DB01142)|Doxorubicin(DB00997)|Doxycycline(DB00254)|Dronabinol(DB00470)|Dronedarone(DB04855)|Dutasteride(DB01126)|Econazole(DB01127)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Epinephrine(DB00668)|Eplerenone(DB00700)|Ergocalciferol(DB00153)|Ergoloid mesylate(DB01049)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Estradiol valerate/Dienogest(DB08866)|Estradiol(DB00783)|Estramustine(DB01196)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Etravirine(DB06414)|Everolimus(DB01590)|Exemestane(DB00990)|Ezetimibe(DB00973)|Famciclovir(DB00426)|Felbamate(DB00949)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Finasteride(DB01216)|Fingolimod(DB08868)|Flucloxacillin(DB00301)|Fluconazole(DB00196)|Flunisolide(DB00180)|Flunitrazepam(DB01544)|Fluorometholone(DB00324)|Fluoxetine(DB00472)|Flurazepam(DB00690)|Flutamide(DB00499)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosamprenavir(DB01319)|Fosphenytoin(DB01320)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Glipizide(DB01067)|Glyburide(DB01016)|Granisetron(DB00889)|Griseofulvin(DB00400)|Guanethidine(DB01170)|Guanfacine(DB01018)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Hydralazine(DB01275)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|Indacaterol(DB05039)|Indapamide(DB00808)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Irinotecan(DB00762)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ixabepilone(DB04845)|Josamycin(DB01321)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Levomethadyl Acetate(DB01227)|Levomilnacipran(DB08918)|Levonorgestrel(DB00367)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Lisuride(DB00589)|Lomitapide(DB08827)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumefantrine(DB06708)|Lurasidone(DB08815)|MACITENTAN(DB08932)|Maraviroc(DB04835)|Mebendazole(DB00643)|Medroxyprogesterone Acetate(DB00603)|Mefloquine(DB00358)|Meloxicam(DB00814)|Mequitazine(DB01071)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Methylergometrine(DB00353)|Methylprednisolone(DB00959)|Methyltestosterone(DB06710)|Metronidazole(DB00916)|Metyrapone(DB01011)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Mitoxantrone(DB01204)|Modafinil(DB00745)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nafcillin(DB00607)|Naloxone(DB01183)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nitric Oxide(DB00435)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Omeprazole(DB00338)|Ondansetron(DB00904)|Orlistat(DB01083)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paramethasone(DB01384)|Paricalcitol(DB00910)|Pazopanib(DB06589)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perampanel(DB08883)|Pergolide(DB01186)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenoxybenzamine(DB00925)|Phenprocoumon(DB00946)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pilocarpine(DB01085)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Prazepam(DB01588)|Praziquantel(DB01058)|Prednisolone(DB00860)|Prednisone(DB00635)|Primaquine(DB01087)|Primidone(DB00794)|Probenecid(DB01032)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Pyridostigmine(DB00545)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Quinupristin(DB01369)|Rabeprazole(DB01129)|Raloxifene(DB00481)|Ramelteon(DB00980)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Regorafenib(DB08896)|Repaglinide(DB00912)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rifapentine(DB01201)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Rimonabant(DB06155)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rivastigmine(DB00989)|Rolitetracycline(DB01301)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosuvastatin(DB01098)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Rufinamide(DB06201)|Ruxolitinib(DB08877)|Salbutamol(DB01001)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sevoflurane(DB01236)|Sibutramine(DB01105)|Sildenafil(DB00203)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Sitaxentan(DB06268)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sufentanil(DB00708)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfanilamide(DB00259)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tasosartan(DB01349)|Telaprevir(DB05521)|Telithromycin(DB00976)|Temazepam(DB00231)|Temozolomide(DB00853)|Temsirolimus(DB06287)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Thiopental(DB00599)|Thiotepa(DB04572)|Tiagabine(DB00906)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tioconazole(DB01007)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tofisopam(DB08811)|Tolterodine(DB01036)|Tolvaptan(DB06212)|Topiramate(DB00273)|Topotecan(DB01030)|Toremifene(DB00539)|Trabectedin(DB05109)|Tramadol(DB00193)|Trametinib(DB08911)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Tretinoin(DB00755)|Triamcinolone(DB00620)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vandetanib(DB05294)|Vardenafil(DB00862)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Zidovudine(DB00495)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)|Zopiclone(DB01198)	GATAGAGGAGCACCAGGCTGA	0.493																																																0			7						C	,	2,4404	4.2+/-10.8	0,2,2201	150	131	138		60,60	0.6	1	7		138	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CYP3A4	NM_001202855.2,NM_017460.5	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	20/503,20/504	99381645	2,13004	2203	4300	6503	99219581	SO:0001819	synonymous_variant	1576			AF280107	CCDS5674.1	7q21.1	2011-06-21	2003-01-14		ENSG00000160868	ENSG00000160868	1.1.1.161	"Cytochrome P450s"	2637	protein-coding gene	gene with protein product		124010	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4"	CYP3A3		8269949, 1391968	Standard	NM_001202855		Approved		uc003urv.2	P08684	OTTHUMG00000156651	ENST00000336411.2:c.60G>A	7.37:g.99381645C>T			99219581	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																				0.493	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1			T	99381645	C	T	99381645	2	4	121	1	0	0	0	0	0	0	0	1	4184	697	25	3		3	CYP3A4	7	99381645	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	11599061	99381645	59757018	118	31888										
ZNF3	7589	hgsc.bcm.edu	37	chr7	99662465	99662465	+	3'UTR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcactggagcagagtcccttCgccacacttagggtcccagt	10	14	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:99662465C>T	ENST00000292450.4	+	0	1811				ZSCAN21_ENST00000456748.2_3'UTR|ZSCAN21_ENST00000543588.1_3'UTR|ZNF3_ENST00000413658.2_Silent_p.A114A	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)			AGAGTCCCTTCGCCACACTTA	0.512																																																0			7											136	144	141					7																	99662465		2118	4233	6351	99500401	SO:0001624	3_prime_UTR_variant	7551			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.*225C>T	7.37:g.99662465C>T			99500401	A4D2A6|D6W5T9|Q9H0B5	Silent	SNP	ENST00000292450.4	37	CCDS5681.1																																																																																				0.512	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		T	99662465	C	T	99662465	1	4	121	0	1	0	0	0	0	0	0	0	17868	871	31	1		1	ZNF3	7	99662465	3'UTR	SNP	C	TCGA-G5-6235-01A-11D-1733-10	280820	99662465	59476198	119	31889										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107689918	107689918	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atggtggaactagtttcattAattttcttttcagcagatga	8	5	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:107689918A>C	ENST00000388781.3	-	27	4058	c.3975T>G	c.(3973-3975)atT>atG	p.I1325M	LAMB4_ENST00000205386.4_Missense_Mutation_p.I1325M|LAMB4_ENST00000388780.3_Missense_Mutation_p.I1325M	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1325	Domain II.				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						TAGTTTCATTAATTTTCTTTT	0.318																																																0			7											171	150	157					7																	107689918		2201	4299	6500	107477154	SO:0001583	missense	22798			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.3975T>G	7.37:g.107689918A>C	ENSP00000373433:p.Ile1325Met		107477154	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	A	7.842	0.722185	0.15372	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.32753	1.44;1.44;1.84;1.46	4.97	-0.585	0.11698	.	1.177410	0.06265	N	0.694547	T	0.18425	0.0442	N	0.19112	0.55	0.09310	N	1	P;P	0.48089	0.905;0.761	B;B	0.43575	0.424;0.275	T	0.09015	-1.0694	10	0.51188	T	0.08	.	0.5668	0.00688	0.332:0.1158:0.188:0.3643	.	1325;1325	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	M	1325;1325;351;1325	ENSP00000205386:I1325M;ENSP00000373433:I1325M;ENSP00000416562:I351M;ENSP00000373432:I1325M	ENSP00000205386:I1325M	I	-	3	3	LAMB4	107477154	0.000000	0.05858	0.000000	0.03702	0.590000	0.36582	-0.681000	0.05191	-0.238000	0.09724	-0.256000	0.11100	ATT		0.318	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		C	107689918	A	C	107689918	3	2	121	1	0	0	0	0	1	0	0	0	8635	358	13	4	1342	4	LAMB4	7	107689918	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	8027453	107689918	51448745	120	31890										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107704331	107704331	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggctgcaggactctggatcgGttacatctatgttgttgttg	13	7	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:107704331G>T	ENST00000388781.3	-	22	3019	c.2936C>A	c.(2935-2937)aCc>aAc	p.T979N	LAMB4_ENST00000205386.4_Missense_Mutation_p.T979N|LAMB4_ENST00000388780.3_Missense_Mutation_p.T979N	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	979	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						CTCTGGATCGGTTACATCTAT	0.507																																																0			7											174	162	166					7																	107704331		2203	4300	6503	107491567	SO:0001583	missense	22798			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.2936C>A	7.37:g.107704331G>T	ENSP00000373433:p.Thr979Asn		107491567	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978930	0.53827	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.62788	0.17;0.17;-0.0;0.17	5.11	3.3	0.37823	EGF-like, laminin (3);	0.408199	0.20762	N	0.086148	T	0.44540	0.1298	N	0.21373	0.66	0.09310	N	0.999999	B	0.26935	0.164	B	0.31442	0.13	T	0.28138	-1.0053	10	0.28530	T	0.3	.	6.2931	0.21071	0.0724:0.1331:0.6564:0.138	.	979	A4D0S4	LAMB4_HUMAN	N	979;979;5;979	ENSP00000205386:T979N;ENSP00000373433:T979N;ENSP00000416562:T5N;ENSP00000373432:T979N	ENSP00000205386:T979N	T	-	2	0	LAMB4	107491567	0.000000	0.05858	0.004000	0.12327	0.940000	0.58332	0.536000	0.23129	0.735000	0.32537	0.563000	0.77884	ACC		0.507	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		T	107704331	G	T	107704331	3	4	121	1	0	0	0	0	1	0	0	0	8635	1261	44	2	2401	2	LAMB4	7	107704331	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	14413	107704331	51434332	121	31891										
MET	4233	hgsc.bcm.edu	37	chr7	116417499	116417499	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acaatgatggcaagaaaattCactgtgctgtgaaatccttg	9	7	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:116417499C>T	ENST00000318493.6	+	16	3557	c.3370C>T	c.(3370-3372)Cac>Tac	p.H1124Y	MET_ENST00000539704.1_5'UTR|MET_ENST00000397752.3_Missense_Mutation_p.H1106Y			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					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)	p.H1124D(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CAAGAAAATTCACTGTGCTGT	0.348			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																														Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	1	Substitution - Missense(1)	kidney(1)	7											200	188	191					7																	116417499		1841	4082	5923	116204735	SO:0001583	missense	8731	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3370C>T	7.37:g.116417499C>T	ENSP00000317272:p.His1124Tyr		116204735	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.120766	0.77436	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	D;D	0.82619	-1.63;-1.63	5.29	5.29	0.74685	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	0.86260	0.5890	N	0.21240	0.645	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.80764	0.979;0.994	D	0.88223	0.2898	10	0.87932	D	0	-15.6536	19.2953	0.94119	0.0:1.0:0.0:0.0	.	1124;1106	P08581-2;P08581	.;MET_HUMAN	Y	1106;1124	ENSP00000380860:H1106Y;ENSP00000317272:H1124Y	ENSP00000317272:H1124Y	H	+	1	0	MET	116204735	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.959000	0.70339	2.628000	0.89032	0.655000	0.94253	CAC		0.348	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116417499	C	T	116417499	3	4	121	1	0	0	0	0	1	0	0	0	9515	826	29	3	3428	3	MET	7	116417499	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	8713168	116417499	42721164	122	31892										
LRGUK	136332	hgsc.bcm.edu	37	chr7	133948672	133948672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctcggtcccagtcatcagtcGcccaggttccaacgtcaaac	8	16	3	0	rs138421011	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:133948672G>A	ENST00000285928.2	+	20	2492	c.2423G>A	c.(2422-2424)cGc>cAc	p.R808H		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	808						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						GTCATCAGTCGCCCAGGTTCC	0.468																																																0			7											160	120	134					7																	133948672		2203	4300	6503	133599212	SO:0001583	missense	136332			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.2423G>A	7.37:g.133948672G>A	ENSP00000285928:p.Arg808His		133599212	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	G	9.996	1.232280	0.22626	.	.	ENSG00000155530	ENST00000285928	T	0.37058	1.22	5.12	-5.66	0.02451	.	1.338460	0.05238	N	0.511617	T	0.15609	0.0376	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.17592	-1.0364	10	0.27785	T	0.31	5.3275	5.351	0.16036	0.5142:0.0:0.2567:0.2291	.	808	Q96M69	LRGUK_HUMAN	H	808	ENSP00000285928:R808H	ENSP00000285928:R808H	R	+	2	0	LRGUK	133599212	0.000000	0.05858	0.000000	0.03702	0.151000	0.21798	-1.215000	0.02985	-1.361000	0.02169	-0.137000	0.14449	CGC		0.468	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		A	133948672	G	A	133948672	3	1	121	1	0	0	0	0	1	0	0	0	8972	1087	38	1	2501	1	LRGUK	7	133948672	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	17531173	133948672	25189991	123	31893										
OR2A5	393046	hgsc.bcm.edu	37	chr7	143747768	143747768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gcttgaacaagagaaaaacaAtctcctttgtcccatgcaca	6	11	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:143747768A>G	ENST00000408906.2	+	1	308	c.274A>G	c.(274-276)Atc>Gtc	p.I92V		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	92						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)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					GAGAAAAACAATCTCCTTTGT	0.433																																																0			7											136	136	136					7																	143747768		2156	4276	6432	143378701	SO:0001583	missense	393046			U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.274A>G	7.37:g.143747768A>G	ENSP00000386208:p.Ile92Val		143378701	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	A	6.722	0.501942	0.12822	.	.	ENSG00000221836	ENST00000408906	T	0.00469	7.21	5.37	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00815	0.0027	M	0.80422	2.495	0.27823	N	0.941739	B	0.16603	0.018	B	0.33339	0.162	T	0.18461	-1.0336	9	0.72032	D	0.01	.	11.7778	0.51995	0.9232:0.0:0.0768:0.0	.	92	Q96R48	OR2A5_HUMAN	V	92	ENSP00000386208:I92V	ENSP00000386208:I92V	I	+	1	0	OR2A5	143378701	0.972000	0.33761	0.281000	0.24762	0.195000	0.23768	2.564000	0.45931	0.481000	0.27557	-1.162000	0.01777	ATC		0.433	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			G	143747768	A	G	143747768	3	3	121	1	0	0	0	0	1	0	0	0	11012	101	4	4	276	4	OR2A5	7	143747768	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	9799096	143747768	15390895	124	31894			2	42		3	3	446	N	T_C_A	7.385178e-06
OR2A5	393046	hgsc.bcm.edu	37	chr7	143748026	143748026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cccatgaaatcaaccacttcTtctgtgaaatcctgtctgtc	5	13	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:143748026T>C	ENST00000408906.2	+	1	566	c.532T>C	c.(532-534)Ttc>Ctc	p.F178L		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	178						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)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CAACCACTTCTTCTGTGAAAT	0.557																																																0			7											185	188	187					7																	143748026		2036	4209	6245	143378959	SO:0001583	missense	393046			U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.532T>C	7.37:g.143748026T>C	ENSP00000386208:p.Phe178Leu		143378959	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.125402	0.77436	.	.	ENSG00000221836	ENST00000408906	T	0.00220	8.52	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33438	U	0.004917	T	0.00328	0.0010	M	0.71581	2.175	0.33693	D	0.613515	P	0.40180	0.705	P	0.46975	0.533	T	0.69022	-0.5255	10	0.42905	T	0.14	.	13.1424	0.59442	0.0:0.0:0.0:1.0	.	178	Q96R48	OR2A5_HUMAN	L	178	ENSP00000386208:F178L	ENSP00000386208:F178L	F	+	1	0	OR2A5	143378959	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.795000	0.55499	2.202000	0.70862	0.455000	0.32223	TTC		0.557	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			C	143748026	T	C	143748026	3	2	121	1	0	0	0	0	1	0	0	0	11012	1609	56	4	534	4	OR2A5	7	143748026	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	258	143748026	15390637	125	31895			2	42		3	3	446	N	T_C_A	7.385178e-06
OR2A5	393046	hgsc.bcm.edu	37	chr7	143748213	143748213	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccgcagaaaggccttctccaCctgctcctcccacctttgca	6	19	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr7:143748213C>A	ENST00000408906.2	+	1	753	c.719C>A	c.(718-720)aCc>aAc	p.T240N		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	240						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)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					GCCTTCTCCACCTGCTCCTCC	0.632																																																0			7											98	99	99					7																	143748213		2034	4197	6231	143379146	SO:0001583	missense	393046			U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.719C>A	7.37:g.143748213C>A	ENSP00000386208:p.Thr240Asn		143379146	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692803	0.88735	.	.	ENSG00000221836	ENST00000408906	T	0.40476	1.03	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32868	U	0.005552	T	0.68081	0.2962	M	0.93462	3.42	0.49130	D	0.999754	P	0.49961	0.93	P	0.53988	0.739	T	0.77048	-0.2732	10	0.87932	D	0	.	16.6572	0.85231	0.0:1.0:0.0:0.0	.	240	Q96R48	OR2A5_HUMAN	N	240	ENSP00000386208:T240N	ENSP00000386208:T240N	T	+	2	0	OR2A5	143379146	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.522000	0.60539	2.797000	0.96272	0.650000	0.86243	ACC		0.632	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			A	143748213	C	A	143748213	3	1	121	1	0	0	0	0	1	0	0	0	11012	507	18	2	721	2	OR2A5	7	143748213	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	187	143748213	15390450	126	31896			2	42		3	3	446	N	T_C_A	7.385178e-06
PRKDC	5591	hgsc.bcm.edu	37	chr8	48794060	48794060	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaatgaaccatgacttgtatTaaaagatacagatgaatcaa	7	5	1	5			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:48794060T>A	ENST00000314191.2	-	39	5037	c.4981A>T	c.(4981-4983)Aat>Tat	p.N1661Y	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Missense_Mutation_p.N1661Y	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	1662					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)	p.N1662H(1)		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)	TGACTTGTATTAAAAGATACA	0.313								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)											1	Substitution - Missense(1)	ovary(1)	8											44	43	43					8																	48794060		1818	4062	5880	48956613	SO:0001583	missense	5591				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		ENST00000314191.2:c.4981A>T	8.37:g.48794060T>A	ENSP00000313420:p.Asn1661Tyr		48956613	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	T	15.89	2.966372	0.53507	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.65364	-0.15;-0.15	5.43	4.28	0.50868	Armadillo-like helical (1);Armadillo-type fold (1);	0.244417	0.40640	N	0.001041	T	0.65637	0.2710	M	0.65975	2.015	0.37673	D	0.923212	D;D	0.55385	0.971;0.971	P;P	0.50617	0.646;0.646	T	0.70927	-0.4739	10	0.72032	D	0.01	.	7.929	0.29891	0.0:0.1605:0.0:0.8395	.	1661;1662	E7EUY0;P78527	.;PRKDC_HUMAN	Y	1661	ENSP00000313420:N1661Y;ENSP00000345182:N1661Y	ENSP00000313420:N1661Y	N	-	1	0	PRKDC	48956613	1.000000	0.71417	0.787000	0.31911	0.598000	0.36846	2.036000	0.41165	0.914000	0.36822	0.523000	0.50628	AAT		0.313	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		A	48794060	T	A	48794060	3	1	121	1	0	0	0	0	1	0	0	0	12555	1754	61	5	7598	5	PRKDC	8	48794060	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10		48794060	97569962	127	31897										
UBXN2B	137886	hgsc.bcm.edu	37	chr8	59358550	59358550	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gcagttgttcttattgatgaTtcagtgccaacaacaaaaat	7	7	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:59358550T>C	ENST00000399598.2	+	7	878	c.756T>C	c.(754-756)gaT>gaC	p.D252D		NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	252	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						TTATTGATGATTCAGTGCCAA	0.368																																																0			8											141	123	129					8																	59358550		1859	4091	5950	59521104	SO:0001819	synonymous_variant	137886			AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"UBX domain containing"	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.756T>C	8.37:g.59358550T>C			59521104	B3KWZ3	Silent	SNP	ENST00000399598.2	37	CCDS43741.1																																																																																				0.368	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619		C	59358550	T	C	59358550	2	2	121	1	0	0	0	0	0	0	0	1	16955	1490	52	4		4	UBXN2B	8	59358550	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	10564490	59358550	87005472	128	31898										
TOX	9760	hgsc.bcm.edu	37	chr8	59750765	59750765	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acgaaagaataacgcataggCagacacaggcttctggggct	12	9	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:59750765C>T	ENST00000361421.1	-	5	1019	c.799G>A	c.(799-801)Gcc>Acc	p.A267T		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	267			A -> T (found in a renal cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:21248752}.			nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A267T(2)		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)				AACGCATAGGCAGACACAGGC	0.483																																					Pancreas(161;610 1969 17913 21374 22725)											2	Substitution - Missense(2)	kidney(2)	8											111	111	111					8																	59750765		2203	4300	6503	59913319	SO:0001583	missense	9760				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.799G>A	8.37:g.59750765C>T	ENSP00000354842:p.Ala267Thr		59913319	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	35	5.589510	0.96590	.	.	ENSG00000198846	ENST00000361421;ENST00000456290	T	0.59772	0.24	5.59	5.59	0.84812	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.82701	0.5094	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86232	0.1638	9	.	.	.	.	19.5961	0.95538	0.0:1.0:0.0:0.0	.	267	O94900	TOX_HUMAN	T	267;25	ENSP00000354842:A267T	.	A	-	1	0	TOX	59913319	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.621000	0.88768	0.591000	0.81541	GCC		0.483	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59750765	C	T	59750765	3	4	121	1	0	0	0	0	1	0	0	0	16417	710	25	3	801	3	TOX	8	59750765	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	392215	59750765	86613257	129	31899										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848938	73848938	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccaaaaggaacggaagcatcGtttctatgaacttaaaagat	8	7	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:73848938G>A	ENST00000523207.1	+	3	1936	c.1348G>A	c.(1348-1350)Gtt>Att	p.V450I		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	450			V -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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.V450I(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)	CGGAAGCATCGTTTCTATGAA	0.473																																																1	Substitution - Missense(1)	large_intestine(1)	8											76	81	79					8																	73848938		2203	4300	6503	74011492	SO:0001583	missense	9312			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.1348G>A	8.37:g.73848938G>A	ENSP00000430846:p.Val450Ile		74011492	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.296133	0.81025	.	.	ENSG00000182674	ENST00000523207	D	0.97279	-4.32	5.74	5.74	0.90152	.	0.178810	0.26620	N	0.023364	D	0.97798	0.9277	M	0.72894	2.215	0.80722	D	1	D	0.57571	0.98	P	0.55391	0.775	D	0.97927	1.0318	10	0.56958	D	0.05	.	19.91	0.97023	0.0:0.0:1.0:0.0	.	450	Q92953	KCNB2_HUMAN	I	450	ENSP00000430846:V450I	ENSP00000430846:V450I	V	+	1	0	KCNB2	74011492	1.000000	0.71417	0.931000	0.37212	0.913000	0.54294	8.022000	0.88759	2.702000	0.92279	0.655000	0.94253	GTT		0.473	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73848938	G	A	73848938	3	1	121	1	0	0	0	0	1	0	0	0	8034	1145	40	1	1354	1	KCNB2	8	73848938	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	14098173	73848938	72515084	130	31900										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125015536	125015536	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggcccatgatgttcccattcCtatggcctccaccactcacc	6	18	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:125015536C>G	ENST00000522917.1	+	13	1855	c.1649C>G	c.(1648-1650)cCt>cGt	p.P550R	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.P550R	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	550						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)			GTTCCCATTCCTATGGCCTCC	0.527																																																0			8											55	55	55					8																	125015536		1957	4151	6108	125084717	SO:0001583	missense	654463			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.1649C>G	8.37:g.125015536C>G	ENSP00000428280:p.Pro550Arg		125084717		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923411	0.33908	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.82167	-1.58;-1.58	5.46	5.46	0.80206	.	1.065020	0.07395	U	0.889854	D	0.82701	0.5094	L	0.53249	1.67	0.22639	N	0.998906	P	0.39717	0.684	B	0.35727	0.209	T	0.74783	-0.3548	10	0.42905	T	0.14	.	18.9144	0.92499	0.0:1.0:0.0:0.0	.	550	Q2WGJ9	FR1L6_HUMAN	R	550	ENSP00000428280:P550R;ENSP00000381982:P550R	ENSP00000381982:P550R	P	+	2	0	FER1L6	125084717	0.149000	0.22717	0.032000	0.17829	0.459000	0.32528	4.895000	0.63214	2.559000	0.86315	0.655000	0.94253	CCT		0.527	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	125015536	C	G	125015536	3	3	121	1	0	0	0	0	1	0	0	0	5834	681	24	5	1695	5	FER1L6	8	125015536	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	51166598	125015536	21348486	131	31901										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139164971	139164971	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cctgtctaatccatacttatCtctagagctcctactctcat	3	14	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:139164971C>A	ENST00000395297.1	-	13	1917	c.1747G>T	c.(1747-1749)Gat>Tat	p.D583Y		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	583										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)			CCATACTTATCTCTAGAGCTC	0.458										HNSCC(54;0.14)																																						0			8											153	145	148					8																	139164971		1900	4119	6019	139234153	SO:0001583	missense	51059			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.1747G>T	8.37:g.139164971C>A	ENSP00000378710:p.Asp583Tyr		139234153	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	14.62	2.590648	0.46214	.	.	ENSG00000147724	ENST00000395297	T	0.16897	2.31	5.45	3.61	0.41365	.	1.013200	0.07872	N	0.968042	T	0.23727	0.0574	L	0.44542	1.39	0.09310	N	1	D;P;P	0.53462	0.96;0.919;0.779	P;P;B	0.51550	0.673;0.525;0.177	T	0.14727	-1.0462	10	0.62326	D	0.03	-1.7504	7.0725	0.25187	0.0:0.6997:0.1672:0.1331	.	583;583;583	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	Y	583	ENSP00000378710:D583Y	ENSP00000276737:D583Y	D	-	1	0	FAM135B	139234153	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	0.393000	0.20817	1.423000	0.47198	-0.176000	0.13171	GAT		0.458	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		A	139164971	C	A	139164971	3	1	121	1	0	0	0	0	1	0	0	0	5465	913	32	2	2505	2	FAM135B	8	139164971	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	14149435	139164971	7199051	132	31902										
EEF1D	1936	hgsc.bcm.edu	37	chr8	144663283	144663283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttctccagcacgttcagccGggcctccagcttggagatgg	12	14	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr8:144663283G>A	ENST00000529272.1	-	5	731	c.331C>T	c.(331-333)Cgg>Tgg	p.R111W	NAPRT1_ENST00000449291.2_5'Flank|EEF1D_ENST00000423316.2_Missense_Mutation_p.R477W|EEF1D_ENST00000419152.2_Missense_Mutation_p.R111W|EEF1D_ENST00000532741.1_Missense_Mutation_p.R527W|EEF1D_ENST00000442189.2_Missense_Mutation_p.R477W|EEF1D_ENST00000528610.1_Missense_Mutation_p.R87W|EEF1D_ENST00000531621.1_Missense_Mutation_p.R68W|EEF1D_ENST00000395119.3_Missense_Mutation_p.R111W|EEF1D_ENST00000526838.1_Missense_Mutation_p.R92W|NAPRT1_ENST00000276844.7_5'Flank|EEF1D_ENST00000532400.1_Intron|NAPRT1_ENST00000435154.3_5'Flank|NAPRT1_ENST00000426292.3_5'Flank|RP11-661A12.7_ENST00000529247.1_RNA|EEF1D_ENST00000317198.6_Missense_Mutation_p.R111W|EEF1D_ENST00000524624.1_Missense_Mutation_p.R87W			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	111	Leucine-zipper.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	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)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			ACGTTCAGCCGGGCCTCCAGC	0.677																																																0			8											42	43	43					8																	144663283		2203	4298	6501	144734426	SO:0001583	missense	1936			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.331C>T	8.37:g.144663283G>A	ENSP00000434872:p.Arg111Trp		144734426	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512686	0.85389	.	.	ENSG00000104529	ENST00000419152;ENST00000532741;ENST00000526838;ENST00000442189;ENST00000528610;ENST00000395119;ENST00000529272;ENST00000423316;ENST00000356793;ENST00000317198;ENST00000337369;ENST00000531621;ENST00000524624;ENST00000534380;ENST00000534377;ENST00000533204;ENST00000530191;ENST00000531218;ENST00000533494;ENST00000530445;ENST00000529516;ENST00000533749	.	.	.	4.8	2.78	0.32641	.	0.000000	0.85682	D	0.000000	T	0.79311	0.4424	M	0.87827	2.91	0.80722	D	1	P;D;D;B;D;D	0.89917	0.877;1.0;0.999;0.203;1.0;1.0	B;D;P;B;D;D	0.97110	0.232;0.997;0.908;0.022;1.0;0.999	T	0.81988	-0.0680	9	0.87932	D	0	.	10.9683	0.47424	0.0:0.0:0.6466:0.3533	.	92;477;405;111;527;477	E9PBQ9;D3DWK1;F8W934;P29692;E9PRY8;P29692-2	.;.;.;EF1D_HUMAN;.;.	W	111;527;92;477;87;111;111;477;405;111;477;68;87;111;87;111;111;111;111;111;92;127	.	ENSP00000317399:R111W	R	-	1	2	EEF1D	144734426	0.987000	0.35691	1.000000	0.80357	0.926000	0.56050	1.877000	0.39598	1.110000	0.41699	0.455000	0.32223	CGG		0.677	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		A	144663283	G	A	144663283	3	1	121	1	0	0	0	0	1	0	0	0	4937	1115	39	1	530	1	EEF1D	8	144663283	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	5498312	144663283	1700739	133	31903										
DMRT3	58524	hgsc.bcm.edu	37	chr9	990868	990868	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gctcgcccgtccttcctgccCgcgccacggaagaccctcgg	11	20	0	1	rs141821476	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:990868C>A	ENST00000190165.2	+	2	1320	c.1282C>A	c.(1282-1284)Cgc>Agc	p.R428S		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	428					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)	p.R428C(2)		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)		CCTTCCTGCCCGCGCCACGGA	0.552																																																2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	9											85	72	76					9																	990868		2203	4300	6503	980868	SO:0001583	missense	58524			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.1282C>A	9.37:g.990868C>A	ENSP00000190165:p.Arg428Ser		980868	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.581684	0.46006	.	.	ENSG00000064218	ENST00000190165	T	0.38887	1.11	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.52805	0.1757	L	0.32530	0.975	0.54753	D	0.999987	D	0.89917	1.0	D	0.81914	0.995	T	0.54774	-0.8243	10	0.66056	D	0.02	-34.3542	13.7296	0.62779	0.1538:0.8462:0.0:0.0	.	428	Q9NQL9	DMRT3_HUMAN	S	428	ENSP00000190165:R428S	ENSP00000190165:R428S	R	+	1	0	DMRT3	980868	0.998000	0.40836	0.096000	0.21009	0.357000	0.29423	4.120000	0.57897	2.424000	0.82194	0.655000	0.94253	CGC		0.552	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		A	990868	C	A	990868	3	1	121	1	0	0	0	0	1	0	0	0	4598	652	23	2	1288	2	DMRT3	9	990868	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10		990868	140222563	134	31904										
IFNA4	3441	hgsc.bcm.edu	37	chr9	21187176	21187176	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctgtatcacacatgcttccaGgtcattcagttgctggtaaa	8	10	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:21187176G>T	ENST00000421715.1	-	1	422	c.355C>A	c.(355-357)Ctg>Atg	p.L119M		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	119					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)	p.L119L(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CATGCTTCCAGGTCATTCAGT	0.478																																					NSCLC(154;890 1986 23660 27800 51138)											1	Substitution - coding silent(1)	ovary(1)	9											27	29	29					9																	21187176		2163	4261	6424	21177176	SO:0001583	missense	3441				CCDS6498.1	9p22	2010-08-24			ENSG00000236637	ENSG00000236637		"Interferons"	5425	protein-coding gene	gene with protein product		147564				1385305	Standard	NM_021068		Approved	MGC142200, IFN-alpha4a	uc003zon.2	P05014	OTTHUMG00000019660	ENST00000421715.1:c.355C>A	9.37:g.21187176G>T	ENSP00000412897:p.Leu119Met		21177176	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	37	CCDS6498.1	.	.	.	.	.	.	.	.	.	.	N	11.65	1.703278	0.30232	.	.	ENSG00000236637	ENST00000421715	T	0.13657	2.57	2.96	2.05	0.26809	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.177446	0.37219	N	0.002186	T	0.44435	0.1293	H	0.96489	3.83	0.09310	N	1	D	0.76494	0.999	D	0.72338	0.977	T	0.37619	-0.9698	10	0.87932	D	0	.	7.6581	0.28388	0.1299:0.0:0.8701:0.0	.	119	P05014	IFNA4_HUMAN	M	119	ENSP00000412897:L119M	ENSP00000412897:L119M	L	-	1	2	IFNA4	21177176	0.002000	0.14202	0.013000	0.15412	0.036000	0.12997	0.281000	0.18810	0.571000	0.29365	-0.443000	0.05667	CTG		0.478	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068		T	21187176	G	T	21187176	3	4	121	1	0	0	0	0	1	0	0	0	7560	991	35	2	218	2	IFNA4	9	21187176	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	20196308	21187176	120026255	135	31905										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543970	32543970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agaagcatttcgttcccttgTcagagttgtacggtagcgaa	11	8	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:32543970T>C	ENST00000360538.2	-	3	669	c.553A>G	c.(553-555)Aca>Gca	p.T185A	TOPORS_ENST00000379858.1_Missense_Mutation_p.T120A	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	185	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)		CGTTCCCTTGTCAGAGTTGTA	0.463																																																0			9											135	116	122					9																	32543970		2203	4300	6503	32533970	SO:0001583	missense	10210			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.553A>G	9.37:g.32543970T>C	ENSP00000353735:p.Thr185Ala		32533970	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.316678	0.40996	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.18657	2.2;2.21	5.21	5.21	0.72293	.	0.000000	0.47455	D	0.000234	T	0.31638	0.0803	L	0.55481	1.735	0.39957	D	0.974616	D	0.58620	0.983	P	0.51016	0.656	T	0.11084	-1.0602	10	0.62326	D	0.03	-15.1247	14.3756	0.66874	0.0:0.0:0.0:1.0	.	185	Q9NS56	TOPRS_HUMAN	A	185;120	ENSP00000353735:T185A;ENSP00000369187:T120A	ENSP00000353735:T185A	T	-	1	0	TOPORS	32533970	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	7.610000	0.82949	2.092000	0.63282	0.460000	0.39030	ACA		0.463	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32543970	T	C	32543970	3	2	121	1	0	0	0	0	1	0	0	0	16410	1667	58	4	2588	4	TOPORS	9	32543970	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	11356794	32543970	108669461	136	31906										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74305087	74305087	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaccgttttttccgtcaagcGgaatggaacgctgcacggat	11	10	1	0	rs374049571		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:74305087G>A	ENST00000377044.4	-	22	4311	c.3772C>T	c.(3772-3774)Cgc>Tgc	p.R1258C	TMEM2_ENST00000377066.5_Missense_Mutation_p.R1195C|TMEM2_ENST00000396272.3_Missense_Mutation_p.R251C	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1258					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)		TCCGTCAAGCGGAATGGAACG	0.478																																																0			9						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	139	118	125		3583,3772	6	1	9		125	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TMEM2	NM_001135820.1,NM_013390.2	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	1195/1321,1258/1384	74305087	1,13005	2203	4300	6503	73494907	SO:0001583	missense	23670				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.3772C>T	9.37:g.74305087G>A	ENSP00000366243:p.Arg1258Cys		73494907	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.473965	0.63737	0.0	1.16E-4	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272	T;T;T	0.74002	-0.8;-0.74;2.43	5.98	5.98	0.97165	.	0.164580	0.53938	D	0.000048	T	0.67353	0.2884	L	0.44542	1.39	0.52501	D	0.99995	B;B	0.26002	0.086;0.139	B;B	0.20184	0.012;0.028	T	0.66081	-0.6012	10	0.87932	D	0	.	13.1544	0.59509	0.0:0.0:0.8014:0.1986	.	1258;1195	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	C	1258;1195;251	ENSP00000366243:R1258C;ENSP00000366266:R1195C;ENSP00000379569:R251C	ENSP00000366243:R1258C	R	-	1	0	TMEM2	73494907	0.995000	0.38212	1.000000	0.80357	0.440000	0.31957	2.314000	0.43743	2.835000	0.97688	0.650000	0.86243	CGC		0.478	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		A	74305087	G	A	74305087	3	1	121	1	0	0	0	0	1	0	0	0	16160	1116	39	1	391	1	TMEM2	9	74305087	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	41761117	74305087	66908344	137	31907										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77457189	77457189	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccattgttcactttctttacCcttggcagctgagatggtcc	8	12	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:77457189C>A	ENST00000360774.1	-	4	460	c.223G>T	c.(223-225)Ggt>Tgt	p.G75C	TRPM6_ENST00000451710.3_Missense_Mutation_p.G75C|TRPM6_ENST00000376871.3_Missense_Mutation_p.G75C|TRPM6_ENST00000376864.4_Missense_Mutation_p.G75C|TRPM6_ENST00000359047.2_Missense_Mutation_p.G75C|TRPM6_ENST00000376872.3_Missense_Mutation_p.G75C|TRPM6_ENST00000361255.3_Missense_Mutation_p.G70C|TRPM6_ENST00000449912.2_Missense_Mutation_p.G70C	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	75			G -> V (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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						CTTTCTTTACCCTTGGCAGCT	0.428																																																0			9											195	184	188					9																	77457189		2203	4300	6503	76647009	SO:0001583	missense	140803			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.223G>T	9.37:g.77457189C>A	ENSP00000354006:p.Gly75Cys		76647009	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429196	0.43122	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17	5.44	1.19	0.21007	.	1.205580	0.05608	N	0.577620	T	0.65533	0.2700	M	0.64404	1.975	0.09310	N	1	P;P;P;P;D;P	0.55172	0.82;0.82;0.82;0.939;0.97;0.518	B;B;B;P;P;P	0.54460	0.416;0.298;0.416;0.753;0.447;0.649	T	0.49476	-0.8936	10	0.59425	D	0.04	.	6.4974	0.22150	0.0:0.5603:0.127:0.3127	.	75;75;75;75;75;70	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	C	75;75;75;75;70;70;74;75;75	ENSP00000354006:G75C;ENSP00000407341:G75C;ENSP00000366068:G75C;ENSP00000366067:G75C;ENSP00000396672:G70C;ENSP00000354962:G70C;ENSP00000366060:G75C;ENSP00000351942:G75C	ENSP00000351942:G75C	G	-	1	0	TRPM6	76647009	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.528000	0.23002	-0.048000	0.13401	-0.390000	0.06520	GGT		0.428	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77457189	C	A	77457189	3	1	121	1	0	0	0	0	1	0	0	0	16630	623	22	2	5989	2	TRPM6	9	77457189	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3152102	77457189	63756242	138	31908										
CENPP	401541	hgsc.bcm.edu	37	chr9	95094529	95094529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tctgaaaaatcagcttggacAtttagaatcagaactttcat	6	7	4	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:95094529A>G	ENST00000375587.3	+	2	700	c.185A>G	c.(184-186)cAt>cGt	p.H62R		NM_001012267.1	NP_001012267.1	Q6IPU0	CENPP_HUMAN	centromere protein P	62					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(1)	16						CAGCTTGGACATTTAGAATCA	0.343																																																0			9											72	69	70					9																	95094529		2203	4300	6503	94134350	SO:0001583	missense	401541			AK091247	CCDS35063.1, CCDS69618.1	9q22.31	2013-11-05			ENSG00000188312	ENSG00000188312			32933	protein-coding gene	gene with protein product		611505				16622419, 16622420	Standard	NM_001286969		Approved	RP11-19J3.3, CENP-P	uc004arz.3	Q6IPU0	OTTHUMG00000020228	ENST00000375587.3:c.185A>G	9.37:g.95094529A>G	ENSP00000364737:p.His62Arg		94134350	B3KRA5|B3KS17|Q5T9F8|Q5T9F9	Missense_Mutation	SNP	ENST00000375587.3	37	CCDS35063.1	.	.	.	.	.	.	.	.	.	.	A	7.029	0.560263	0.13498	.	.	ENSG00000188312	ENST00000375587	.	.	.	5.16	1.5	0.22942	.	0.922896	0.09246	N	0.828575	T	0.45478	0.1344	L	0.42245	1.32	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.18398	-1.0338	9	0.22706	T	0.39	-1.7998	6.739	0.23424	0.6867:0.0:0.3133:0.0	.	62	Q6IPU0	CENPP_HUMAN	R	62	.	ENSP00000364737:H62R	H	+	2	0	CENPP	94134350	0.816000	0.29132	0.989000	0.46669	0.555000	0.35460	0.358000	0.20216	0.144000	0.18951	0.450000	0.29827	CAT		0.343	CENPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053098.1	NM_001012267		G	95094529	A	G	95094529	3	3	121	1	0	0	0	0	1	0	0	0	3246	217	8	4	191	4	CENPP	9	95094529	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	17637340	95094529	46118902	139	31909										
DBC1	1620	hgsc.bcm.edu	37	chr9	121929513	121929513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agtccagctggggtttccccGgggccacaggaggggccagg	18	12	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:121929513G>A	ENST00000265922.3	-	8	2596	c.2135C>T	c.(2134-2136)cCg>cTg	p.P712L	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	712			P -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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.P712L(1)									GGGTTTCCCCGGGGCCACAGG	0.557																																																1	Substitution - Missense(1)	kidney(1)	9											86	94	91					9																	121929513		2203	4300	6503	120969334	SO:0001583	missense	57805			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.2135C>T	9.37:g.121929513G>A	ENSP00000265922:p.Pro712Leu		120969334	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.531209	0.64972	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.19250	2.16	5.64	4.73	0.59995	.	0.100848	0.64402	D	0.000001	T	0.23727	0.0574	M	0.61703	1.905	0.80722	D	1	P	0.35433	0.501	B	0.28011	0.085	T	0.07121	-1.0789	10	0.87932	D	0	-22.0002	16.2315	0.82344	0.0:0.0:0.8659:0.1341	.	712	O60477	DBC1_HUMAN	L	712	ENSP00000265922:P712L	ENSP00000265922:P712L	P	-	2	0	DBC1	120969334	1.000000	0.71417	0.961000	0.40146	0.998000	0.95712	7.234000	0.78134	1.508000	0.48769	0.585000	0.79938	CCG		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		A	121929513	G	A	121929513	3	1	121	1	0	0	0	0	1	0	0	0	4253	1116	39	1	154	1	DBC1	9	121929513	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	26834984	121929513	19283918	140	31910										
C9orf171	389799	hgsc.bcm.edu	37	chr9	135447838	135447838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agagagcattaaaagcccacCgggaagagtgtgccgtgcgc	14	10	0	2	rs370319315		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:135447838C>T	ENST00000343036.2	+	7	952	c.904C>T	c.(904-906)Cgg>Tgg	p.R302W	C9orf171_ENST00000393216.2_Missense_Mutation_p.R266W	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	302										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						AAAAGCCCACCGGGAAGAGTG	0.627																																																0			9						C	TRP/ARG	0,4406		0,0,2203	60	57	58		904	0.8	0	9		58	1,8599	1.2+/-3.3	0,1,4299	no	missense	C9orf171	NM_207417.1	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	302/321	135447838	1,13005	2203	4300	6503	134437659	SO:0001583	missense	389799			AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.904C>T	9.37:g.135447838C>T	ENSP00000343290:p.Arg302Trp		134437659	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	C	11.84	1.757720	0.31137	0.0	1.16E-4	ENSG00000188523	ENST00000343036;ENST00000393216	T;T	0.24151	1.87;1.87	5.53	0.786	0.18590	.	1.178800	0.06184	N	0.680006	T	0.11623	0.0283	N	0.08118	0	0.09310	N	1	P;P	0.48407	0.608;0.91	B;B	0.40101	0.241;0.319	T	0.09751	-1.0660	10	0.38643	T	0.18	.	2.4411	0.04494	0.1567:0.5106:0.1437:0.189	.	266;302	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	W	302;266	ENSP00000343290:R302W;ENSP00000376909:R266W	ENSP00000343290:R302W	R	+	1	2	C9orf171	134437659	0.009000	0.17119	0.017000	0.16124	0.760000	0.43138	0.508000	0.22692	0.238000	0.21222	-0.282000	0.10007	CGG		0.627	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		T	135447838	C	T	135447838	3	4	121	1	0	0	0	0	1	0	0	0	2476	643	23	1	930	1	C9orf171	9	135447838	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	13518325	135447838	5765593	141	31911										
BARHL1	56751	hgsc.bcm.edu	37	chr9	135458566	135458566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagcccctgagcctgggggcCgccttgcggccaaggccgcg	16	17	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr9:135458566C>T	ENST00000263610.2	+	1	995	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	BARHL1_ENST00000542090.1_Missense_Mutation_p.R128C	NM_020064.3	NP_064448.1	Q9BZE3	BARH1_HUMAN	BarH-like homeobox 1	128					midbrain development (GO:0030901)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|sensory perception of sound (GO:0007605)	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(1)|large_intestine(2)|lung(2)|skin(3)	8				OV - Ovarian serous cystadenocarcinoma(145;1.79e-06)|Epithelial(140;3.12e-05)		GCCTGGGGGCCGCCTTGCGGC	0.607																																																0			9											29	38	35					9																	135458566		2182	4274	6456	134448387	SO:0001583	missense	56751			AJ237816	CCDS6950.1	9q34.13	2011-06-20	2007-07-09		ENSG00000125492	ENSG00000125492		"Homeoboxes / ANTP class : NKL subclass"	953	protein-coding gene	gene with protein product		605211	"BarH (Drosophila)-like 1"				Standard	NM_020064		Approved		uc004cbp.1	Q9BZE3	OTTHUMG00000020839	ENST00000263610.2:c.382C>T	9.37:g.135458566C>T	ENSP00000263610:p.Arg128Cys		134448387	Q5T6V2|Q9NY88	Missense_Mutation	SNP	ENST00000263610.2	37	CCDS6950.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.573576	0.28092	.	.	ENSG00000125492	ENST00000263610;ENST00000542090	D;D	0.91237	-2.81;-2.81	4.24	4.24	0.50183	.	0.060098	0.64402	D	0.000007	T	0.75503	0.3858	N	0.03115	-0.41	0.58432	D	0.999999	B	0.13145	0.007	B	0.06405	0.002	T	0.71185	-0.4667	10	0.52906	T	0.07	.	5.2538	0.15537	0.2041:0.6925:0.0:0.1034	.	128	Q9BZE3	BARH1_HUMAN	C	128	ENSP00000263610:R128C;ENSP00000444704:R128C	ENSP00000263610:R128C	R	+	1	0	BARHL1	134448387	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	2.711000	0.47177	2.180000	0.69256	0.643000	0.83706	CGC		0.607	BARHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054789.2			T	135458566	C	T	135458566	3	4	121	1	0	0	0	0	1	0	0	0	1314	652	23	1	384	1	BARHL1	9	135458566	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	10728	135458566	5754865	142	31912										
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24873346	24873346	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggacatacccccagtttaaaGacagggatgaaactctgctt	9	10	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:24873346G>T	ENST00000396432.2	-	26	6358	c.5872C>A	c.(5872-5874)Ctt>Att	p.L1958I		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1957					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)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CCAGTTTAAAGACAGGGATGA	0.408																																																0			10											89	86	87					10																	24873346		2203	4300	6503	24913352	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.5872C>A	10.37:g.24873346G>T	ENSP00000379709:p.Leu1958Ile		24913352	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	G	18.27	3.586058	0.66105	.	.	ENSG00000107863	ENST00000396432;ENST00000447364	T	0.13089	2.62	5.55	4.62	0.57501	.	0.069015	0.64402	D	0.000016	T	0.13713	0.0332	L	0.43923	1.385	0.80722	D	1	P	0.48294	0.908	B	0.37692	0.256	T	0.02059	-1.1221	10	0.87932	D	0	.	16.0791	0.80989	0.0:0.1344:0.8656:0.0	.	1957	Q5T5U3	RHG21_HUMAN	I	1958;1407	ENSP00000379709:L1958I	ENSP00000379709:L1958I	L	-	1	0	ARHGAP21	24913352	1.000000	0.71417	0.939000	0.37840	0.957000	0.61999	4.934000	0.63491	1.264000	0.44198	0.655000	0.94253	CTT		0.408	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		T	24873346	G	T	24873346	3	4	121	1	0	0	0	0	1	0	0	0	871	942	33	2	8	2	ARHGAP21	10	24873346	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10		24873346	110661401	143	31913										
TMEM72	643236	hgsc.bcm.edu	37	chr10	45429195	45429195	+	5'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggtggcctgcttcctccaccCggtcctggtctggcacgtga	13	15	1	1	rs369873974		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:45429195C>T	ENST00000544540.1	+	0	450				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						TTCCTCCACCCGGTCCTGGTC	0.627																																																0			10						C	LEU/PRO	1,3135		0,1,1567	50	52	52		320	5.6	1	10		52	0,7164		0,0,3582	no	missense	TMEM72	NM_001123376.1	98	0,1,5149	TT,TC,CC		0.0,0.0319,0.0097	probably-damaging	107/276	45429195	1,10299	1568	3582	5150	44749201	SO:0001623	5_prime_UTR_variant	643236			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.-35C>T	10.37:g.45429195C>T			44749201	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	37		.	.	.	.	.	.	.	.	.	.	C	23.0	4.359703	0.82353	3.19E-4	0.0	ENSG00000187783	ENST00000389583	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.78886	0.4354	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80513	-0.1349	9	0.87932	D	0	-28.2346	15.4555	0.75311	0.0:1.0:0.0:0.0	.	107	A0PK05	TMM72_HUMAN	L	107	.	ENSP00000374234:P107L	P	+	2	0	TMEM72	44749201	0.999000	0.42202	0.997000	0.53966	0.815000	0.46073	5.357000	0.66058	2.793000	0.96121	0.655000	0.94253	CCG		0.627	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		T	45429195	C	T	45429195	1	4	121	0	1	0	0	0	0	0	0	0	16240	652	23	1		1	TMEM72	10	45429195	5'UTR	SNP	C	TCGA-G5-6235-01A-11D-1733-10	20555849	45429195	90105552	144	31914										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50678894	50678894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaaggctggttgaatccttcTttttagatggcatttgggtg	12	5	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:50678894T>C	ENST00000355832.5	-	18	3190	c.3112A>G	c.(3112-3114)Aga>Gga	p.R1038G	RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank|ERCC6_ENST00000542458.1_Missense_Mutation_p.R408G	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1038			R -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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						TGAATCCTTCTTTTTAGATGG	0.388								Direct reversal of damage;Nucleotide excision repair (NER)																																								0			10											126	127	127					10																	50678894		2203	4300	6503	50348900	SO:0001583	missense	2074			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.3112A>G	10.37:g.50678894T>C	ENSP00000348089:p.Arg1038Gly		50348900	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	9.409	1.080124	0.20309	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83419	-1.72;-1.46	5.95	4.8	0.61643	.	.	.	.	.	T	0.79695	0.4490	M	0.64404	1.975	0.23809	N	0.996785	B;B	0.13145	0.002;0.007	B;B	0.08055	0.001;0.003	T	0.65146	-0.6239	9	0.25106	T	0.35	-18.2246	11.3011	0.49306	0.0:0.0:0.3622:0.6378	.	1038;415	Q03468;Q59FF6	ERCC6_HUMAN;.	G	1038;415;408	ENSP00000348089:R1038G;ENSP00000445134:R408G	ENSP00000348089:R1038G	R	-	1	2	ERCC6	50348900	0.994000	0.37717	0.351000	0.25721	0.072000	0.16883	1.898000	0.39809	1.039000	0.40074	0.533000	0.62120	AGA		0.388	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50678894	T	C	50678894	3	2	121	1	0	0	0	0	1	0	0	0	5230	1617	56	4	1385	4	ERCC6	10	50678894	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	5249699	50678894	84855853	145	31915										
PRF1	5551	hgsc.bcm.edu	37	chr10	72360291	72360291	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tccagtcgttgcggatgctaCgagccgcatcccgggccaca	12	15	0	0	rs139336186		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:72360291C>A	ENST00000441259.1	-	2	528	c.368G>T	c.(367-369)cGt>cTt	p.R123L	PRF1_ENST00000373209.2_Missense_Mutation_p.R123L	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	123	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		R -> H. {ECO:0000269|PubMed:16959974}.		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)	p.R123H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						GCGGATGCTACGAGCCGCATC	0.642			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																													yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	1	Substitution - Missense(1)	large_intestine(1)	10	GRCh37	CM071929	PRF1	M	rs139336186						44	42	42					10																	72360291		2203	4299	6502	72030297	SO:0001583	missense	55893	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	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.368G>T	10.37:g.72360291C>A	ENSP00000398568:p.Arg123Leu		72030297	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.543579	0.45280	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91295	-2.82;-2.82	5.65	-6.67	0.01783	Membrane attack complex component/perforin (MACPF) domain (1);	2.273180	0.01260	N	0.009149	D	0.82600	0.5072	N	0.22421	0.69	0.09310	N	1	B	0.14012	0.009	B	0.06405	0.002	T	0.70528	-0.4847	10	0.40728	T	0.16	0.2052	9.5638	0.39385	0.0:0.1071:0.2941:0.5988	.	123	P14222	PERF_HUMAN	L	123	ENSP00000362305:R123L;ENSP00000398568:R123L	ENSP00000316746:R123L	R	-	2	0	PRF1	72030297	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.444000	0.21661	-1.374000	0.02131	-0.136000	0.14681	CGT		0.642	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		A	72360291	C	A	72360291	3	1	121	1	0	0	0	0	1	0	0	0	12512	536	19	2	1307	2	PRF1	10	72360291	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	21681397	72360291	63174456	146	31916										
ZMIZ1	57178	hgsc.bcm.edu	37	chr10	81058323	81058323	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	caagccaaatatgagcgctcTgccaccacccccaggtgagg	10	15	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:81058323T>A	ENST00000334512.5	+	15	2224	c.1652T>A	c.(1651-1653)cTg>cAg	p.L551Q		NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	551	Pro-rich.		L -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			ATGAGCGCTCTGCCACCACCC	0.672																																																0			10											85	85	85					10																	81058323		2203	4300	6503	80728329	SO:0001583	missense	57178			AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.1652T>A	10.37:g.81058323T>A	ENSP00000334474:p.Leu551Gln		80728329	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	37	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022392	0.75275	.	.	ENSG00000108175	ENST00000334512;ENST00000360331;ENST00000372347	T	0.49720	0.77	5.12	5.12	0.69794	.	0.000000	0.32314	N	0.006280	T	0.35364	0.0929	N	0.13043	0.29	0.80722	D	1	P	0.42010	0.768	B	0.42112	0.376	T	0.23762	-1.0179	10	0.40728	T	0.16	-11.7383	14.9189	0.70818	0.0:0.0:0.0:1.0	.	551	Q9ULJ6	ZMIZ1_HUMAN	Q	551;481;458	ENSP00000334474:L551Q	ENSP00000334474:L551Q	L	+	2	0	ZMIZ1	80728329	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	7.630000	0.83225	1.936000	0.56123	0.379000	0.24179	CTG		0.672	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		A	81058323	T	A	81058323	3	1	121	1	0	0	0	0	1	0	0	0	17735	1580	55	5	1694	5	ZMIZ1	10	81058323	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	8698032	81058323	54476424	147	31917										
PTEN	5728	hgsc.bcm.edu	37	chr10	89692918	89692918	+	Missense_Mutation	SNP	G	G	A													0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagggacgaactggtgtaatGatatgtgcatatttattaca							TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:89692918G>A	ENST00000371953.3	+	5	1759	c.402G>A	c.(400-402)atG>atA	p.M134I		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	134	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		M -> L (in prostate cancer; no effect on protein phosphatase activity; reduced phosphatase activity towards Ins(1,3,4,5)P3 but retains PtdIns(3,4,5)P3 phosphatase activity). {ECO:0000269|PubMed:9072974}.		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.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.A121_F145del(1)|p.T131fs*42(1)|p.F56fs*2(1)|p.M134I(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)		CTGGTGTAATGATATGTGCAT	0.393		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)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	53	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)|Substitution - Missense(1)|Deletion - In frame(1)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											129	121	124					10																	89692918		2203	4300	6503	89682898	SO:0001583	missense	5728	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.402G>A	10.37:g.89692918G>A	ENSP00000361021:p.Met134Ile		89682898	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	32	5.122120	0.94429	.	.	ENSG00000171862	ENST00000371953	D	0.83992	-1.79	5.22	5.22	0.72569	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89518	0.6738	L	0.58428	1.81	0.80722	D	1	D	0.59357	0.985	D	0.72338	0.977	D	0.88569	0.3128	9	.	.	.	-2.5011	18.7776	0.91918	0.0:0.0:1.0:0.0	.	134	P60484	PTEN_HUMAN	I	134	ENSP00000361021:M134I	.	M	+	3	0	PTEN	89682898	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.429000	0.97481	2.411000	0.81874	0.655000	0.94253	ATG		0.393	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89692918	G	A	89692918	3	1	121	1	0	0	0	0	1	0	0	0	12772	1290	45	3	420	3	PTEN	10	89692918	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	8634595	89692918	45841829	148	31918	57	2								
PTEN	5728	hgsc.bcm.edu	37	chr10	89692923	89692923	+	Missense_Mutation	SNP	G	G	A													0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acgaactggtgtaatgatatGtgcatatttattacatcggg							TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:89692923G>A	ENST00000371953.3	+	5	1764	c.407G>A	c.(406-408)tGt>tAt	p.C136Y		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	136	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		C -> Y (in CWS1; loss of phosphatase activity towards Ins(1,3,4,5)P3). {ECO:0000269|PubMed:9735393}.		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.C136Y(8)|p.C136F(5)|p.?(5)|p.R55fs*1(5)|p.C136fs*1(2)|p.Y27fs*1(2)|p.I135_A137>T(1)|p.A121_F145del(1)|p.I135fs*6(1)|p.T131fs*42(1)|p.F56fs*2(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)		GTAATGATATGTGCATATTTA	0.393		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)																												yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	69	Whole gene deletion(37)|Substitution - Missense(13)|Deletion - Frameshift(10)|Unknown(5)|Insertion - Frameshift(2)|Deletion - In frame(1)|Complex - deletion inframe(1)	prostate(16)|central_nervous_system(14)|endometrium(10)|breast(8)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(3)|meninges(1)|soft_tissue(1)|urinary_tract(1)	10	GRCh37	CM983501	PTEN	M							123	117	119					10																	89692923		2203	4300	6503	89682903	SO:0001583	missense	5728	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.407G>A	10.37:g.89692923G>A	ENSP00000361021:p.Cys136Tyr		89682903	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658698	0.88154	.	.	ENSG00000171862	ENST00000371953	D	0.98747	-5.11	5.22	5.22	0.72569	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99489	0.9818	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98145	1.0438	9	.	.	.	-4.1412	18.7776	0.91918	0.0:0.0:1.0:0.0	.	136	P60484	PTEN_HUMAN	Y	136	ENSP00000361021:C136Y	.	C	+	2	0	PTEN	89682903	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.429000	0.97481	2.411000	0.81874	0.655000	0.94253	TGT		0.393	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		A	89692923	G	A	89692923	3	1	121	1	0	0	0	0	1	0	0	0	12772	1377	48	3	425	3	PTEN	10	89692923	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	5	89692923	45841824	149	31919	57	2								
ALDH18A1	5832	hgsc.bcm.edu	37	chr10	97387287	97387287	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccagacacctttgggtgggtTccattggcaataacaacaga	10	10	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:97387287T>G	ENST00000371224.2	-	9	1127	c.990A>C	c.(988-990)ggA>ggC	p.G330G	ALDH18A1_ENST00000371221.3_Silent_p.G328G	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	330	Glutamate 5-kinase.				cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|glutamate metabolic process (GO:0006536)|L-proline biosynthetic process (GO:0055129)|ornithine biosynthetic process (GO:0006592)|proline biosynthetic process (GO:0006561)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate 5-kinase activity (GO:0004349)|glutamate-5-semialdehyde dehydrogenase activity (GO:0004350)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(9)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)		TTGGGTGGGTTCCATTGGCAA	0.463																																																0			10											156	153	154					10																	97387287		2203	4300	6503	97377277	SO:0001819	synonymous_variant	5832			X94453	CCDS7443.1, CCDS31257.1	10q24.3-q24.6	2004-08-12	2004-08-12	2004-08-12	ENSG00000059573	ENSG00000059573		"Aldehyde dehydrogenases"	9722	protein-coding gene	gene with protein product		138250	"pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)"	GSAS, PYCS		8921385	Standard	XM_006717933		Approved	P5CS	uc001kkz.3	P54886	OTTHUMG00000018815	ENST00000371224.2:c.990A>C	10.37:g.97387287T>G			97377277	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Silent	SNP	ENST00000371224.2	37	CCDS7443.1																																																																																				0.463	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860		G	97387287	T	G	97387287	2	3	121	1	0	0	0	0	0	0	0	1	489	1770	62	4		4	ALDH18A1	10	97387287	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	7694364	97387287	38147460	150	31920										
PCGF6	84108	hgsc.bcm.edu	37	chr10	105086323	105086323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atcaagacccatttttcttcTgaggaatttttctacatgtc	5	9	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:105086323T>C	ENST00000369847.3	-	8	944	c.877A>G	c.(877-879)Aga>Gga	p.R293G	PCGF6_ENST00000337211.4_Missense_Mutation_p.R218G|PCGF6_ENST00000490296.1_5'UTR	NM_001011663.1	NP_001011663.1	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6	293					negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R293G(1)		autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)	8		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		ATTTTTCTTCTGAGGAATTTT	0.353																																																1	Substitution - Missense(1)	kidney(1)	10											88	87	87					10																	105086323		2203	4300	6503	105076313	SO:0001583	missense	84108			AB047006	CCDS7546.1, CCDS31275.1	10q24.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000156374	ENSG00000156374		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	21156	protein-coding gene	gene with protein product		607816	"ring finger protein 134"	RNF134		12167161	Standard	NM_032154		Approved	MBLR	uc001kwt.3	Q9BYE7	OTTHUMG00000018982	ENST00000369847.3:c.877A>G	10.37:g.105086323T>C	ENSP00000358862:p.Arg293Gly		105076313	A8K3R4|Q5SYD1|Q5SYD6|Q96ID9|Q96SJ1	Missense_Mutation	SNP	ENST00000369847.3	37	CCDS31275.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657497	0.47467	.	.	ENSG00000156374	ENST00000369847;ENST00000337211	T;T	0.35605	1.3;1.37	5.0	0.945	0.19543	.	0.000000	0.85682	D	0.000000	T	0.51261	0.1664	M	0.83118	2.625	0.30729	N	0.747404	D;D	0.62365	0.99;0.991	P;P	0.58013	0.794;0.831	T	0.55879	-0.8071	10	0.66056	D	0.02	.	7.5775	0.27944	0.1312:0.0:0.4047:0.4641	.	218;293	Q9BYE7-3;Q9BYE7	.;PCGF6_HUMAN	G	293;218	ENSP00000358862:R293G;ENSP00000338845:R218G	ENSP00000338845:R218G	R	-	1	2	PCGF6	105076313	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.932000	0.28884	0.222000	0.20900	0.379000	0.24179	AGA		0.353	PCGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050132.1	NM_032154		C	105086323	T	C	105086323	3	2	121	1	0	0	0	0	1	0	0	0	11609	1588	55	4	187	4	PCGF6	10	105086323	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	7699036	105086323	30448424	151	31921										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123274795	123274795	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtaaatggctatctccaggtAgtctggggaagctgtaatct	12	7	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:123274795A>G	ENST00000358487.5	-	9	1395	c.1123T>C	c.(1123-1125)Tac>Cac	p.Y375H	FGFR2_ENST00000457416.2_Missense_Mutation_p.Y376H|FGFR2_ENST00000369061.4_Missense_Mutation_p.Y263H|FGFR2_ENST00000369056.1_Missense_Mutation_p.Y376H|FGFR2_ENST00000369059.1_Missense_Mutation_p.Y261H|FGFR2_ENST00000351936.6_Missense_Mutation_p.Y375H|FGFR2_ENST00000490349.1_5'Flank|FGFR2_ENST00000360144.3_Missense_Mutation_p.Y287H|FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000356226.4_Missense_Mutation_p.Y260H|FGFR2_ENST00000346997.2_Missense_Mutation_p.Y375H|FGFR2_ENST00000478859.1_Missense_Mutation_p.Y147H|FGFR2_ENST00000357555.5_Missense_Mutation_p.Y286H	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	375			Y -> C (in PS and BSTVS). {ECO:0000269|PubMed:11781872, ECO:0000269|PubMed:12000365, ECO:0000269|PubMed:8696350}.		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)	ATCTCCAGGTAGTCTGGGGAA	0.488		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																														Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											108	114	112					10																	123274795		2203	4300	6503	123264785	SO:0001583	missense	2263	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.1123T>C	10.37:g.123274795A>G	ENSP00000351276:p.Tyr375His		123264785	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	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.650986	0.87958	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	D;D;D;D;D;D;D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.93400	0.7895	M	0.84326	2.69	0.80722	D	1	B;D;D;D;D;B;D	0.69078	0.273;0.985;0.99;0.991;0.994;0.117;0.997	B;P;P;D;P;B;D	0.67548	0.04;0.905;0.881;0.926;0.896;0.086;0.952	D	0.93560	0.6894	10	0.49607	T	0.09	.	16.2041	0.82108	1.0:0.0:0.0:0.0	.	394;376;286;260;375;287;376	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17	.;.;.;.;FGFR2_HUMAN;.;.	H	286;378;263;375;260;261;375;376;375;287;376;376;286	ENSP00000350166:Y286H;ENSP00000358057:Y263H;ENSP00000351276:Y375H;ENSP00000348559:Y260H;ENSP00000358055:Y261H;ENSP00000263451:Y375H;ENSP00000410294:Y376H;ENSP00000309878:Y375H;ENSP00000353262:Y287H;ENSP00000358052:Y376H;ENSP00000358054:Y376H;ENSP00000337665:Y286H	ENSP00000337665:Y286H	Y	-	1	0	FGFR2	123264785	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.248000	0.95456	2.219000	0.72066	0.533000	0.62120	TAC		0.488	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		G	123274795	A	G	123274795	3	3	121	1	0	0	0	0	1	0	0	0	5885	420	15	4	1486	4	FGFR2	10	123274795	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	18188472	123274795	12259952	152	31922										
CUZD1	50624	hgsc.bcm.edu	37	chr10	124598699	124598699	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggcccattgctggaggttccGtcaaagactttaatgttttc	10	9	1	1	rs141440856		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr10:124598699G>A	ENST00000368904.1	-	5	1231	c.282C>T	c.(280-282)gaC>gaT	p.D94D	CUZD1_ENST00000392790.1_Silent_p.D94D|CUZD1_ENST00000545804.1_Silent_p.D94D					CUB and zona pellucida-like domains 1									p.D94D(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|stomach(1)	39		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		TGGAGGTTCCGTCAAAGACTT	0.433													G|||	1	0.000199681	8e-04	0	5008	,	,		20863	0		0	False		,,,				2504	0															1	Substitution - coding silent(1)	ovary(1)	10						G		0,4406		0,0,2203	181	169	173		282	-2.7	0	10	dbSNP_134	173	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CUZD1	NM_022034.5		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		94/608	124598699	2,13004	2203	4300	6503	124588689	SO:0001819	synonymous_variant	50624			AF305835	CCDS7631.1	10q26.13	2003-11-18			ENSG00000138161	ENSG00000138161			17937	protein-coding gene	gene with protein product						10542259	Standard	NM_022034		Approved	ERG-1, UO-44		Q86UP6	OTTHUMG00000019195	ENST00000368904.1:c.282C>T	10.37:g.124598699G>A			124588689		Silent	SNP	ENST00000368904.1	37	CCDS7631.1																																																																																				0.433	CUZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050829.2	NM_022034		A	124598699	G	A	124598699	2	1	121	1	0	0	0	0	0	0	0	1	4072	1136	40	1		1	CUZD1	10	124598699	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1323904	124598699	10936048	153	31923										
OR51E1	143503	hgsc.bcm.edu	37	chr11	4674315	4674315	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cctactgcctacaccaagatGtcatgaagctggcctgtgat	9	12	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:4674315G>T	ENST00000396952.5	+	2	1209	c.559G>T	c.(559-561)Gtc>Ttc	p.V187F	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACACCAAGATGTCATGAAGCT	0.542																																																0			11											230	197	208					11																	4674315		2201	4298	6499	4630891	SO:0001583	missense	143503			AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"GPCR / Class A : Olfactory receptors"	15194	protein-coding gene	gene with protein product		611267	"olfactory receptor, family 51, subfamily E, member 1 pseudogene"	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000396952.5:c.559G>T	11.37:g.4674315G>T	ENSP00000380155:p.Val187Phe		4630891	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	37	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	G	16.59	3.164451	0.57476	.	.	ENSG00000180785	ENST00000396952	T	0.72505	-0.66	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.284575	0.25494	N	0.030289	D	0.83188	0.5200	M	0.87547	2.89	0.80722	D	1	D	0.67145	0.996	D	0.72982	0.979	D	0.84734	0.0747	10	0.87932	D	0	.	7.4055	0.26987	0.1741:0.0:0.8259:0.0	.	186	Q8TCB6	O51E1_HUMAN	F	187	ENSP00000380155:V187F	ENSP00000380155:V187F	V	+	1	0	OR51E1	4630891	0.007000	0.16637	1.000000	0.80357	0.996000	0.88848	0.051000	0.14141	2.605000	0.88082	0.655000	0.94253	GTC		0.542	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430		T	4674315	G	T	4674315	3	4	121	1	0	0	0	0	1	0	0	0	11125	1377	48	2	561	2	OR51E1	11	4674315	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10		4674315	130332201	154	31924										
OR51I1	390063	hgsc.bcm.edu	37	chr11	5462306	5462306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttggtaaggatgcccagacCcatagccaatatacggttgt	10	10	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:5462306C>A	ENST00000380211.1	-	1	438	c.439G>T	c.(439-441)Ggt>Tgt	p.G147C	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	147					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)		ATGCCCAGACCCATAGCCAAT	0.478																																																0			11											135	105	116					11																	5462306		2201	4297	6498	5418882	SO:0001583	missense	390063			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.439G>T	11.37:g.5462306C>A	ENSP00000369559:p.Gly147Cys		5418882	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609116	0.28623	.	.	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.35236	1.32	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000026	T	0.54615	0.1869	M	0.93678	3.445	0.39406	D	0.966662	P	0.39326	0.668	B	0.42882	0.401	T	0.66889	-0.5809	10	0.87932	D	0	.	12.0476	0.53489	0.0:0.9209:0.0:0.0791	.	147	Q9H343	O51I1_HUMAN	C	132;144;147	ENSP00000369559:G147C	ENSP00000348350:G132C	G	-	1	0	OR51I1	5418882	0.098000	0.21812	0.968000	0.41197	0.342000	0.28953	3.381000	0.52455	2.742000	0.94016	0.551000	0.68910	GGT		0.478	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		A	5462306	C	A	5462306	3	1	121	1	0	0	0	0	1	0	0	0	11131	623	22	2	509	2	OR51I1	11	5462306	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	787991	5462306	129544210	155	31925										
CCDC73	493860	hgsc.bcm.edu	37	chr11	32636242	32636242	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctgtttctattgctgtatctAacactacaaaatgattattt	4	7	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:32636242A>G	ENST00000335185.5	-	16	1665	c.1622T>C	c.(1621-1623)tTa>tCa	p.L541S	CCDC73_ENST00000534415.1_5'Flank	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	541										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)					TGCTGTATCTAACACTACAAA	0.299																																																0			11											129	116	120					11																	32636242		1814	4074	5888	32592818	SO:0001583	missense	493860			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.1622T>C	11.37:g.32636242A>G	ENSP00000335325:p.Leu541Ser		32592818	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	A	3.003	-0.205650	0.06180	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.19	-0.635	0.11512	.	0.746134	0.11499	N	0.557867	T	0.13586	0.0329	N	0.08118	0	0.09310	N	1	B	0.28933	0.228	B	0.24394	0.053	T	0.25363	-1.0134	9	0.17369	T	0.5	.	3.7258	0.08474	0.4109:0.0:0.4302:0.1588	.	541	Q6ZRK6	CCD73_HUMAN	S	541	.	ENSP00000335325:L541S	L	-	2	0	CCDC73	32592818	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	0.174000	0.16743	-0.487000	0.06735	0.482000	0.46254	TTA		0.299	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		G	32636242	A	G	32636242	3	3	121	1	0	0	0	0	1	0	0	0	2852	372	13	4	1629	4	CCDC73	11	32636242	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	27173936	32636242	102370274	156	31926										
MADD	4607	hgsc.bcm.edu	37	chr11	47350685	47350685	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agatctcagaaccccgccccGgcctgtctctagctgatgga	10	15	2	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:47350685G>A	ENST00000545968.1	-	0	4217				MADD_ENST00000407859.3_Missense_Mutation_p.R1561Q|MADD_ENST00000349238.3_Missense_Mutation_p.R1604Q|MADD_ENST00000311027.5_Missense_Mutation_p.R1643Q|MADD_ENST00000395336.3_3'UTR|MADD_ENST00000395344.3_Missense_Mutation_p.R1537Q|MADD_ENST00000402799.1_Missense_Mutation_p.R1541Q|MADD_ENST00000406482.1_3'UTR|MADD_ENST00000342922.4_Missense_Mutation_p.R1584Q|MADD_ENST00000402192.2_Missense_Mutation_p.R1583Q	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac						cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		ACCCCGCCCCGGCCTGTCTCT	0.597																																																0			11											95	97	96					11																	47350685		2201	4298	6499	47307261	SO:0001628	intergenic_variant	8567			X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7551	protein-coding gene	gene with protein product		600958	"myosin-binding protein C, cardiac"	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896			11.37:g.47350685G>A			47307261	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	G	36	5.836323	0.97009	.	.	ENSG00000110514	ENST00000342922;ENST00000402799;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000402192	T;T;T;T;T;T;T	0.08008	3.27;3.14;3.26;3.18;3.14;3.14;3.27	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.25158	0.0611	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.999;0.998;1.0	D;D;D;D;D;D;D	0.83275	0.978;0.978;0.99;0.996;0.993;0.99;0.996	T	0.00115	-1.2038	10	0.72032	D	0.01	-17.409	20.0016	0.97412	0.0:0.0:1.0:0.0	.	1537;1537;1541;1604;1561;1643;1584	B5MEE5;A8K8S7;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;MADD_HUMAN;.	Q	1584;1541;1604;1643;1561;1537;1583	ENSP00000343902:R1584Q;ENSP00000385585:R1541Q;ENSP00000304505:R1604Q;ENSP00000310933:R1643Q;ENSP00000384204:R1561Q;ENSP00000378753:R1537Q;ENSP00000384287:R1583Q	ENSP00000310933:R1643Q	R	+	2	0	MADD	47307261	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.706000	0.74649	2.731000	0.93534	0.555000	0.69702	CGG		0.597	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			A	47350685	G	A	47350685	1	1	121	0	1	0	0	0	0	0	0	0	9182	1116	39	1		1	MADD	11	47350685	IGR	SNP	G	TCGA-G5-6235-01A-11D-1733-10	14714443	47350685	87655831	157	31927										
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322678	55322678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctgtggatctcacattgctgTtgtgattttgttctttgtcc	9	8	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:55322678T>C	ENST00000314644.2	+	1	896	c.896T>C	c.(895-897)gTt>gCt	p.V299A		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	245						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						CACATTGCTGTTGTGATTTTG	0.418										HNSCC(20;0.049)																																						0			11											244	234	238					11																	55322678		2201	4296	6497	55079254	SO:0001583	missense	81309			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.896T>C	11.37:g.55322678T>C	ENSP00000324958:p.Val299Ala		55079254	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.610630	0.66558	.	.	ENSG00000181939	ENST00000314644	T	0.00237	8.47	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00496	0.0016	M	0.75085	2.285	0.29568	N	0.850109	D	0.61697	0.99	D	0.65573	0.936	T	0.50750	-0.8791	9	0.62326	D	0.03	.	12.7227	0.57152	0.0:0.0:0.0:1.0	.	245	Q8NGM1	OR4CF_HUMAN	A	299	ENSP00000324958:V299A	ENSP00000324958:V299A	V	+	2	0	OR4C15	55079254	0.001000	0.12720	0.860000	0.33809	0.610000	0.37248	0.837000	0.27558	2.107000	0.64212	0.317000	0.21355	GTT		0.418	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		C	55322678	T	C	55322678	3	2	121	1	0	0	0	0	1	0	0	0	11079	1725	60	4	898	4	OR4C15	11	55322678	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	7971993	55322678	79683838	158	31928										
OR9Q2	219957	hgsc.bcm.edu	37	chr11	57958121	57958121	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctcctgatccgtggcgatcgTcggctccacaccccgatgta	10	16	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:57958121T>C	ENST00000311591.3	+	1	216	c.159T>C	c.(157-159)cgT>cgC	p.R53R		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	53						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)				GTGGCGATCGTCGGCTCCACA	0.532																																																0			11											122	88	99					11																	57958121		2201	4296	6497	57714697	SO:0001819	synonymous_variant	219957			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.159T>C	11.37:g.57958121T>C			57714697		Silent	SNP	ENST00000311591.3	37	CCDS31544.1																																																																																				0.532	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283		C	57958121	T	C	57958121	2	2	121	1	0	0	0	0	0	0	0	1	11287	1654	58	4		4	OR9Q2	11	57958121	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	2635443	57958121	77048395	159	31929										
OR5AN1	390195	hgsc.bcm.edu	37	chr11	59132243	59132243	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgtattattcagtactttatCttttcaacgatgggactgag	8	6	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:59132243C>A	ENST00000313940.2	+	1	359	c.312C>A	c.(310-312)atC>atA	p.I104I		NM_001004729.1	NP_001004729.1	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN, member 1	104						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(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	21						AGTACTTTATCTTTTCAACGA	0.428																																																0			11											206	188	194					11																	59132243		2201	4295	6496	58888819	SO:0001819	synonymous_variant	390195			AB065806	CCDS31559.1	11q12.1	2012-08-09			ENSG00000176495	ENSG00000176495		"GPCR / Class A : Olfactory receptors"	15255	protein-coding gene	gene with protein product		615702					Standard	NM_001004729		Approved		uc010rks.2	Q8NGI8	OTTHUMG00000167337	ENST00000313940.2:c.312C>A	11.37:g.59132243C>A			58888819	B9EIS2|Q6IEV4	Silent	SNP	ENST00000313940.2	37	CCDS31559.1																																																																																				0.428	OR5AN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394231.1	NM_001004729		A	59132243	C	A	59132243	2	1	121	1	0	0	0	0	0	0	0	1	11174	903	32	2		2	OR5AN1	11	59132243	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1174122	59132243	75874273	160	31930										
PLAC1L	219990	hgsc.bcm.edu	37	chr11	59811020	59811020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagaaatctgtatatatttgCggatgaattacatctgggaa	9	5	2	2	rs375351184		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:59811020C>T	ENST00000278855.2	+	2	328	c.143C>T	c.(142-144)gCg>gTg	p.A48V	PLAC1L_ENST00000532905.1_Missense_Mutation_p.A17V	NM_173801.3	NP_776162.2	Q86WS3	OOSP2_HUMAN		48						extracellular region (GO:0005576)				breast(1)|lung(9)|ovary(2)|prostate(2)|skin(1)	15						TATATATTTGCGGATGAATTA	0.398																																																0			11						C	VAL/ALA	0,4402		0,0,2201	120	118	118		143	0.2	0	11		118	1,8589	1.2+/-3.3	0,1,4294	no	missense	PLAC1L	NM_173801.3	64	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	48/159	59811020	1,12991	2201	4295	6496	59567596	SO:0001583	missense	219990																														ENST00000278855.2:c.143C>T	11.37:g.59811020C>T	ENSP00000278855:p.Ala48Val		59567596	E9PJA4|Q8N9U6	Missense_Mutation	SNP	ENST00000278855.2	37	CCDS7979.1	.	.	.	.	.	.	.	.	.	.	C	15.52	2.857310	0.51376	0.0	1.16E-4	ENSG00000149507	ENST00000278855;ENST00000532905	D;D	0.81996	-1.56;-1.56	3.4	0.161	0.14977	.	0.671038	0.12343	N	0.477297	T	0.82010	0.4944	L	0.50333	1.59	0.09310	N	1	D	0.65815	0.995	P	0.52793	0.709	T	0.71076	-0.4697	10	0.39692	T	0.17	-3.3017	8.9142	0.35572	0.5885:0.4115:0.0:0.0	.	48	Q86WS3	PLACL_HUMAN	V	48;17	ENSP00000278855:A48V;ENSP00000433831:A17V	ENSP00000278855:A48V	A	+	2	0	PLAC1L	59567596	0.008000	0.16893	0.026000	0.17262	0.725000	0.41563	0.192000	0.17096	0.043000	0.15746	0.557000	0.71058	GCG		0.398	PLAC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394411.1			T	59811020	C	T	59811020	3	4	121	1	0	0	0	0	1	0	0	0	12044	768	27	1	149	1	PLAC1L	11	59811020	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	678777	59811020	75195496	161	31931										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62298674	62298674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtcctttaagatccaggtcaAcatctggcaaagacatctta	7	10	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:62298674A>G	ENST00000378024.4	-	5	3489	c.3215T>C	c.(3214-3216)gTt>gCt	p.V1072A	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1072					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)				ATCCAGGTCAACATCTGGCAA	0.458																																																0			11											123	120	121					11																	62298674		2202	4299	6501	62055250	SO:0001583	missense	79026			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.3215T>C	11.37:g.62298674A>G	ENSP00000367263:p.Val1072Ala		62055250	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	a	10.28	1.306781	0.23821	.	.	ENSG00000124942	ENST00000378024	T	0.05025	3.51	4.76	4.76	0.60689	.	0.411457	0.23217	N	0.050620	T	0.06690	0.0171	L	0.46819	1.47	0.23827	N	0.996734	B	0.12630	0.006	B	0.16289	0.015	T	0.37197	-0.9716	10	0.09590	T	0.72	-10.1736	12.5425	0.56179	1.0:0.0:0.0:0.0	.	1072	Q09666	AHNK_HUMAN	A	1072	ENSP00000367263:V1072A	ENSP00000367263:V1072A	V	-	2	0	AHNAK	62055250	0.000000	0.05858	0.936000	0.37596	0.100000	0.18952	1.055000	0.30467	1.788000	0.52465	0.454000	0.30748	GTT		0.458	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		G	62298674	A	G	62298674	3	3	121	1	0	0	0	0	1	0	0	0	414	43	2	4	14577	4	AHNAK	11	62298674	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	2487654	62298674	72707842	162	31932										
SCYL1	57410	hgsc.bcm.edu	37	chr11	65303520	65303520	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcctgggctttgctgccaccCacaacctctactcaatgaac	6	16	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:65303520C>T	ENST00000270176.5	+	11	1560	c.1483C>T	c.(1483-1485)Cac>Tac	p.H495Y	SCYL1_ENST00000533862.1_Missense_Mutation_p.H495Y|SCYL1_ENST00000527009.1_Missense_Mutation_p.H352Y|SCYL1_ENST00000279270.6_Missense_Mutation_p.H495Y|SCYL1_ENST00000524944.1_Missense_Mutation_p.H495Y|SCYL1_ENST00000525364.1_Missense_Mutation_p.H495Y|SCYL1_ENST00000420247.2_Missense_Mutation_p.H495Y	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	495			H -> Y (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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)	p.H495Y(1)		ovary(1)|skin(1)	2						TGCTGCCACCCACAACCTCTA	0.592																																																1	Substitution - Missense(1)	skin(1)	11											89	91	90					11																	65303520		1980	4152	6132	65060096	SO:0001583	missense	57410			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.1483C>T	11.37:g.65303520C>T	ENSP00000270176:p.His495Tyr		65060096	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	37	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.335543	0.24253	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009	T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (1);	0.104625	0.64402	D	0.000005	T	0.45915	0.1366	L	0.56769	1.78	0.80722	D	1	B;D;B;B;P	0.57571	0.038;0.98;0.232;0.232;0.928	B;P;B;B;P	0.54706	0.085;0.759;0.113;0.113;0.579	T	0.33369	-0.9871	10	0.49607	T	0.09	-11.242	16.7806	0.85562	0.0:1.0:0.0:0.0	.	495;495;495;495;495	E9PS17;Q96KG9-4;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;.;NTKL_HUMAN	Y	495;495;495;495;495;495;495;495;352	ENSP00000270176:H495Y;ENSP00000431635:H495Y;ENSP00000408192:H495Y;ENSP00000437254:H495Y;ENSP00000433450:H495Y;ENSP00000279270:H495Y;ENSP00000432175:H495Y;ENSP00000436993:H352Y	ENSP00000270176:H495Y	H	+	1	0	SCYL1	65060096	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.079000	0.64431	2.577000	0.86979	0.462000	0.41574	CAC		0.592	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		T	65303520	C	T	65303520	3	4	121	1	0	0	0	0	1	0	0	0	13984	594	21	3	1525	3	SCYL1	11	65303520	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3004846	65303520	69702996	163	31933										
NARS2	79731	hgsc.bcm.edu	37	chr11	78279747	78279747	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acattttgccttttggatggActttttatcagctgcccttg	8	9	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:78279747A>G	ENST00000281038.5	-	3	678	c.303T>C	c.(301-303)agT>agC	p.S101S	NARS2_ENST00000528850.1_5'UTR	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	101					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TTTTGGATGGACTTTTTATCA	0.338																																																0			11											176	170	172					11																	78279747		2200	4291	6491	77957395	SO:0001819	synonymous_variant	79731			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.303T>C	11.37:g.78279747A>G			77957395	G3V178	Silent	SNP	ENST00000281038.5	37	CCDS8261.1																																																																																				0.338	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		G	78279747	A	G	78279747	2	3	121	1	0	0	0	0	0	0	0	1	10201	272	10	4		4	NARS2	11	78279747	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	12976227	78279747	56726769	164	31934										
GRM5	2915	hgsc.bcm.edu	37	chr11	88242010	88242010	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagccgcctgcgcccctgccGcgggctgcgcgcctcccgtg	14	21	0	0	rs543797881		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:88242010G>A	ENST00000305447.4	-	9	3538	c.3389C>T	c.(3388-3390)gCg>gTg	p.A1130V	GRM5-AS1_ENST00000531994.1_RNA|GRM5-AS1_ENST00000526448.1_RNA|GRM5_ENST00000418177.2_Missense_Mutation_p.A1130V|GRM5_ENST00000455756.2_Missense_Mutation_p.A1098V|GRM5_ENST00000393297.1_Intron|GRM5_ENST00000305432.5_Missense_Mutation_p.A1098V	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	1130					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)	CGCCCCTGCCGCGGGCTGCGC	0.711													G|||	1	0.000199681	8e-04	0	5008	,	,		8276	0		0	False		,,,				2504	0															0			11											7	7	7					11																	88242010		2097	4169	6266	87881658	SO:0001583	missense	2915			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.3389C>T	11.37:g.88242010G>A	ENSP00000306138:p.Ala1130Val		87881658	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340533	0.24339	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447	D;D;D;D	0.87966	-2.28;-2.32;-2.32;-2.28	4.54	2.52	0.30459	.	1.674510	0.03380	U	0.200282	T	0.76004	0.3927	N	0.12182	0.205	0.23030	N	0.998401	B;B	0.11235	0.004;0.002	B;B	0.08055	0.003;0.001	T	0.62445	-0.6853	9	.	.	.	.	6.0486	0.19773	0.1679:0.1556:0.6765:0.0	.	1098;1130	P41594-2;P41594	.;GRM5_HUMAN	V	1130;1098;1098;1130	ENSP00000402912:A1130V;ENSP00000405690:A1098V;ENSP00000305905:A1098V;ENSP00000306138:A1130V	.	A	-	2	0	GRM5	87881658	.	.	0.784000	0.31847	0.681000	0.39784	.	.	0.891000	0.36235	-0.244000	0.11960	GCG		0.711	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88242010	G	A	88242010	3	1	121	1	0	0	0	0	1	0	0	0	6821	1087	38	1	253	1	GRM5	11	88242010	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	9962263	88242010	46764506	165	31935										
FAT3	120114	hgsc.bcm.edu	37	chr11	92534211	92534211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atacagtgctttcgttctttGtcaaagcagtagatgggggc	12	7	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:92534211G>A	ENST00000298047.6	+	9	8049	c.8032G>A	c.(8032-8034)Gtc>Atc	p.V2678I	FAT3_ENST00000525166.1_Missense_Mutation_p.V2528I|FAT3_ENST00000409404.2_Missense_Mutation_p.V2678I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2678	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)				TTCGTTCTTTGTCAAAGCAGT	0.478										TCGA Ovarian(4;0.039)																																						0			11											49	46	47					11																	92534211		1917	4124	6041	92173859	SO:0001583	missense	120114			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.8032G>A	11.37:g.92534211G>A	ENSP00000298047:p.Val2678Ile		92173859	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	20.8	4.054813	0.75960	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.64803	-0.12;-0.12;-0.12	6.17	6.17	0.99709	.	.	.	.	.	T	0.76941	0.4058	L	0.60067	1.865	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.68447	-0.5406	9	0.22706	T	0.39	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	2678	Q8TDW7-3	.	I	2678;2678;2528	ENSP00000298047:V2678I;ENSP00000387040:V2678I;ENSP00000432586:V2528I	ENSP00000298047:V2678I	V	+	1	0	FAT3	92173859	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.787000	0.99055	2.941000	0.99782	0.655000	0.94253	GTC		0.478	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92534211	G	A	92534211	3	1	121	1	0	0	0	0	1	0	0	0	5710	1377	48	3	8066	3	FAT3	11	92534211	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	4292201	92534211	42472305	166	31936										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93808490	93808490	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tccaattaaggacaccagctCtggcctggtagggcctttgc	11	12	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:93808490C>A	ENST00000315765.9	+	9	1663	c.1655C>A	c.(1654-1656)tCt>tAt	p.S552Y		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	552	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)				GACACCAGCTCTGGCCTGGTA	0.512																																																0			11											90	86	87					11																	93808490		1948	4134	6082	93448138	SO:0001583	missense	341208			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.1655C>A	11.37:g.93808490C>A	ENSP00000313699:p.Ser552Tyr		93448138	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.749316	0.89753	.	.	ENSG00000181333	ENST00000315765	D	0.99032	-5.35	5.39	5.39	0.77823	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.171616	0.53938	D	0.000056	D	0.99342	0.9769	M	0.85462	2.755	0.45852	D	0.99871	D	0.71674	0.998	D	0.72982	0.979	D	0.99253	1.0888	10	0.87932	D	0	.	19.1613	0.93533	0.0:1.0:0.0:0.0	.	552	Q6MZM0	HPHL1_HUMAN	Y	552	ENSP00000313699:S552Y	ENSP00000313699:S552Y	S	+	2	0	HEPHL1	93448138	0.999000	0.42202	1.000000	0.80357	0.979000	0.70002	7.332000	0.79203	2.517000	0.84864	0.650000	0.86243	TCT		0.512	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		A	93808490	C	A	93808490	3	1	121	1	0	0	0	0	1	0	0	0	7076	913	32	2	1689	2	HEPHL1	11	93808490	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1274279	93808490	41198026	167	31937										
BIRC3	330	hgsc.bcm.edu	37	chr11	102195608	102195608	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agtaacaaattccacacactCattacttccgggtacagaaa	5	11	1	1	rs572690185		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:102195608C>T	ENST00000263464.3	+	2	3118	c.368C>T	c.(367-369)tCa>tTa	p.S123L	BIRC3_ENST00000532808.1_Missense_Mutation_p.S123L	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	123					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)			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)		TCCACACACTCATTACTTCCG	0.408			T	MALT1	MALT																																		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	0			11											171	179	176					11																	102195608		2203	4299	6502	101700818	SO:0001583	missense	330			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.368C>T	11.37:g.102195608C>T	ENSP00000263464:p.Ser123Leu		101700818	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	C	3.937	-0.014949	0.07681	.	.	ENSG00000023445	ENST00000263464;ENST00000532808	T;T	0.21932	1.98;1.98	5.93	0.599	0.17519	.	0.417996	0.29046	N	0.013313	T	0.12944	0.0314	L	0.33485	1.01	0.09310	N	1	B	0.14012	0.009	B	0.15484	0.013	T	0.25047	-1.0143	10	0.25751	T	0.34	.	7.46	0.27289	0.0:0.6434:0.1113:0.2453	.	123	Q13489	BIRC3_HUMAN	L	123	ENSP00000263464:S123L;ENSP00000432907:S123L	ENSP00000263464:S123L	S	+	2	0	BIRC3	101700818	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	0.566000	0.23593	0.122000	0.18314	-0.229000	0.12294	TCA		0.408	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102195608	C	T	102195608	3	4	121	1	0	0	0	0	1	0	0	0	1437	838	29	3	370	3	BIRC3	11	102195608	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	8387118	102195608	32810908	168	31938										
ATM	472	hgsc.bcm.edu	37	chr11	108216545	108216545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaaattttcaaccagttttcCgttacttctgcatggaaaaa	5	8	2	0	rs587779872		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:108216545C>T	ENST00000452508.2	+	59	8683	c.8494C>T	c.(8494-8496)Cgt>Tgt	p.R2832C	C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.R2832C			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2832	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		R -> C (in AT and B-cell non-Hodgkin lymphoma). {ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:9288106, ECO:0000269|PubMed:9443866}.		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)	p.R2832C(4)		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)	ACCAGTTTTCCGTTACTTCTG	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)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	4	Substitution - Missense(4)	haematopoietic_and_lymphoid_tissue(2)|NS(1)|central_nervous_system(1)	11	GRCh37	CM980159	ATM	M							146	152	150					11																	108216545		2200	4298	6498	107721755	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	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.8494C>T	11.37:g.108216545C>T	ENSP00000388058:p.Arg2832Cys		107721755	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383425	0.82792	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.76186	-1.0;-1.0	5.45	5.45	0.79879	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.88883	0.6558	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.90645	0.4578	10	0.87932	D	0	.	19.2872	0.94084	0.0:1.0:0.0:0.0	.	2832	Q13315	ATM_HUMAN	C	2832	ENSP00000278616:R2832C;ENSP00000388058:R2832C	ENSP00000278616:R2832C	R	+	1	0	ATM	107721755	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.935000	0.63498	2.548000	0.85928	0.650000	0.86243	CGT		0.343	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108216545	C	T	108216545	3	4	121	1	0	0	0	0	1	0	0	0	1110	652	23	1	8720	1	ATM	11	108216545	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	6020937	108216545	26789971	169	31939										
MLL	4297	hgsc.bcm.edu	37	chr11	118359388	118359388	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttttgtttagaggagaacgaGcgccctctggaggaccagct	13	9	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:118359388G>A	ENST00000389506.5	+	11	4392	c.4392G>A	c.(4390-4392)gaG>gaA	p.E1464E	KMT2A_ENST00000354520.4_Silent_p.E1426E|KMT2A_ENST00000534358.1_Silent_p.E1464E			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1464					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)										AGGAGAACGAGCGCCCTCTGG	0.433																																																0			11											135	122	126					11																	118359388		2200	4296	6496	117864598	SO:0001819	synonymous_variant	4297			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.4392G>A	11.37:g.118359388G>A			117864598	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.433	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118359388	G	A	118359388	2	1	121	1	0	0	0	0	0	0	0	1	9650	962	34	3		3	MLL	11	118359388	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	10142843	118359388	16647128	170	31940										
SRPR	6734	hgsc.bcm.edu	37	chr11	126135298	126135298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggctgcagaatctgcaccagGgactcctgtagggcttgctt	13	11	1	1	rs145286251		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:126135298G>A	ENST00000332118.6	-	10	1330	c.1176C>T	c.(1174-1176)tcC>tcT	p.S392S	SRPR_ENST00000532259.1_Silent_p.S364S|SRPR_ENST00000530680.1_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	392					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		TCTGCACCAGGGACTCCTGTA	0.567																																																0			11						G	,	1,4401	2.1+/-5.4	0,1,2200	50	49	49		1092,1176	2	1	11	dbSNP_134	49	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	SRPR	NM_001177842.1,NM_003139.3	,	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	,	364/611,392/639	126135298	1,12999	2201	4299	6500	125640508	SO:0001819	synonymous_variant	6734			BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"signal recognition particle receptor ('docking protein')"			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1176C>T	11.37:g.126135298G>A			125640508	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Silent	SNP	ENST00000332118.6	37	CCDS31717.1																																																																																				0.567	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139		A	126135298	G	A	126135298	2	1	121	1	0	0	0	0	0	0	0	1	15201	1219	43	3		3	SRPR	11	126135298	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	7775910	126135298	8871218	171	31941										
NTM	50863	hgsc.bcm.edu	37	chr11	132016192	132016192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcaggtgcactattgacaacCgggtcacccgggtggcctgg	14	12	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr11:132016192C>T	ENST00000374786.1	+	2	663	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	NTM_ENST00000427481.2_Missense_Mutation_p.R53W|NTM_ENST00000539799.1_Missense_Mutation_p.R62W|NTM_ENST00000374791.3_Missense_Mutation_p.R62W|NTM_ENST00000425719.2_Missense_Mutation_p.R62W|NTM_ENST00000374784.1_Missense_Mutation_p.R62W	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	62	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R62W(2)		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						TATTGACAACCGGGTCACCCG	0.577																																																2	Substitution - Missense(2)	lung(2)	11											110	90	97					11																	132016192		2201	4297	6498	131521402	SO:0001583	missense	50863			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.184C>T	11.37:g.132016192C>T	ENSP00000363918:p.Arg62Trp		131521402	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.162507	0.78226	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.69	5.69	0.88448	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054148	0.64402	D	0.000001	T	0.78059	0.4224	L	0.59436	1.845	0.47276	D	0.999374	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;0.998	D;D;D;D;P;D	0.72625	0.978;0.964;0.962;0.935;0.894;0.94	T	0.77005	-0.2748	10	0.45353	T	0.12	-18.7026	14.6363	0.68692	0.1455:0.8545:0.0:0.0	.	62;53;62;62;62;62	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	W	62;62;53;53;62;62;62	ENSP00000363923:R62W;ENSP00000437668:R62W;ENSP00000448104:R53W;ENSP00000416320:R53W;ENSP00000363918:R62W;ENSP00000396722:R62W;ENSP00000363916:R62W	ENSP00000363916:R62W	R	+	1	2	NTM	131521402	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.766000	0.47629	2.691000	0.91804	0.655000	0.94253	CGG		0.577	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		T	132016192	C	T	132016192	3	4	121	1	0	0	0	0	1	0	0	0	10730	643	23	1	276	1	NTM	11	132016192	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	5880894	132016192	2990324	172	31942										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7586046	7586046	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cggtgttgacattcccagagAgctgactcatttccataaca	8	11	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:7586046A>G	ENST00000313599.3	-	3	426	c.369T>C	c.(367-369)gcT>gcC	p.A123A	CD163L1_ENST00000396630.1_Silent_p.A123A|CD163L1_ENST00000416109.2_Silent_p.A123A			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	123	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.A123A(1)		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						ATTCCCAGAGAGCTGACTCAT	0.423																																																1	Substitution - coding silent(1)	ovary(1)	12											109	103	105					12																	7586046		2203	4300	6503	7477313	SO:0001819	synonymous_variant	283316			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.369T>C	12.37:g.7586046A>G			7477313	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																				0.423	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		G	7586046	A	G	7586046	2	3	121	1	0	0	0	0	0	0	0	1	2974	291	11	4		4	CD163L1	12	7586046	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10		7586046	126265849	173	31943										
LRP6	4040	hgsc.bcm.edu	37	chr12	12303771	12303771	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaaccaagctctcaattaccTggctgccatcttcttgtgcc	7	14	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:12303771T>C	ENST00000261349.4	-	13	3069	c.2993A>G	c.(2992-2994)cAg>cGg	p.Q998R	LRP6_ENST00000543091.1_Splice_Site_p.Q998R	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	998	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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 Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q998R(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CTCAATTACCTGGCTGCCATC	0.448																																																1	Substitution - Missense(1)	lung(1)	12											215	195	202					12																	12303771		2203	4300	6503	12195038	SO:0001630	splice_region_variant	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.2994+1A>G	12.37:g.12303771T>C			12195038	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.014912	0.75161	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91011	-2.77;-2.77	5.74	5.74	0.90152	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000017	D	0.88149	0.6359	L	0.52126	1.63	0.80722	D	1	B;B	0.26445	0.077;0.149	B;B	0.30495	0.042;0.116	D	0.84421	0.0571	10	0.16896	T	0.51	.	16.0257	0.80541	0.0:0.0:0.0:1.0	.	998;998	F5H7J9;O75581	.;LRP6_HUMAN	R	998	ENSP00000261349:Q998R;ENSP00000442472:Q998R	ENSP00000261349:Q998R	Q	-	2	0	LRP6	12195038	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.768000	0.62293	2.187000	0.69744	0.482000	0.46254	CAG		0.448	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		Missense_Mutation	C	12303771	T	C	12303771	5	2	121	1	0	0	0	0	0	0	1	0	8991	1594	55	4	1892	4	LRP6	12	12303771	Splice_Site	SNP	T	TCGA-G5-6235-01A-11D-1733-10	4717725	12303771	121548124	174	31944										
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14650919	14650919	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tggtagcaaatactactttgCagtacgagccaaggatattt	9	7	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:14650919C>A	ENST00000540793.1	+	14	3880	c.3725C>A	c.(3724-3726)gCa>gAa	p.A1242E	ATF7IP_ENST00000261168.4_Missense_Mutation_p.A1242E|ATF7IP_ENST00000544627.1_Missense_Mutation_p.A1250E|ATF7IP_ENST00000536444.1_Missense_Mutation_p.A1241E			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1242	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Interaction with MBD1.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						TACTACTTTGCAGTACGAGCC	0.468																																																0			12											151	142	145					12																	14650919		2203	4300	6503	14542186	SO:0001583	missense	55729			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3725C>A	12.37:g.14650919C>A	ENSP00000444589:p.Ala1242Glu		14542186	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048773	0.93740	.	.	ENSG00000171681	ENST00000261168;ENST00000536444;ENST00000544627;ENST00000540793	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	6.17	6.17	0.99709	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000006	T	0.57359	0.2048	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.54057	-0.8350	10	0.87932	D	0	-25.1396	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1241;1242	G3V1U0;Q6VMQ6	.;MCAF1_HUMAN	E	1242;1241;1250;1242	ENSP00000261168:A1242E;ENSP00000445955:A1241E;ENSP00000440440:A1250E;ENSP00000444589:A1242E	ENSP00000261168:A1242E	A	+	2	0	ATF7IP	14542186	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.813000	0.86123	2.941000	0.99782	0.655000	0.94253	GCA		0.468	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		A	14650919	C	A	14650919	3	1	121	1	0	0	0	0	1	0	0	0	1088	710	25	2	3779	2	ATF7IP	12	14650919	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	2347148	14650919	119200976	175	31945										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398281	25398281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcaaggcactcttgcctacgCcaccagctccaactaccaca	5	18	2	0	rs112445441		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:25398281C>T	ENST00000256078.4	-	2	101	c.38G>A	c.(37-39)gGc>gAc	p.G13D	KRAS_ENST00000556131.1_Missense_Mutation_p.G13D|KRAS_ENST00000557334.1_Missense_Mutation_p.G13D|KRAS_ENST00000311936.3_Missense_Mutation_p.G13D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	13			G -> D (in a breast carcinoma cell line and GASC; somatic mutation). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:3627975}.|G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway). {ECO:0000269|PubMed:16247081}.		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.G13D(3223)|p.G13V(33)|p.G13A(28)|p.G13E(3)|p.G13I(1)|p.G13N(1)|p.G13_V14>DI(1)|p.G13R(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)			CTTGCCTACGCCACCAGCTCC	0.338	G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT116_LARGE_INTESTINE)|G13D(HCT15_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(MDAMB231_BREAST)|G13D(NCIH647_LUNG)|G13D(NCIH747_LARGE_INTESTINE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(T84_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	3291	Substitution - Missense(3290)|Complex - compound substitution(1)	large_intestine(2808)|haematopoietic_and_lymphoid_tissue(94)|lung(92)|endometrium(54)|soft_tissue(38)|ovary(38)|stomach(32)|pancreas(30)|thyroid(27)|biliary_tract(21)|prostate(20)|breast(10)|cervix(4)|gastrointestinal_tract_(site_indeterminate)(3)|upper_aerodigestive_tract(3)|urinary_tract(3)|liver(3)|salivary_gland(3)|small_intestine(3)|oesophagus(2)|skin(1)|genital_tract(1)|bone(1)	12											88	78	82					12																	25398281		2203	4300	6503	25289548	SO:0001583	missense	3845	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	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.38G>A	12.37:g.25398281C>T	ENSP00000256078:p.Gly13Asp		25289548	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867862	0.91587	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.82803	-1.65;-0.7;-0.7;-0.7	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.93062	3.375	0.80722	D	1	B;P	0.43314	0.215;0.803	B;P	0.46172	0.175;0.506	D	0.92106	0.5692	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	13;13	P01116-2;P01116	.;RASK_HUMAN	D	13	ENSP00000308495:G13D;ENSP00000452512:G13D;ENSP00000256078:G13D;ENSP00000451856:G13D	ENSP00000256078:G13D	G	-	2	0	KRAS	25289548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGC		0.338	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398281	C	T	25398281	3	4	121	1	0	0	0	0	1	0	0	0	8459	739	26	3	668	3	KRAS	12	25398281	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	10747362	25398281	108453614	176	31946										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40692100	40692100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	taataaatttacatcatttcCttcttatttgttgaaaatga	3	5	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:40692100C>T	ENST00000298910.7	+	24	3210	c.3152C>T	c.(3151-3153)cCt>cTt	p.P1051L	LRRK2_ENST00000343742.2_Missense_Mutation_p.P1051L	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1051					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)				ACATCATTTCCTTCTTATTTG	0.343																																																0			12											127	125	126					12																	40692100		2203	4300	6503	38978367	SO:0001583	missense	120892			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.3152C>T	12.37:g.40692100C>T	ENSP00000298910:p.Pro1051Leu		38978367	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.680480	0.68042	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.35973	1.51;1.28	5.74	5.74	0.90152	.	0.116756	0.64402	D	0.000014	T	0.75102	0.3804	H	0.97051	3.93	0.80722	D	1	D;B	0.89917	1.0;0.372	D;B	0.85130	0.997;0.082	D	0.83551	0.0101	10	0.87932	D	0	.	19.9044	0.97001	0.0:1.0:0.0:0.0	.	1051;1051	E9PC85;Q5S007	.;LRRK2_HUMAN	L	1051	ENSP00000341930:P1051L;ENSP00000298910:P1051L	ENSP00000298910:P1051L	P	+	2	0	LRRK2	38978367	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.000000	0.76290	2.696000	0.92011	0.655000	0.94253	CCT		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40692100	C	T	40692100	3	4	121	1	0	0	0	0	1	0	0	0	9062	681	24	3	3246	3	LRRK2	12	40692100	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	15293819	40692100	93159795	177	31947										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43771221	43771221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atgcaaacagctgttaatgcAttggtaaacctgagaggaag	11	6	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:43771221A>G	ENST00000389420.3	-	32	4941	c.4942T>C	c.(4942-4944)Tgc>Cgc	p.C1648R		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1648	TSP type-1 14. {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)		CTGTTAATGCATTGGTAAACC	0.408																																																0			12											110	99	103					12																	43771221		2203	4300	6503	42057488	SO:0001583	missense	80070			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.4942T>C	12.37:g.43771221A>G	ENSP00000374071:p.Cys1648Arg		42057488	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	A	15.74	2.922278	0.52653	.	.	ENSG00000173157	ENST00000389420	T	0.59906	0.23	4.99	4.99	0.66335	.	0.000000	0.56097	D	0.000025	T	0.74253	0.3692	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72769	-0.4193	10	0.28530	T	0.3	.	15.3961	0.74794	1.0:0.0:0.0:0.0	.	1648	P59510	ATS20_HUMAN	R	1648	ENSP00000374071:C1648R	ENSP00000374071:C1648R	C	-	1	0	ADAMTS20	42057488	1.000000	0.71417	1.000000	0.80357	0.403000	0.30841	6.539000	0.73856	2.187000	0.69744	0.533000	0.62120	TGC		0.408	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43771221	A	G	43771221	3	3	121	1	0	0	0	0	1	0	0	0	266	217	8	4	821	4	ADAMTS20	12	43771221	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	3079121	43771221	90080674	178	31948										
HDAC7	51564	hgsc.bcm.edu	37	chr12	48189107	48189107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaggcctgacccagagagccGctcggtggtcattaaggact	14	11	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:48189107G>A	ENST00000427332.2	-	11	1183	c.1027C>T	c.(1027-1029)Cgg>Tgg	p.R343W	HDAC7_ENST00000354334.3_Missense_Mutation_p.R345W|HDAC7_ENST00000552960.1_Missense_Mutation_p.R365W|HDAC7_ENST00000380610.4_Missense_Mutation_p.R399W|HDAC7_ENST00000080059.7_Missense_Mutation_p.R382W			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	343	Transcription repression 2. {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)		CCAGAGAGCCGCTCGGTGGTC	0.677																																																0			12											13	17	16					12																	48189107		2196	4280	6476	46475374	SO:0001583	missense	51564			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.1027C>T	12.37:g.48189107G>A	ENSP00000404394:p.Arg343Trp		46475374	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		.	.	.	.	.	.	.	.	.	.	G	20.1	3.938622	0.73557	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.68624	-0.25;-0.13;-0.24;-0.32;-0.34	4.51	3.62	0.41486	.	0.684461	0.14498	N	0.315902	T	0.73853	0.3640	M	0.65975	2.015	0.40242	D	0.977972	D;D;D	0.61697	0.99;0.99;0.99	P;P;P	0.53224	0.721;0.721;0.721	T	0.77153	-0.2692	10	0.87932	D	0	.	13.1009	0.59219	0.0:0.0:0.8383:0.1617	.	382;365;345	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	W	382;345;365;399;343	ENSP00000080059:R382W;ENSP00000351326:R345W;ENSP00000448532:R365W;ENSP00000369984:R399W;ENSP00000404394:R343W	ENSP00000080059:R382W	R	-	1	2	HDAC7	46475374	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	3.696000	0.54757	1.246000	0.43901	-0.268000	0.10319	CGG		0.677	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			A	48189107	G	A	48189107	3	1	121	1	0	0	0	0	1	0	0	0	7033	1086	38	1	1895	1	HDAC7	12	48189107	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	4417886	48189107	85662788	179	31949										
MLL2	8085	hgsc.bcm.edu	37	chr12	49416545	49416545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tccattcggtgcgcagccgcCggtactgagatgacttggag	14	11	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:49416545C>T	ENST00000301067.7	-	51	16165	c.16166G>A	c.(16165-16167)cGg>cAg	p.R5389Q		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5389					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)										GCGCAGCCGCCGGTACTGAGA	0.557																																																0			12											104	116	112					12																	49416545		2086	4220	6306	47702812	SO:0001583	missense	9757			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.16166G>A	12.37:g.49416545C>T	ENSP00000301067:p.Arg5389Gln		47702812	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.433569	0.62955	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	D;D	0.86497	-2.13;-2.13	5.09	5.09	0.68999	.	0.000000	0.32640	N	0.005833	D	0.91365	0.7276	L	0.45581	1.43	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.92209	0.5774	10	0.87932	D	0	.	17.6392	0.88130	0.0:1.0:0.0:0.0	.	5389	O14686	MLL2_HUMAN	Q	5389;70	ENSP00000301067:R5389Q;ENSP00000435714:R70Q	ENSP00000301067:R5389Q	R	-	2	0	MLL2	47702812	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.734000	0.84928	2.546000	0.85860	0.591000	0.81541	CGG		0.557	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49416545	C	T	49416545	3	4	121	1	0	0	0	0	1	0	0	0	9651	652	23	1	463	1	MLL2	12	49416545	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1227438	49416545	84435350	180	31950										
DIP2B	57609	hgsc.bcm.edu	37	chr12	51069160	51069160	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaaaatccagcagcttctgaAcactctgaaacgacccaaaa	5	12	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:51069160A>T	ENST00000301180.5	+	7	879	c.845A>T	c.(844-846)aAc>aTc	p.N282I		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	282						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						CAGCTTCTGAACACTCTGAAA	0.348																																																0			12											89	92	91					12																	51069160		2203	4300	6503	49355427	SO:0001583	missense	57609			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.845A>T	12.37:g.51069160A>T	ENSP00000301180:p.Asn282Ile		49355427	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.580547	0.86645	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.45276	0.9	5.03	5.03	0.67393	.	0.040269	0.85682	D	0.000000	T	0.65933	0.2739	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69045	-0.5249	10	0.48119	T	0.1	-18.4275	14.9228	0.70854	1.0:0.0:0.0:0.0	.	282;292	Q9P265;E9PHD6	DIP2B_HUMAN;.	I	292;282	ENSP00000301180:N282I	ENSP00000301180:N282I	N	+	2	0	DIP2B	49355427	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.083000	0.71326	2.106000	0.64143	0.460000	0.39030	AAC		0.348	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		T	51069160	A	T	51069160	3	4	121	1	0	0	0	0	1	0	0	0	4539	43	2	5	871	5	DIP2B	12	51069160	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	1652615	51069160	82782735	181	31951										
CSAD	51380	hgsc.bcm.edu	37	chr12	53552447	53552447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggagccctccttcaccatgcGctccttgagcacgggggcca	12	16	1	1	rs374597733		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:53552447G>A	ENST00000444623.1	-	17	1597	c.1330C>T	c.(1330-1332)Cgc>Tgc	p.R444C	CSAD_ENST00000379846.1_Missense_Mutation_p.R297C|CSAD_ENST00000267085.4_Missense_Mutation_p.R471C|CSAD_ENST00000379843.3_Missense_Mutation_p.R297C|CSAD_ENST00000453446.2_Missense_Mutation_p.R444C|RP11-1136G11.8_ENST00000550908.1_lincRNA	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	444					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)	p.R444C(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	TTCACCATGCGCTCCTTGAGC	0.622													G|||	1	0.000199681	0	0.0014	5008	,	,		18748	0		0	False		,,,				2504	0				Ovarian(109;252 1546 16882 28524 44645)											1	Substitution - Missense(1)	large_intestine(1)	12											53	41	45					12																	53552447		2203	4300	6503	51838714	SO:0001583	missense	51380			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.1330C>T	12.37:g.53552447G>A	ENSP00000415485:p.Arg444Cys		51838714	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	37	CCDS58235.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	4.004875|4.004875	0.74932|0.74932	.|.	.|.	ENSG00000139631|ENSG00000139631	ENST00000379850|ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	.|T;T;T;T;T	.|0.42131	.|0.98;0.98;0.98;0.98;0.98	4.49|4.49	4.49|4.49	0.54785|0.54785	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65080|0.65080	0.2657|0.2657	M|M	0.90759|0.90759	3.145|3.145	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.989;0.999	.|P;P;P	.|0.62491	.|0.89;0.779;0.903	T|T	0.71451|0.71451	-0.4589|-0.4589	5|10	.|0.72032	.|D	.|0.01	-15.5893|-15.5893	10.233|10.233	0.43266|0.43266	0.0:0.0:0.6914:0.3086|0.0:0.0:0.6914:0.3086	.|.	.|471;444;297	.|Q9Y600-3;Q9Y600;Q9Y600-2	.|.;CSAD_HUMAN;.	V|C	469|533;297;471;297;444;405;444	.|ENSP00000369172:R297C;ENSP00000267085:R471C;ENSP00000369175:R297C;ENSP00000415485:R444C;ENSP00000410648:R444C	.|ENSP00000267085:R471C	A|R	-|-	2|1	0|0	CSAD|CSAD	51838714|51838714	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.936000|0.936000	0.57629|0.57629	2.630000|2.630000	0.46494|0.46494	2.505000|2.505000	0.84491|0.84491	0.442000|0.442000	0.29010|0.29010	GCG|CGC		0.622	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		A	53552447	G	A	53552447	3	1	121	1	0	0	0	0	1	0	0	0	3931	1087	38	1	155	1	CSAD	12	53552447	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	2483287	53552447	80299448	182	31952										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	82147821	82147821	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atgacatcctgaagtctttgCtgggcaagtgagaggctttc	12	8	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr12:82147821C>T	ENST00000549396.1	-	3	340	c.180G>A	c.(178-180)caG>caA	p.Q60Q	PPFIA2_ENST00000549325.1_Silent_p.Q60Q|PPFIA2_ENST00000552948.1_Silent_p.Q60Q|PPFIA2_ENST00000333447.7_Silent_p.Q60Q|PPFIA2_ENST00000550584.2_Silent_p.Q60Q|PPFIA2_ENST00000548586.1_Silent_p.Q60Q	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	60					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						GAAGTCTTTGCTGGGCAAGTG	0.502																																																0			12											61	64	63					12																	82147821		1951	4144	6095	80671952	SO:0001819	synonymous_variant	8499			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.180G>A	12.37:g.82147821C>T			80671952	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1																																																																																				0.502	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	82147821	C	T	82147821	2	4	121	1	0	0	0	0	0	0	0	1	12341	796	28	3		3	PPFIA2	12	82147821	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	28595374	82147821	51704074	183	31953										
PAN3	255967	hgsc.bcm.edu	37	chr13	28851445	28851445	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tctttggcaggaattcagcgAgagaatttacagaaagccat	10	7	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:28851445A>G	ENST00000380958.3	+	15	2273	c.2121A>G	c.(2119-2121)cgA>cgG	p.R707R	PAN3_ENST00000282391.5_Silent_p.R395R|PAN3_ENST00000399613.1_Silent_p.R507R	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)		GAATTCAGCGAGAGAATTTAC	0.343																																																0			13											112	115	114					13																	28851445		2203	4300	6503	27749445	SO:0001819	synonymous_variant	255967			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.2121A>G	13.37:g.28851445A>G			27749445		Silent	SNP	ENST00000380958.3	37	CCDS9329.2																																																																																				0.343	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		G	28851445	A	G	28851445	2	3	121	1	0	0	0	0	0	0	0	1	11446	291	11	4		4	PAN3	13	28851445	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10		28851445	86318433	184	31954										
C13orf26	122046	hgsc.bcm.edu	37	chr13	31540436	31540436	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aacctccagacactgaattcCgaaggaattaccaaattcca	5	12	0	2	rs193234818	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:31540436C>T	ENST00000380473.3	+	5	560	c.547C>T	c.(547-549)Cga>Tga	p.R183*	TEX26_ENST00000530916.1_Intron	NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26	183								p.R183*(2)									CACTGAATTCCGAAGGAATTA	0.423													C|||	3	0.000599042	0	0.0014	5008	,	,		17160	0		0	False		,,,				2504	0.002															2	Substitution - Nonsense(2)	ovary(1)|lung(1)	13											80	77	78					13																	31540436		2203	4300	6503	30438436	SO:0001587	stop_gained	122046			BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 26"	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.547C>T	13.37:g.31540436C>T	ENSP00000369840:p.Arg183*		30438436		Nonsense_Mutation	SNP	ENST00000380473.3	37	CCDS9339.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	25.2	4.615390	0.87359	.	.	ENSG00000175664	ENST00000380473	.	.	.	5.41	3.58	0.41010	.	0.100459	0.42821	D	0.000658	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.9032	7.5701	0.27902	0.1625:0.7485:0.0:0.089	.	.	.	.	X	183	.	ENSP00000369840:R183X	R	+	1	2	C13orf26	30438436	1.000000	0.71417	0.988000	0.46212	0.709000	0.40893	1.359000	0.34113	1.410000	0.46936	0.650000	0.86243	CGA		0.423	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325		T	31540436	C	T	31540436	4	4	121	1	0	0	0	0	0	1	0	0	1726	644	23	1	565	1	C13orf26	13	31540436	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	2688991	31540436	83629442	185	31955										
SMAD9	4093	hgsc.bcm.edu	37	chr13	37453599	37453599	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgggacacctgcagccgcccGtccagggagcggggaatcgt	16	13	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:37453599G>A	ENST00000399275.2	-	1	367	c.228C>T	c.(226-228)gaC>gaT	p.D76D	SMAD9_ENST00000379826.4_Silent_p.D76D|SMAD9_ENST00000483941.1_5'UTR|SMAD9_ENST00000350148.5_Silent_p.D76D			O15198	SMAD9_HUMAN	SMAD family member 9	76	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		GCAGCCGCCCGTCCAGGGAGC	0.642																																																0			13											43	47	46					13																	37453599		2203	4300	6503	36351599	SO:0001819	synonymous_variant	4093				CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"SMADs"	6774	protein-coding gene	gene with protein product		603295	"MAD, mothers against decapentaplegic homolog 9 (Drosophila)", "SMAD, mothers against DPP homolog 9 (Drosophila)"	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.228C>T	13.37:g.37453599G>A			36351599	A2A2Y6|O14989|Q5TBA1	Silent	SNP	ENST00000399275.2	37	CCDS45032.1																																																																																				0.642	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		A	37453599	G	A	37453599	2	1	121	1	0	0	0	0	0	0	0	1	14801	1136	40	1		1	SMAD9	13	37453599	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	5913163	37453599	77716279	186	31956										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37679002	37679002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	taatgtctcggtgtagaaaaTtctttgtatgcacgtattca	8	6	3	1	rs375626846		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:37679002T>C	ENST00000379800.3	-	1	801	c.392A>G	c.(391-393)aAt>aGt	p.N131S		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	131	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)		GTGTAGAAAATTCTTTGTATG	0.383																																																0			13						T	SER/ASN	0,4406		0,0,2203	190	174	179		392	-0.3	0	13		179	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSNK1A1L	NM_145203.5	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	131/338	37679002	1,13005	2203	4300	6503	36577002	SO:0001583	missense	122011			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.392A>G	13.37:g.37679002T>C	ENSP00000369126:p.Asn131Ser		36577002	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	T	1.081	-0.666946	0.03428	0.0	1.16E-4	ENSG00000180138	ENST00000379800	T	0.21361	2.01	1.01	-0.268	0.12934	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.048510	0.85682	N	0.000000	T	0.10165	0.0249	N	0.25485	0.75	0.31767	N	0.632625	B	0.23249	0.082	B	0.22152	0.038	T	0.27872	-1.0061	10	0.15066	T	0.55	.	4.4455	0.11595	0.0:0.2201:0.0:0.7799	.	131	Q8N752	KC1AL_HUMAN	S	131	ENSP00000369126:N131S	ENSP00000369126:N131S	N	-	2	0	CSNK1A1L	36577002	1.000000	0.71417	0.005000	0.12908	0.399000	0.30720	3.932000	0.56537	-0.111000	0.12001	-0.411000	0.06167	AAT		0.383	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		C	37679002	T	C	37679002	3	2	121	1	0	0	0	0	1	0	0	0	3957	1493	52	4	625	4	CSNK1A1L	13	37679002	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	225403	37679002	77490876	187	31957										
FREM2	341640	hgsc.bcm.edu	37	chr13	39425912	39425912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttataagaattccagtgattCgccaaggagacacttcaaag	8	8	1	3	rs375661157		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:39425912C>T	ENST00000280481.7	+	11	7048	c.6832C>T	c.(6832-6834)Cgc>Tgc	p.R2278C		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2278	Calx-beta 5.				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)		TCCAGTGATTCGCCAAGGAGA	0.453																																																0			13						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	69	70	70		6832	5.6	1	13		70	0,8600		0,0,4300	no	missense	FREM2	NM_207361.4	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2278/3170	39425912	1,13005	2203	4300	6503	38323912	SO:0001583	missense	341640			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.6832C>T	13.37:g.39425912C>T	ENSP00000280481:p.Arg2278Cys		38323912	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182222	0.78677	2.27E-4	0.0	ENSG00000150893	ENST00000280481	T	0.43688	0.94	5.62	5.62	0.85841	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.73783	0.3631	M	0.91406	3.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.79685	-0.1700	10	0.87932	D	0	.	19.655	0.95832	0.0:1.0:0.0:0.0	.	2278;2278	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	C	2278	ENSP00000280481:R2278C	ENSP00000280481:R2278C	R	+	1	0	FREM2	38323912	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.761000	0.62243	2.650000	0.89964	0.650000	0.86243	CGC		0.453	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39425912	C	T	39425912	3	4	121	1	0	0	0	0	1	0	0	0	6064	884	31	1	6874	1	FREM2	13	39425912	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1746910	39425912	75743966	188	31958										
SPERT	220082	hgsc.bcm.edu	37	chr13	46288409	46288409	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agaagctggtcattgacaccGtgaccgaggtcaccgcgcgc	13	13	2	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:46288409G>A	ENST00000310521.1	+	3	1329	c.1249G>A	c.(1249-1251)Gtg>Atg	p.V417M	SPERT_ENST00000378966.3_Missense_Mutation_p.V381M	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	417						cytoplasmic membrane-bounded vesicle (GO:0016023)		p.V417M(1)		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)		CATTGACACCGTGACCGAGGT	0.612																																																1	Substitution - Missense(1)	large_intestine(1)	13											26	24	25					13																	46288409		2202	4300	6502	45186410	SO:0001583	missense	220082			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.1249G>A	13.37:g.46288409G>A	ENSP00000309189:p.Val417Met		45186410	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	37	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626994	0.66901	.	.	ENSG00000174015	ENST00000310521;ENST00000378966	T;T	0.57107	0.43;0.42	5.17	5.17	0.71159	.	0.000000	0.50627	D	0.000119	T	0.54013	0.1832	N	0.08118	0	0.32204	N	0.577393	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.65191	-0.6228	10	0.72032	D	0.01	.	15.512	0.75789	0.0:0.0:1.0:0.0	.	381;417	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	M	417;381	ENSP00000309189:V417M;ENSP00000368249:V381M	ENSP00000309189:V417M	V	+	1	0	SPERT	45186410	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.530000	0.45641	2.680000	0.91292	0.609000	0.83330	GTG		0.612	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		A	46288409	G	A	46288409	3	1	121	1	0	0	0	0	1	0	0	0	15078	1145	40	1	1259	1	SPERT	13	46288409	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6862497	46288409	68881469	189	31959										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61986437	61986437	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtacttttctttctcttctcGgtccagctgagtagaaactg	8	10	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:61986437G>A	ENST00000409186.1	-	5	3900	c.1795C>T	c.(1795-1797)Cga>Tga	p.R599*	PCDH20_ENST00000409204.4_Nonsense_Mutation_p.R599*			Q8N6Y1	PCD20_HUMAN	protocadherin 20	599	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)|poly(A) RNA binding (GO:0044822)	p.R572R(1)		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)		TTCTCTTCTCGGTCCAGCTGA	0.463																																																1	Substitution - coding silent(1)	ovary(1)	13											112	110	110					13																	61986437		2203	4300	6503	60884438	SO:0001587	stop_gained	64881			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.1795C>T	13.37:g.61986437G>A	ENSP00000386653:p.Arg599*		60884438	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Nonsense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	G	40	8.030738	0.98619	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	.	.	.	5.94	3.84	0.44239	.	0.000000	0.56097	D	0.000034	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6506	0.62308	0.0:0.0:0.5205:0.4795	.	.	.	.	X	599;599;345	.	ENSP00000351500:R345X	R	-	1	2	PCDH20	60884438	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.222000	0.51223	1.295000	0.44724	0.557000	0.71058	CGA		0.463	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		A	61986437	G	A	61986437	4	1	121	1	0	0	0	0	0	1	0	0	11546	1124	39	1	1064	1	PCDH20	13	61986437	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	15698028	61986437	53183441	190	31960										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67799663	67799663	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	caacccccaacaaaggtgttGtccaaagggagttcctgaat	9	11	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr13:67799663G>A	ENST00000377865.2	-	1	3044	c.2910C>T	c.(2908-2910)gaC>gaT	p.D970D	PCDH9_ENST00000377861.3_Silent_p.D970D|PCDH9_ENST00000328454.5_Silent_p.D970D|PCDH9_ENST00000456367.1_Silent_p.D970D|PCDH9_ENST00000544246.1_Silent_p.D970D			Q9HC56	PCDH9_HUMAN	protocadherin 9	970					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)	p.D970E(1)		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)		CAAAGGTGTTGTCCAAAGGGA	0.483																																																1	Substitution - Missense(1)	ovary(1)	13											145	142	143					13																	67799663		2203	4300	6503	66697664	SO:0001819	synonymous_variant	5101			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.2910C>T	13.37:g.67799663G>A			66697664	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																				0.483	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	67799663	G	A	67799663	2	1	121	1	0	0	0	0	0	0	0	1	11549	1368	48	3		3	PCDH9	13	67799663	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	5813226	67799663	47370215	191	31961										
OR11H12	440153	hgsc.bcm.edu	37	chr14	19377700	19377700	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccaaggtttcacttgtgagtGgacaattcagatcttcctct	8	10	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:19377700G>T	ENST00000550708.1	+	1	179	c.107G>T	c.(106-108)tGg>tTg	p.W36L		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W36*(1)		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)		ACTTGTGAGTGGACAATTCAG	0.433																																																1	Substitution - Nonsense(1)	ovary(1)	14											67	68	68					14																	19377700		2199	4296	6495	18447700	SO:0001583	missense	440153				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.107G>T	14.37:g.19377700G>T	ENSP00000449002:p.Trp36Leu		18447700		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	g	2.826	-0.243683	0.05906	.	.	ENSG00000257115	ENST00000550708	T	0.00892	5.57	.	.	.	.	0.431515	0.17171	U	0.184292	T	0.00754	0.0025	L	0.35288	1.05	0.26066	N	0.981283	B	0.06786	0.001	B	0.09377	0.004	T	0.33471	-0.9867	8	0.09084	T	0.74	.	6.4784	0.22049	2.0E-4:0.0:0.9998:0.0	.	36	B2RN74	O11HC_HUMAN	L	36	ENSP00000449002:W36L	ENSP00000449002:W36L	W	+	2	0	CR383656.1	18447700	0.000000	0.05858	0.593000	0.28771	0.151000	0.21798	-2.602000	0.00891	0.413000	0.25759	0.064000	0.15345	TGG		0.433	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354		T	19377700	G	T	19377700	3	4	121	1	0	0	0	0	1	0	0	0	10958	1357	47	2	109	2	OR11H12	14	19377700	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10		19377700	87971840	192	31962										
OR4N5	390437	hgsc.bcm.edu	37	chr14	20612745	20612745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	catctttcctttgatgaaccCtgttatttatacgcttcgca	5	11	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:20612745C>T	ENST00000333629.1	+	1	851	c.851C>T	c.(850-852)cCt>cTt	p.P284L	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P284H(1)		endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		TTGATGAACCCTGTTATTTAT	0.408																																																1	Substitution - Missense(1)	ovary(1)	14											117	117	117					14																	20612745		2203	4300	6503	19682585	SO:0001583	missense	390437				CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.851C>T	14.37:g.20612745C>T	ENSP00000332110:p.Pro284Leu		19682585	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	37	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550088	0.65311	.	.	ENSG00000184394	ENST00000333629	T	0.63417	-0.04	4.0	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	D	0.000563	D	0.83677	0.5306	H	0.94658	3.565	0.49915	D	0.999838	D	0.89917	1.0	D	0.91635	0.999	D	0.88383	0.3003	10	0.87932	D	0	.	13.9851	0.64328	0.0:1.0:0.0:0.0	.	284	Q8IXE1	OR4N5_HUMAN	L	284	ENSP00000332110:P284L	ENSP00000332110:P284L	P	+	2	0	OR4N5	19682585	0.975000	0.34042	1.000000	0.80357	0.959000	0.62525	4.159000	0.58157	2.219000	0.72066	0.655000	0.94253	CCT		0.408	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			T	20612745	C	T	20612745	3	4	121	1	0	0	0	0	1	0	0	0	11110	681	24	3	853	3	OR4N5	14	20612745	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1235045	20612745	86736795	193	31963										
RNASE13	440163	hgsc.bcm.edu	37	chr14	21502341	21502341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	taaccctgggatagtcaatgCttaaggtatagaagttcctg	10	7	1	1	rs549619794		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:21502341C>T	ENST00000382951.3	-	2	244	c.107G>A	c.(106-108)aGc>aAc	p.S36N	NDRG2_ENST00000403829.3_Intron	NM_001012264.3	NP_001012264.1	Q5GAN3	RNS13_HUMAN	ribonuclease, RNase A family, 13 (non-active)	36						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|lung(5)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	12	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.019)		ATAGTCAATGCTTAAGGTATA	0.493													C|||	1	0.000199681	0	0	5008	,	,		19579	0		0	False		,,,				2504	0.001															0			14											102	93	96					14																	21502341		2203	4300	6503	20572181	SO:0001583	missense	440163			AY665808	CCDS32039.1	14q11.1	2011-02-10			ENSG00000206150	ENSG00000206150		"Ribonucleases, RNase A"	25285	protein-coding gene	gene with protein product							Standard	NM_001012264		Approved		uc001vzj.3	Q5GAN3		ENST00000382951.3:c.107G>A	14.37:g.21502341C>T	ENSP00000372410:p.Ser36Asn		20572181		Missense_Mutation	SNP	ENST00000382951.3	37	CCDS32039.1	.	.	.	.	.	.	.	.	.	.	C	7.965	0.747868	0.15710	.	.	ENSG00000206150	ENST00000382951	T	0.72725	-0.68	5.05	2.59	0.31030	Ribonuclease A, domain (2);	1.282440	0.05333	N	0.528613	T	0.45074	0.1324	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	10	0.38643	T	0.18	-7.3868	4.6503	0.12592	0.1669:0.0923:0.0:0.7408	.	36	Q5GAN3	RNS13_HUMAN	N	36	ENSP00000372410:S36N	ENSP00000372410:S36N	S	-	2	0	RNASE13	20572181	0.014000	0.17966	0.000000	0.03702	0.001000	0.01503	0.882000	0.28186	0.341000	0.23771	-0.300000	0.09419	AGC		0.493	RNASE13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411744.1			T	21502341	C	T	21502341	3	4	121	1	0	0	0	0	1	0	0	0	13440	797	28	3	367	3	RNASE13	14	21502341	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	889596	21502341	85847199	194	31964										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30046614	30046614	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttcatgggtgatgtagcgctCcccgattttgcattccagct	10	11	1	1	rs368061812		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:30046614C>A	ENST00000331968.5	-	18	2798	c.2569G>T	c.(2569-2571)Gag>Tag	p.E857*	PRKD1_ENST00000415220.2_Nonsense_Mutation_p.E865*	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	857			E -> K (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.E857K(1)		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)		ATGTAGCGCTCCCCGATTTTG	0.468																																																1	Substitution - Missense(1)	large_intestine(1)	14											131	118	123					14																	30046614		2203	4300	6503	29116365	SO:0001587	stop_gained	5587				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.2569G>T	14.37:g.30046614C>A	ENSP00000333568:p.Glu857*		29116365	A6NL64|B2RAF6	Nonsense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	C	40	8.034123	0.98621	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-29.324	20.5568	0.99304	0.0:1.0:0.0:0.0	.	.	.	.	X	857;865	.	ENSP00000333568:E857X	E	-	1	0	PRKD1	29116365	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	GAG		0.468	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30046614	C	A	30046614	4	1	121	1	0	0	0	0	0	1	0	0	12552	864	30	2	173	2	PRKD1	14	30046614	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	8544273	30046614	77302926	195	31965										
NPAS3	64067	hgsc.bcm.edu	37	chr14	33684439	33684439	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gatgctgctcgctcccgccgGggaaaagaaaactttgagtt	12	10	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:33684439G>T	ENST00000356141.4	+	3	192	c.192G>T	c.(190-192)cgG>cgT	p.R64R	NPAS3_ENST00000547068.1_5'UTR|NPAS3_ENST00000346562.2_Silent_p.R34R|NPAS3_ENST00000548645.1_Silent_p.R34R|NPAS3_ENST00000551008.1_5'UTR|NPAS3_ENST00000357798.5_Silent_p.R34R|NPAS3_ENST00000551492.1_Silent_p.R71R|NPAS3_ENST00000341321.4_Silent_p.R64R			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	64	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)	p.R34R(2)|p.R64R(1)		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)		GCTCCCGCCGGGGAAAAGAAA	0.458																																																3	Substitution - coding silent(3)	lung(3)	14											68	73	72					14																	33684439		2203	4300	6503	32754190	SO:0001819	synonymous_variant	64067			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.192G>T	14.37:g.33684439G>T			32754190	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	37	CCDS53891.1																																																																																				0.458	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			T	33684439	G	T	33684439	2	4	121	1	0	0	0	0	0	0	0	1	10595	1219	43	2		2	NPAS3	14	33684439	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	3637825	33684439	73665101	196	31966										
MDGA2	161357	hgsc.bcm.edu	37	chr14	47530617	47530617	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agtctgtgtaatgaccatccGctcagaacttcttaatggac	8	10	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:47530617G>T	ENST00000399232.2	-	7	1517	c.1153C>A	c.(1153-1155)Cgg>Agg	p.R385R	MDGA2_ENST00000357362.3_Silent_p.R156R|MDGA2_ENST00000426342.1_Silent_p.R156R|MDGA2_ENST00000439988.3_Silent_p.R454R	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	385	Ig-like 4.				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						ATGACCATCCGCTCAGAACTT	0.418																																																0			14											155	140	145					14																	47530617		1895	4112	6007	46600367	SO:0001819	synonymous_variant	161357			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.1153C>A	14.37:g.47530617G>T			46600367	F6W3S7|J3KPX6	Silent	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	G	8.092	0.774805	0.16051	.	.	ENSG00000139915	ENST00000554762	.	.	.	5.64	1.35	0.21983	.	.	.	.	.	T	0.68348	0.2991	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66571	-0.5890	4	.	.	.	.	14.7054	0.69186	0.0:0.0:0.2732:0.7268	.	.	.	.	E	159	.	.	A	-	2	0	MDGA2	46600367	0.999000	0.42202	0.996000	0.52242	0.995000	0.86356	1.688000	0.37690	0.261000	0.21753	-0.274000	0.10170	GCG		0.418	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47530617	G	T	47530617	2	4	121	1	0	0	0	0	0	0	0	1	9437	1086	38	2		2	MDGA2	14	47530617	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	13846178	47530617	59818923	197	31967										
DAAM1	23002	hgsc.bcm.edu	37	chr14	59821990	59821990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ataaaggtcaaagagggaatGcatatggattcaagatatct	10	4	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr14:59821990G>A	ENST00000395125.1	+	20	2517	c.2494G>A	c.(2494-2496)Gca>Aca	p.A832T	DAAM1_ENST00000360909.3_Missense_Mutation_p.A822T|DAAM1_ENST00000351081.1_Missense_Mutation_p.A832T|DAAM1_ENST00000553966.1_3'UTR	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	832	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AAGAGGGAATGCATATGGATT	0.433																																																0			14											148	137	140					14																	59821990		2203	4300	6503	58891743	SO:0001583	missense	23002			AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2494G>A	14.37:g.59821990G>A	ENSP00000378557:p.Ala832Thr		58891743	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	37	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	G	36	5.644441	0.96704	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125	T;T;T	0.36157	1.27;1.27;1.27	5.81	5.81	0.92471	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.092055	0.85682	D	0.000000	T	0.65144	0.2663	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.62539	-0.6833	10	0.44086	T	0.13	.	20.4375	0.99097	0.0:0.0:1.0:0.0	.	822;832	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	T	822;832;801;832	ENSP00000354162:A822T;ENSP00000247170:A832T;ENSP00000378557:A832T	ENSP00000247170:A832T	A	+	1	0	DAAM1	58891743	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.813000	0.99286	2.906000	0.99361	0.655000	0.94253	GCA		0.433	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59821990	G	A	59821990	3	1	121	1	0	0	0	0	1	0	0	0	4221	1319	46	3	2572	3	DAAM1	14	59821990	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	12291373	59821990	47527550	198	31968										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49284715	49284715	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	caattctactattgagctgcActtctacagatatgggttca	7	9	3	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr15:49284715A>G	ENST00000559471.1	-	18	3295	c.3032T>C	c.(3031-3033)gTg>gCg	p.V1011A	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.V966A	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	1011							poly(A) RNA binding (GO:0044822)	p.V966E(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						ATTGAGCTGCACTTCTACAGA	0.443																																																1	Substitution - Missense(1)	breast(1)	15											85	83	83					15																	49284715		2197	4295	6492	47072007	SO:0001583	missense	9728			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.3032T>C	15.37:g.49284715A>G	ENSP00000453854:p.Val1011Ala		47072007	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	A	18.78	3.696571	0.68386	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.73897	-0.79	5.19	5.19	0.71726	.	0.153691	0.45867	D	0.000329	T	0.75627	0.3875	N	0.24115	0.695	0.39308	D	0.965024	P;D	0.61697	0.824;0.99	B;D	0.73380	0.239;0.98	T	0.73322	-0.4019	10	0.21540	T	0.41	.	13.7729	0.63036	1.0:0.0:0.0:0.0	.	1011;966	Q93073;Q93073-2	SBP2L_HUMAN;.	A	966;1011	ENSP00000261847:V966A	ENSP00000261847:V966A	V	-	2	0	SECISBP2L	47072007	1.000000	0.71417	0.953000	0.39169	0.961000	0.63080	7.759000	0.85235	2.183000	0.69458	0.533000	0.62120	GTG		0.443	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		G	49284715	A	G	49284715	3	3	121	1	0	0	0	0	1	0	0	0	14044	159	6	4	277	4	SECISBP2L	15	49284715	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10		49284715	53246677	199	31969										
MNS1	55329	hgsc.bcm.edu	37	chr15	56721366	56721366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	actcttcaccaagcagatcaAtatcatcctcttttttaaat	2	11	5	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr15:56721366A>G	ENST00000260453.3	-	10	1585	c.1421T>C	c.(1420-1422)aTt>aCt	p.I474T	MNS1_ENST00000566386.1_5'UTR|TEX9_ENST00000537232.1_Intron|TEX9_ENST00000352903.2_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	474					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.I474T(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)		AAGCAGATCAATATCATCCTC	0.313																																																1	Substitution - Missense(1)	ovary(1)	15											96	91	93					15																	56721366		2191	4285	6476	54508658	SO:0001583	missense	55329			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.1421T>C	15.37:g.56721366A>G	ENSP00000260453:p.Ile474Thr		54508658	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	A	15.76	2.929003	0.52759	.	.	ENSG00000138587	ENST00000260453	T	0.14640	2.49	6.08	6.08	0.98989	.	0.672261	0.15854	N	0.241362	T	0.14570	0.0352	L	0.44542	1.39	0.32864	D	0.508349	B	0.32245	0.361	B	0.25140	0.058	T	0.09037	-1.0693	10	0.59425	D	0.04	-1.9293	15.8323	0.78764	1.0:0.0:0.0:0.0	.	474	Q8NEH6	MNS1_HUMAN	T	474	ENSP00000260453:I474T	ENSP00000260453:I474T	I	-	2	0	MNS1	54508658	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	6.099000	0.71466	2.333000	0.79357	0.482000	0.46254	ATT		0.313	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		G	56721366	A	G	56721366	3	3	121	1	0	0	0	0	1	0	0	0	9707	101	4	4	70	4	MNS1	15	56721366	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	7436651	56721366	45810026	200	31970										
HEXA	3073	hgsc.bcm.edu	37	chr15	72638893	72638893	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aatgccaggggttccactatGtagaaatccttccagtcagg	10	10	1	1	rs587779406		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr15:72638893G>T	ENST00000268097.5	-	11	1808	c.1305C>A	c.(1303-1305)taC>taA	p.Y435*	RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|HEXA_ENST00000457859.2_Intron|HEXA_ENST00000566304.1_Nonsense_Mutation_p.Y446*|HEXA_ENST00000567159.1_Nonsense_Mutation_p.Y435*|HEXA_ENST00000429918.2_Nonsense_Mutation_p.Y262*	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)	435					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)	p.Y435Y(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	24						GTTCCACTATGTAGAAATCCT	0.572																																																1	Substitution - coding silent(1)	ovary(1)	15											101	109	107					15																	72638893		2199	4297	6496	70425947	SO:0001587	stop_gained	3073			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.1305C>A	15.37:g.72638893G>T	ENSP00000268097:p.Tyr435*		70425947	B4DKE7|E7ENH7|Q53HS8|Q6AI32	Nonsense_Mutation	SNP	ENST00000268097.5	37	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	G	38	6.762285	0.97821	.	.	ENSG00000213614	ENST00000268097;ENST00000429918	.	.	.	5.88	2.7	0.31948	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.1925	9.9799	0.41806	0.3062:0.0:0.6938:0.0	.	.	.	.	X	435;262	.	ENSP00000268097:Y435X	Y	-	3	2	HEXA	70425947	1.000000	0.71417	0.067000	0.19924	0.922000	0.55478	3.432000	0.52824	0.267000	0.21916	0.655000	0.94253	TAC		0.572	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	NM_000520		T	72638893	G	T	72638893	4	4	121	1	0	0	0	0	0	1	0	0	7094	1372	48	2	300	2	HEXA	15	72638893	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	15917527	72638893	29892499	201	31971										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88472472	88472472	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggacatgccgaagtccccaaTcttcactagcagattcgctc	8	14	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr15:88472472T>A	ENST00000360948.2	-	16	2244	c.2083A>T	c.(2083-2085)Att>Ttt	p.I695F	NTRK3_ENST00000557856.1_Missense_Mutation_p.I687F|NTRK3_ENST00000355254.2_Missense_Mutation_p.I695F|NTRK3_ENST00000394480.2_Missense_Mutation_p.I695F|NTRK3_ENST00000357724.2_Missense_Mutation_p.I687F|NTRK3_ENST00000558676.1_Missense_Mutation_p.I687F|NTRK3_ENST00000542733.2_Missense_Mutation_p.I597F	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	695	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.I695V(1)	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)			AAGTCCCCAATCTTCACTAGC	0.557			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																													Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	1	Substitution - Missense(1)	large_intestine(1)	15											111	102	105					15																	88472472		2201	4299	6500	86273476	SO:0001583	missense	4916			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.2083A>T	15.37:g.88472472T>A	ENSP00000354207:p.Ile695Phe		86273476	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.729113	0.89390	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733	D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04	5.16	5.16	0.70880	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	0.97380	0.9143	H	0.96943	3.91	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.97;0.999;0.97	D;D;D;D;D	0.87578	0.998;0.996;0.927;0.994;0.927	D	0.98591	1.0654	10	0.87932	D	0	.	14.1992	0.65690	0.0:0.0:0.0:1.0	.	597;687;687;695;695	B7Z7U4;E9PG56;B7Z4C5;Q16288-3;Q16288	.;.;.;.;NTRK3_HUMAN	F	695;695;687;695;597	ENSP00000377990:I695F;ENSP00000354207:I695F;ENSP00000350356:I687F;ENSP00000347397:I695F;ENSP00000437773:I597F	ENSP00000347397:I695F	I	-	1	0	NTRK3	86273476	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.853000	0.86934	1.952000	0.56665	0.533000	0.62120	ATT		0.557	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				A	88472472	T	A	88472472	3	1	121	1	0	0	0	0	1	0	0	0	10739	1435	50	5	452	5	NTRK3	15	88472472	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	15833579	88472472	14058920	202	31972										
TPSG1	8912	hgsc.bcm.edu	37	chr16	1272011	1272011	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agactcccggcctgttggggCggccgcagccctcaccccag	13	18	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr16:1272011C>T	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.R248H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						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)	CCTGTTGGGGCGGCCGCAGCC	0.667																																																0			16											25	35	32					16																	1272011		2191	4298	6489	1212012	SO:0001628	intergenic_variant	25823			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			16.37:g.1272011C>T			1212012	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	c	16.16	3.045512	0.55110	.	.	ENSG00000116176	ENST00000234798	D	0.89123	-2.47	4.28	-3.03	0.05429	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.90981	0.7164	M	0.65677	2.01	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.82293	-0.0529	9	0.52906	T	0.07	.	6.3073	0.21145	0.0:0.3286:0.1364:0.535	.	248	Q9NRR2	TRYG1_HUMAN	H	248	ENSP00000234798:R248H	ENSP00000234798:R248H	R	-	2	0	TPSG1	1212012	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.742000	0.00378	-0.533000	0.06323	-0.147000	0.13772	CGC		0.667	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1272011	C	T	1272011	1	4	121	0	1	0	0	0	0	0	0	0	16466	768	27	1		1	TPSG1	16	1272011	IGR	SNP	C	TCGA-G5-6235-01A-11D-1733-10		1272011	89082742	203	31973										
DCI	1632	hgsc.bcm.edu	37	chr16	2289989	2289989	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cagcccaatcgttagcctttTtcttctttgagcctctctaa	5	13	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr16:2289989T>G	ENST00000301729.4	-	7	947	c.900A>C	c.(898-900)gaA>gaC	p.E300D	ECI1_ENST00000570258.1_Missense_Mutation_p.E241D|RP11-304L19.11_ENST00000565709.1_RNA|ECI1_ENST00000562238.1_Missense_Mutation_p.E283D	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	300					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|intramolecular oxidoreductase activity (GO:0016860)			endometrium(1)|large_intestine(2)|lung(6)	9						GTTAGCCTTTTTCTTCTTTGA	0.512																																																0			16											106	104	105					16																	2289989		2198	4300	6498	2229990	SO:0001583	missense	1632				CCDS10464.1, CCDS58410.1	16p13.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000167969	ENSG00000167969	5.3.3.8		2703	protein-coding gene	gene with protein product	"3,2 trans-enoyl-CoA isomerase"	600305	"dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme A isomerase)", "dodecenoyl-CoA isomerase"	DCI		7829074	Standard	NM_001178029		Approved		uc002cpr.3	P42126	OTTHUMG00000128830	ENST00000301729.4:c.900A>C	16.37:g.2289989T>G	ENSP00000301729:p.Glu300Asp		2229990	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Missense_Mutation	SNP	ENST00000301729.4	37	CCDS10464.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.523723	0.44866	.	.	ENSG00000167969	ENST00000301729	T	0.63913	-0.07	4.9	-1.82	0.07857	.	0.546966	0.19645	N	0.109347	T	0.32704	0.0838	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.001;0.006	T	0.10222	-1.0639	10	0.51188	T	0.08	-11.8868	3.6218	0.08099	0.2793:0.3119:0.0:0.4088	.	283;300	P42126-2;P42126	.;ECI1_HUMAN	D	300	ENSP00000301729:E300D	ENSP00000301729:E300D	E	-	3	2	ECI1	2229990	0.017000	0.18338	0.000000	0.03702	0.125000	0.20455	-0.070000	0.11523	-0.384000	0.07845	-0.119000	0.15052	GAA		0.512	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1			G	2289989	T	G	2289989	3	3	121	1	0	0	0	0	1	0	0	0	4295	1838	64	4	12	4	DCI	16	2289989	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	1017978	2289989	88064764	204	31974										
USP7	7874	hgsc.bcm.edu	37	chr16	9024253	9024253	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggtgggtcatctgtatctccCgctttaaagaagaaaaagaa	10	7	3	3	rs62031302		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr16:9024253C>A	ENST00000344836.4	-	2	279	c.81G>T	c.(79-81)gcG>gcT	p.A27A	USP7_ENST00000566224.1_5'UTR|USP7_ENST00000535863.1_5'UTR|USP7_ENST00000381886.4_Splice_Site_p.A11A	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	27	Interaction with TSPYL5.				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						CTGTATCTCCCGCTTTAAAGA	0.403																																																0			16											106	81	89					16																	9024253		2197	4300	6497	8931754	SO:0001630	splice_region_variant	7874			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.80-1G>T	16.37:g.9024253C>A			8931754	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																				0.403	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		Silent	A	9024253	C	A	9024253	5	1	121	1	0	0	0	0	0	0	1	0	17128	666	23	2	3347	2	USP7	16	9024253	Splice_Site	SNP	C	TCGA-G5-6235-01A-11D-1733-10	6734264	9024253	81330500	205	31975										
CYLD	1540	hgsc.bcm.edu	37	chr16	50826584	50826584	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	taaaaaaatttttccttctcTggaattaaatataacagatt	3	5	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr16:50826584T>A	ENST00000427738.3	+	15	2523	c.2318T>A	c.(2317-2319)cTg>cAg	p.L773Q	RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000540145.1_Missense_Mutation_p.L773Q|CYLD_ENST00000398568.2_Missense_Mutation_p.L770Q|CYLD_ENST00000566206.1_Missense_Mutation_p.L770Q|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000568704.2_Missense_Mutation_p.L588Q|CYLD_ENST00000569418.1_Missense_Mutation_p.L770Q|CYLD_ENST00000311559.9_Missense_Mutation_p.L773Q|CYLD_ENST00000564326.1_Missense_Mutation_p.L770Q			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	773	USP.				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)				TTTCCTTCTCTGGAATTAAAT	0.274			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																													yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											36	32	34					16																	50826584		1769	4036	5805	49384085	SO:0001583	missense	1540	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.2318T>A	16.37:g.50826584T>A	ENSP00000392025:p.Leu773Gln		49384085	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	T	19.24	3.789019	0.70337	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.29917	1.55;1.55;1.55	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.39517	0.1081	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.17561	-1.0365	10	0.21014	T	0.42	-13.2987	15.6083	0.76692	0.0:0.0:0.0:1.0	.	770;770	A8KAB0;Q9NQC7-2	.;.	Q	773;773;770;770	ENSP00000445447:L773Q;ENSP00000308928:L773Q;ENSP00000381574:L770Q	ENSP00000308928:L773Q	L	+	2	0	CYLD	49384085	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.638000	0.83328	2.167000	0.68274	0.455000	0.32223	CTG		0.274	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			A	50826584	T	A	50826584	3	1	121	1	0	0	0	0	1	0	0	0	4149	1580	55	5	2372	5	CYLD	16	50826584	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	41802331	50826584	39528169	206	31976										
CDH1	999	hgsc.bcm.edu	37	chr16	68835630	68835630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctatttttccctcgacacccGattcaaagtgggcacagatg	8	12	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr16:68835630G>A	ENST00000261769.5	+	3	412	c.221G>A	c.(220-222)cGa>cAa	p.R74Q	CDH1_ENST00000422392.2_Missense_Mutation_p.R74Q|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	74					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.?(2)		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)		CTCGACACCCGATTCAAAGTG	0.468			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																													yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	2	Unknown(2)	breast(2)	16											192	174	180					16																	68835630		2198	4300	6498	67393131	SO:0001583	missense	51343	Familial Cancer Database	HDGC	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.221G>A	16.37:g.68835630G>A	ENSP00000261769:p.Arg74Gln		67393131	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.901183	0.72754	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.43688	0.94;0.94	5.43	3.47	0.39725	Cadherin prodomain-like (1);Cadherin-like (1);	0.214104	0.23710	N	0.045326	T	0.57770	0.2076	M	0.71581	2.175	0.37809	D	0.927992	D;D	0.71674	0.998;0.987	P;P	0.62560	0.904;0.603	T	0.63616	-0.6597	10	0.59425	D	0.04	.	11.0197	0.47711	0.1542:0.0:0.8458:0.0	.	74;74	Q9UII8;P12830	.;CADH1_HUMAN	Q	74	ENSP00000261769:R74Q;ENSP00000414946:R74Q	ENSP00000261769:R74Q	R	+	2	0	CDH1	67393131	0.805000	0.28982	0.994000	0.49952	0.884000	0.51177	1.645000	0.37238	0.774000	0.33427	0.561000	0.74099	CGA		0.468	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		A	68835630	G	A	68835630	3	1	121	1	0	0	0	0	1	0	0	0	3101	1058	37	1	231	1	CDH1	16	68835630	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	18009046	68835630	21519123	207	31977										
AP1G1	164	hgsc.bcm.edu	37	chr16	71808376	71808376	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aaaagtaagacttacttcttGatacagttggtcatgagaag	9	5	2	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr16:71808376G>T	ENST00000299980.4	-	3	762	c.321C>A	c.(319-321)atC>atA	p.I107I	AP1G1_ENST00000569748.1_Silent_p.I107I|AP1G1_ENST00000393512.3_Silent_p.I107I|AP1G1_ENST00000433195.2_Silent_p.I130I|AP1G1_ENST00000423132.2_Silent_p.I107I	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	107					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)				CTTACTTCTTGATACAGTTGG	0.378																																																0			16											143	140	141					16																	71808376		2198	4300	6498	70365877	SO:0001819	synonymous_variant	164			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.321C>A	16.37:g.71808376G>T			70365877	O75709|O75842|Q9UG09|Q9Y3U4	Silent	SNP	ENST00000299980.4	37	CCDS32480.1																																																																																				0.378	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			T	71808376	G	T	71808376	2	4	121	1	0	0	0	0	0	0	0	1	732	1280	45	2		2	AP1G1	16	71808376	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	2972746	71808376	18546377	208	31978										
TP53	7157	hgsc.bcm.edu	37	chr17	7577545	7577545	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaggatgggcctccggttcaTgccgcccatgcaggaactgt	14	12	1	0	rs483352695|rs397516437		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:7577545T>C	ENST00000269305.4	-	7	925	c.736A>G	c.(736-738)Atg>Gtg	p.M246V	TP53_ENST00000455263.2_Missense_Mutation_p.M246V|TP53_ENST00000359597.4_Missense_Mutation_p.M246V|TP53_ENST00000420246.2_Missense_Mutation_p.M246V|TP53_ENST00000445888.2_Missense_Mutation_p.M246V|TP53_ENST00000413465.2_Missense_Mutation_p.M246V|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	246	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		M -> I (in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (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.M246V(34)|p.0?(8)|p.?(5)|p.M246L(3)|p.G244_M246>V(3)|p.M246fs*1(2)|p.M153V(2)|p.M246_P250delMNRRP(2)|p.G151_M153>V(1)|p.G244fs*17(1)|p.C242fs*98(1)|p.G245fs*17(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*14(1)|p.G245fs*16(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)	CTCCGGTTCATGCCGCCCATG	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)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	67	Substitution - Missense(39)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)	liver(8)|haematopoietic_and_lymphoid_tissue(7)|large_intestine(6)|biliary_tract(6)|lung(6)|ovary(6)|breast(5)|stomach(4)|bone(4)|upper_aerodigestive_tract(3)|urinary_tract(3)|oesophagus(3)|soft_tissue(2)|central_nervous_system(2)|pancreas(2)	17	GRCh37	CM942294	TP53	M							152	113	126					17																	7577545		2203	4300	6503	7518270	SO:0001583	missense	7157	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.736A>G	17.37:g.7577545T>C	ENSP00000269305:p.Met246Val		7518270	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	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945888	0.73672	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99784	-6.74;-6.74;-6.74;-6.74;-6.74;-6.74;-6.74;-6.74	4.62	3.54	0.40534	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	0.99684	0.9881	M	0.87971	2.92	0.53005	D	0.999962	D;P;P;D;P;D	0.76494	0.993;0.889;0.832;0.994;0.931;0.999	D;P;B;D;D;D	0.80764	0.972;0.545;0.403;0.984;0.947;0.994	D	0.98572	1.0646	10	0.87932	D	0	-28.5667	8.419	0.32690	0.0:0.0941:0.0:0.9059	.	246;246;153;246;246;246	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	V	246;246;246;246;246;246;235;153;114;153	ENSP00000410739:M246V;ENSP00000352610:M246V;ENSP00000269305:M246V;ENSP00000398846:M246V;ENSP00000391127:M246V;ENSP00000391478:M246V;ENSP00000425104:M114V;ENSP00000423862:M153V	ENSP00000269305:M246V	M	-	1	0	TP53	7518270	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.824000	0.86668	0.914000	0.36822	0.379000	0.24179	ATG		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577545	T	C	7577545	3	2	121	1	0	0	0	0	1	0	0	0	16421	1464	51	4	554	4	TP53	17	7577545	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10		7577545	73617665	209	31979										
TP53	7157	hgsc.bcm.edu	37	chr17	7579536	7579536	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtcttcagtgaaccattgttCaatatcgtccggggacagca	10	10	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:7579536C>A	ENST00000269305.4	-	4	340	c.151G>T	c.(151-153)Gaa>Taa	p.E51*	TP53_ENST00000455263.2_Nonsense_Mutation_p.E51*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E51*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E51*|TP53_ENST00000445888.2_Nonsense_Mutation_p.E51*|TP53_ENST00000413465.2_Nonsense_Mutation_p.E51*|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	51	Interaction with HRMT1L2.				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.E51*(6)|p.E51fs*6(3)|p.E51fs*59(1)|p.I50fs*4(1)|p.D48fs*55(1)|p.E51fs*72(1)|p.P13fs*18(1)|p.S33fs*23(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)	AACCATTGTTCAATATCGTCC	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)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	23	Whole gene deletion(8)|Substitution - Nonsense(6)|Deletion - Frameshift(6)|Insertion - Frameshift(3)	ovary(5)|bone(4)|skin(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|kidney(1)|breast(1)|prostate(1)|pancreas(1)	17											169	168	168					17																	7579536		2203	4300	6503	7520261	SO:0001587	stop_gained	7157	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.151G>T	17.37:g.7579536C>A	ENSP00000269305:p.Glu51*		7520261	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	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.718125	0.48622	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	3.77	0.663	0.17885	.	1.997220	0.02241	N	0.065738	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	0.6634	5.7343	0.18057	0.0:0.6465:0.0:0.3535	.	.	.	.	X	51	.	ENSP00000269305:E51X	E	-	1	0	TP53	7520261	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.943000	0.03917	0.194000	0.20326	0.561000	0.74099	GAA		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7579536	C	A	7579536	4	1	121	1	0	0	0	0	0	1	0	0	16421	835	29	2	1151	2	TP53	17	7579536	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1991	7579536	73615674	210	31980										
MYH2	4620	hgsc.bcm.edu	37	chr17	10428144	10428144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgcggttggcatggttcagcTggatttccatttcattgagg	13	7	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:10428144T>C	ENST00000245503.5	-	34	5285	c.4901A>G	c.(4900-4902)cAg>cGg	p.Q1634R	MYH2_ENST00000397183.2_Missense_Mutation_p.Q1634R|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1634					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)	p.Q1634L(1)		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						ATGGTTCAGCTGGATTTCCAT	0.517																																																1	Substitution - Missense(1)	ovary(1)	17											205	177	187					17																	10428144		2203	4298	6501	10368869	SO:0001583	missense	4620				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.4901A>G	17.37:g.10428144T>C	ENSP00000245503:p.Gln1634Arg		10368869	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.408615	0.83340	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.78707	-1.2;-1.2	5.44	5.44	0.79542	Myosin tail (1);	0.000000	0.37304	U	0.002144	D	0.87394	0.6166	H	0.96269	3.795	0.54753	D	0.999985	P	0.38250	0.624	B	0.43155	0.41	D	0.90284	0.4317	10	0.66056	D	0.02	.	15.662	0.77193	0.0:0.0:0.0:1.0	.	1634	Q9UKX2	MYH2_HUMAN	R	1634	ENSP00000245503:Q1634R;ENSP00000380367:Q1634R	ENSP00000245503:Q1634R	Q	-	2	0	MYH2	10368869	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.778000	0.85637	2.277000	0.76020	0.482000	0.46254	CAG		0.517	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		C	10428144	T	C	10428144	3	2	121	1	0	0	0	0	1	0	0	0	10065	1580	55	4	952	4	MYH2	17	10428144	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	2848608	10428144	70767066	211	31981										
COPS3	8533	hgsc.bcm.edu	37	chr17	17150847	17150847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctggtccatggctttcagccGctcatccagctcaatgcact	8	15	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:17150847G>A	ENST00000268717.5	-	11	1271	c.1165C>T	c.(1165-1167)Cgg>Tgg	p.R389W	COPS3_ENST00000539941.2_Missense_Mutation_p.R369W|COPS3_ENST00000439936.2_Missense_Mutation_p.R311W	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	389					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						GCTTTCAGCCGCTCATCCAGC	0.498																																																0			17											194	181	185					17																	17150847		2203	4300	6503	17091572	SO:0001583	missense	8533			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.1165C>T	17.37:g.17150847G>A	ENSP00000268717:p.Arg389Trp		17091572	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	37	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228800	0.39399	.	.	ENSG00000141030	ENST00000268717;ENST00000539941	.	.	.	5.53	4.55	0.56014	.	0.055983	0.64402	D	0.000002	T	0.41789	0.1174	N	0.19112	0.55	0.40468	D	0.980316	P	0.48694	0.914	P	0.44561	0.453	T	0.47368	-0.9123	9	0.66056	D	0.02	-20.8034	12.6347	0.56677	0.0:0.0:0.699:0.301	.	389	Q9UNS2	CSN3_HUMAN	W	389;369	.	ENSP00000268717:R389W	R	-	1	2	COPS3	17091572	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.784000	0.62411	1.298000	0.44778	0.655000	0.94253	CGG		0.498	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2			A	17150847	G	A	17150847	3	1	121	1	0	0	0	0	1	0	0	0	3740	1086	38	1	114	1	COPS3	17	17150847	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6722703	17150847	64044363	212	31982										
SEZ6	124925	hgsc.bcm.edu	37	chr17	27286098	27286098	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agcactgaggtcccggggtcCgactggaactgaatggtgac	15	10	0	3	rs372776647		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:27286098C>T	ENST00000317338.12	-	10	2480	c.2052G>A	c.(2050-2052)tcG>tcA	p.S684S	SEZ6_ENST00000335960.6_Intron|SEZ6_ENST00000442608.3_Silent_p.S684S|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000360295.9_Silent_p.S684S			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	684	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)		p.S684S(1)		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)			TCCCGGGGTCCGACTGGAACT	0.597																																																1	Substitution - coding silent(1)	large_intestine(1)	17						C	,	1,3911		0,1,1955	54	61	59		2052,2052	-8.6	0.9	17		59	0,8290		0,0,4145	no	coding-synonymous,coding-synonymous	SEZ6	NM_001098635.1,NM_178860.4	,	0,1,6100	TT,TC,CC		0.0,0.0256,0.0082	,	684/994,684/995	27286098	1,12201	1956	4145	6101	24310224	SO:0001819	synonymous_variant	124925			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.2052G>A	17.37:g.27286098C>T			24310224	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Silent	SNP	ENST00000317338.12	37	CCDS45639.1																																																																																				0.597	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3			T	27286098	C	T	27286098	2	4	121	1	0	0	0	0	0	0	0	1	14179	639	23	1		1	SEZ6	17	27286098	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	10135251	27286098	53909112	213	31983										
BLMH	642	hgsc.bcm.edu	37	chr17	28612457	28612457	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	atttctcctttggttgctccActgtgtaccaggttccgcag	9	12	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:28612457A>C	ENST00000261714.6	-	6	768	c.594T>G	c.(592-594)agT>agG	p.S198R	BLMH_ENST00000394819.3_Missense_Mutation_p.S111R|BLMH_ENST00000582669.1_5'UTR|RNU6-1267P_ENST00000410747.1_RNA	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	198					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	TGGTTGCTCCACTGTGTACCA	0.428																																					Pancreas(127;628 1772 12912 33293 36203)											0			17											156	141	146					17																	28612457		2203	4300	6503	25636583	SO:0001583	missense	642			X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.594T>G	17.37:g.28612457A>C	ENSP00000261714:p.Ser198Arg		25636583	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.901357	0.52227	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.42131	0.98;0.98	5.83	3.61	0.41365	.	0.072064	0.85682	D	0.000000	T	0.36331	0.0963	L	0.49455	1.56	0.42116	D	0.991405	B;B	0.19331	0.035;0.009	B;B	0.17722	0.019;0.013	T	0.15009	-1.0452	10	0.56958	D	0.05	-17.9855	9.8594	0.41105	0.8611:0.0:0.1389:0.0	.	111;198	E7EMN3;Q13867	.;BLMH_HUMAN	R	198;111	ENSP00000261714:S198R;ENSP00000378296:S111R	ENSP00000261714:S198R	S	-	3	2	BLMH	25636583	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.423000	0.34837	0.470000	0.27294	-0.297000	0.09499	AGT		0.428	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386		C	28612457	A	C	28612457	3	2	121	1	0	0	0	0	1	0	0	0	1447	156	6	4	801	4	BLMH	17	28612457	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	1326359	28612457	52582753	214	31984										
NF1	4763	hgsc.bcm.edu	37	chr17	29562775	29562775	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agcttggccagtaaaataatGacattctgtttcaaggtttg	9	6	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:29562775G>T	ENST00000358273.4	+	28	4238	c.3855G>T	c.(3853-3855)atG>atT	p.M1285I	NF1_ENST00000356175.3_Missense_Mutation_p.M1285I	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1285	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				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)		GTAAAATAATGACATTCTGTT	0.403			"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)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	17											136	132	133					17																	29562775		2203	4300	6503	26586901	SO:0001583	missense	4763	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.3855G>T	17.37:g.29562775G>T	ENSP00000351015:p.Met1285Ile		26586901	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.796023	0.90453	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.80214	-0.02;-1.35;-1.35	6.16	6.16	0.99307	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (3);	0.078863	0.85682	D	0.000000	D	0.86916	0.6048	L	0.43646	1.37	0.80722	D	1	D;B;P;B	0.76494	0.999;0.032;0.656;0.408	D;B;P;B	0.74023	0.982;0.049;0.679;0.335	D	0.83835	0.0254	10	0.36615	T	0.2	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1285;335;1285;1285	E1P657;Q59FX3;P21359-2;P21359	.;.;.;NF1_HUMAN	I	1285;1285;951	ENSP00000351015:M1285I;ENSP00000348498:M1285I;ENSP00000389907:M951I	ENSP00000348498:M1285I	M	+	3	0	NF1	26586901	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.278000	0.95766	2.937000	0.99478	0.650000	0.86243	ATG		0.403	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		T	29562775	G	T	29562775	3	4	121	1	0	0	0	0	1	0	0	0	10387	1290	45	2	4026	2	NF1	17	29562775	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	950318	29562775	51632435	215	31985										
NF1	4763	hgsc.bcm.edu	37	chr17	29677294	29677294	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tatttcaatggaaaatgttcCtatggatacatatcccattc	5	8	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:29677294C>A	ENST00000358273.4	+	50	7798	c.7415C>A	c.(7414-7416)cCt>cAt	p.P2472H	NF1_ENST00000417592.2_Missense_Mutation_p.P185H|NF1_ENST00000444181.2_Missense_Mutation_p.P265H|NF1_ENST00000356175.3_Missense_Mutation_p.P2451H	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2472					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)|p.P2472H(1)	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)		GAAAATGTTCCTATGGATACA	0.348			"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)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|prostate(1)|central_nervous_system(1)	17											130	115	120					17																	29677294		2203	4300	6503	26701420	SO:0001583	missense	4763	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.7415C>A	17.37:g.29677294C>A	ENSP00000351015:p.Pro2472His		26701420	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843226	0.91197	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181;ENST00000417592	T;T;T;T	0.46451	3.14;3.3;2.99;0.87	5.57	5.57	0.84162	Armadillo-type fold (1);	0.176816	0.50627	D	0.000103	T	0.50360	0.1611	L	0.44542	1.39	0.80722	D	1	P;B	0.47409	0.895;0.383	P;B	0.51079	0.658;0.136	T	0.44802	-0.9304	10	0.49607	T	0.09	.	19.5321	0.95234	0.0:1.0:0.0:0.0	.	2451;2472	P21359-2;P21359	.;NF1_HUMAN	H	2472;2451;2117;265;185	ENSP00000351015:P2472H;ENSP00000348498:P2451H;ENSP00000389907:P2117H;ENSP00000396481:P265H	ENSP00000348498:P2451H	P	+	2	0	NF1	26701420	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.056000	0.76662	2.626000	0.88956	0.563000	0.77884	CCT		0.348	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29677294	C	A	29677294	3	1	121	1	0	0	0	0	1	0	0	0	10387	681	24	2	7674	2	NF1	17	29677294	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	114519	29677294	51517916	216	31986										
SYNRG	11276	hgsc.bcm.edu	37	chr17	35900630	35900630	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctttatcaccaaggctcaaaCtcctcttgtgtgatcctggg	8	12	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:35900630C>G	ENST00000339208.6	-	16	3358	c.3218G>C	c.(3217-3219)aGt>aCt	p.S1073T	SYNRG_ENST00000345615.4_Missense_Mutation_p.S995T|SYNRG_ENST00000591288.1_Missense_Mutation_p.S867T|SYNRG_ENST00000502449.2_Missense_Mutation_p.S950T|SYNRG_ENST00000394378.2_Missense_Mutation_p.S995T|SYNRG_ENST00000585472.1_Missense_Mutation_p.S994T|SYNRG_ENST00000346661.4_Missense_Mutation_p.S1073T	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1073					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						AAGGCTCAAACTCCTCTTGTG	0.493																																																0			17											86	90	89					17																	35900630		2203	4300	6503	32974743	SO:0001583	missense	0			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.3218G>C	17.37:g.35900630C>G	ENSP00000343610:p.Ser1073Thr		32974743	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.703388	0.88924	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378	T;T	0.54866	1.1;0.55	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.70343	0.3213	M	0.63843	1.955	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.996;0.996	D;D;D;D;D;D	0.83275	0.996;0.996;0.996;0.996;0.99;0.99	T	0.68488	-0.5395	10	0.38643	T	0.18	-9.1744	17.94	0.89024	0.0:1.0:0.0:0.0	.	867;995;995;995;1073;1073	B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;SYNRG_HUMAN	T	1073;867;1073;995;995	ENSP00000005279:S1073T;ENSP00000377903:S995T	ENSP00000343610:S867T	S	-	2	0	SYNRG	32974743	1.000000	0.71417	0.995000	0.50966	0.950000	0.60333	7.788000	0.85771	2.475000	0.83589	0.563000	0.77884	AGT		0.493	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		G	35900630	C	G	35900630	3	3	121	1	0	0	0	0	1	0	0	0	15499	565	20	5	827	5	SYNRG	17	35900630	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	6223336	35900630	45294580	217	31987										
CDK12	51755	hgsc.bcm.edu	37	chr17	37676315	37676315	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gcgacttccttaaagatgtcGaactcagcaaaatggctcct	8	11	1	1	rs201479472		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:37676315G>T	ENST00000447079.4	+	11	3103	c.3070G>T	c.(3070-3072)Gaa>Taa	p.E1024*	CDK12_ENST00000430627.2_Nonsense_Mutation_p.E1024*	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1024					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)	p.E1024*(1)		NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						TAAAGATGTCGAACTCAGCAA	0.468			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	1	Substitution - Nonsense(1)	lung(1)	17											133	112	119					17																	37676315		2203	4300	6503	34929841	SO:0001587	stop_gained	0			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.3070G>T	17.37:g.37676315G>T	ENSP00000398880:p.Glu1024*		34929841	A7E2B2|B4DYX4|B9EIQ6|O94978	Nonsense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	G	40	8.374654	0.98784	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	.	.	.	5.56	5.56	0.83823	.	0.341651	0.21039	N	0.081207	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-2.4145	19.5353	0.95251	0.0:0.0:1.0:0.0	.	.	.	.	X	1024	.	ENSP00000407720:E1024X	E	+	1	0	CDK12	34929841	1.000000	0.71417	0.440000	0.26846	0.928000	0.56348	9.824000	0.99380	2.607000	0.88179	0.655000	0.94253	GAA		0.468	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37676315	G	T	37676315	4	4	121	1	0	0	0	0	0	1	0	0	3134	1059	37	2	3112	2	CDK12	17	37676315	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1775685	37676315	43518895	218	31988										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38567398	38567398	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cactcaattggcatgttgatCcaaagctcttgggttgtaaa	9	8	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:38567398C>T	ENST00000423485.1	-	10	1324	c.1166G>A	c.(1165-1167)gGa>gAa	p.G389E		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	389					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)	GCATGTTGATCCAAAGCTCTT	0.333																																																0			17											109	96	100					17																	38567398		1807	4078	5885	35820924	SO:0001583	missense	7153				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.1166G>A	17.37:g.38567398C>T	ENSP00000411532:p.Gly389Glu		35820924	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849006	0.91277	.	.	ENSG00000131747	ENST00000423485;ENST00000348049;ENST00000357601	T	0.26810	1.71	5.64	5.64	0.86602	Ribosomal protein S5 domain 2-type fold (1);DNA topoisomerase, type IIA, subunit B, domain 2 (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA topoisomerase, type IIA, subunit B/N-terminal (1);	.	.	.	.	T	0.64560	0.2609	H	0.95260	3.645	0.80722	D	1	D	0.59767	0.986	D	0.64410	0.925	T	0.75918	-0.3148	9	0.87932	D	0	.	19.6803	0.95960	0.0:1.0:0.0:0.0	.	389	P11388	TOP2A_HUMAN	E	389;388;425	ENSP00000411532:G389E	ENSP00000342944:G388E	G	-	2	0	TOP2A	35820924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.653000	0.90120	0.650000	0.86243	GGA		0.333	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			T	38567398	C	T	38567398	3	4	121	1	0	0	0	0	1	0	0	0	16405	855	30	3	3533	3	TOP2A	17	38567398	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	891083	38567398	42627812	219	31989										
KRT35	3886	hgsc.bcm.edu	37	chr17	39633380	39633380	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtgcgggctgcactaggaccGcaggaggccgcaggaagaca	17	11	0	1	rs367703815		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:39633380G>A	ENST00000393989.1	-	7	1338	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C	KRT35_ENST00000246639.2_Silent_p.C402C	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	432	Tail.				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)				CACTAGGACCGCAGGAGGCCG	0.587																																																0			17						G		0,3906		0,0,1953	49	56	54		1296	-8.4	0	17		54	1,8291		0,1,4145	no	coding-synonymous	KRT35	NM_002280.4		0,1,6098	AA,AG,GG		0.0121,0.0,0.0082		432/456	39633380	1,12197	1953	4146	6099	36886906	SO:0001819	synonymous_variant	3886			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.1296C>T	17.37:g.39633380G>A			36886906	O76012|Q92651	Silent	SNP	ENST00000393989.1	37	CCDS11394.2																																																																																				0.587	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		A	39633380	G	A	39633380	2	1	121	1	0	0	0	0	0	0	0	1	8493	1079	38	1		1	KRT35	17	39633380	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1065982	39633380	41561830	220	31990										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40647711	40647711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tccctggagtgtttggtggaCcatacccttttggcattgat	11	9	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:40647711C>T	ENST00000343619.4	+	14	1660	c.1537C>T	c.(1537-1539)Cca>Tca	p.P513S	RP11-194N12.2_ENST00000591343.1_RNA|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.P470S|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.P513S|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.P520S|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.P470S|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.P513S|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.P159S|MIR548AT_ENST00000578714.1_RNA	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	513					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)		GTTTGGTGGACCATACCCTTT	0.433																																																0			17											85	67	73					17																	40647711		2203	4300	6503	37901237	SO:0001583	missense	535			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.1537C>T	17.37:g.40647711C>T	ENSP00000342951:p.Pro513Ser		37901237	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	37	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	C	35	5.567880	0.96540	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.86030	-2.06;-2.06;-2.06;-2.06;-2.06;-2.06	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.94542	0.8242	M	0.90870	3.155	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;0.989;1.0;1.0	D;D;D;D;D	0.97110	0.994;0.967;0.927;1.0;1.0	D	0.94636	0.7826	10	0.87932	D	0	-10.8412	20.6439	0.99570	0.0:1.0:0.0:0.0	.	470;470;520;513;513	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	S	513;513;513;520;470;159	ENSP00000342951:P513S;ENSP00000444676:P513S;ENSP00000377415:P513S;ENSP00000264649:P520S;ENSP00000443991:P470S;ENSP00000446377:P159S	ENSP00000264649:P520S	P	+	1	0	ATP6V0A1	37901237	1.000000	0.71417	0.994000	0.49952	0.973000	0.67179	7.791000	0.85805	2.884000	0.98904	0.655000	0.94253	CCA		0.433	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		T	40647711	C	T	40647711	3	4	121	1	0	0	0	0	1	0	0	0	1169	507	18	3	1608	3	ATP6V0A1	17	40647711	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1014331	40647711	40547499	221	31991										
WIPI1	55062	hgsc.bcm.edu	37	chr17	66429644	66429644	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tccagcttgaagatgtgtacCgtctcggtgttactggaggc	13	9	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:66429644C>A	ENST00000262139.5	-	8	764	c.765G>T	c.(763-765)acG>acT	p.T255T	WIPI1_ENST00000546360.1_Silent_p.T173T|WIPI1_ENST00000589459.1_5'UTR	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	255					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						AGATGTGTACCGTCTCGGTGT	0.498																																																0			17											188	138	155					17																	66429644		2203	4300	6503	63941239	SO:0001819	synonymous_variant	55062				CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"WD repeat domain containing"	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.765G>T	17.37:g.66429644C>A			63941239	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																				0.498	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983		A	66429644	C	A	66429644	2	1	121	1	0	0	0	0	0	0	0	1	17410	639	23	2		2	WIPI1	17	66429644	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	25781933	66429644	14765566	222	31992										
HN1	51155	hgsc.bcm.edu	37	chr17	73132267	73132267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gcactggggccggggccaccGggctgggcacaggcgcagca	19	14	0	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:73132267G>A	ENST00000409753.3	-	5	680	c.395C>T	c.(394-396)cCg>cTg	p.P132L	HN1_ENST00000405458.3_Missense_Mutation_p.P86L|HN1_ENST00000470924.1_Missense_Mutation_p.P86L|HN1_ENST00000476258.1_Missense_Mutation_p.P86L|RP11-649A18.5_ENST00000584339.1_RNA|HN1_ENST00000392566.2_Missense_Mutation_p.P86L|HN1_ENST00000482348.1_Missense_Mutation_p.P86L|HN1_ENST00000481647.1_Missense_Mutation_p.P86L|HN1_ENST00000356033.4_Missense_Mutation_p.R126W	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	132					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					CGGGGCCACCGGGCTGGGCAC	0.592																																																0			17											45	50	48					17																	73132267		2203	4300	6503	70643862	SO:0001583	missense	51155			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.395C>T	17.37:g.73132267G>A	ENSP00000387059:p.Pro132Leu		70643862	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.1|27.1	4.803865|4.803865	0.90623|0.90623	.|.	.|.	ENSG00000189159|ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000392566|ENST00000356033	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	.|1.112010	.|0.06831	.|N	.|0.793973	T|T	0.62720|0.62720	0.2451|0.2451	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999999|0.999999	D|D	0.89917|0.60160	1.0|0.987	D|B	0.87578|0.43783	0.998|0.431	T|T	0.63919|0.63919	-0.6528|-0.6528	7|8	0.87932|0.72032	D|D	0|0.01	4.4765|4.4765	17.8012|17.8012	0.88587|0.88587	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	132|126	Q9UK76|Q9UK76-2	HN1_HUMAN|.	L|W	86;132;86|126	.|.	ENSP00000440912:P86L|ENSP00000348316:R126W	P|R	-|-	2|1	0|2	HN1|HN1	70643862|70643862	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.988000|0.988000	0.76386|0.76386	6.388000|6.388000	0.73195|0.73195	2.624000|2.624000	0.88883|0.88883	0.643000|0.643000	0.83706|0.83706	CCG|CGG		0.592	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032		A	73132267	G	A	73132267	3	1	121	1	0	0	0	0	1	0	0	0	7270	1116	39	1	173	1	HN1	17	73132267	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6702623	73132267	8062943	223	31993										
RNF157	114804	hgsc.bcm.edu	37	chr17	74151352	74151352	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cctctgcatcctgctctccaGctgggaggccagcaaagttg	11	14	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr17:74151352G>T	ENST00000269391.6	-	16	1877	c.1745C>A	c.(1744-1746)gCt>gAt	p.A582D	RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000592748.1_RNA|RNF157_ENST00000319945.6_Intron|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586661.1_RNA	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	582							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)			CTGCTCTCCAGCTGGGAGGCC	0.587																																					GBM(186;507 2120 27388 27773 52994)											0			17											85	84	84					17																	74151352		2203	4300	6503	71662947	SO:0001583	missense	114804			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.1745C>A	17.37:g.74151352G>T	ENSP00000269391:p.Ala582Asp		71662947	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	37	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.062947	0.55432	.	.	ENSG00000141576	ENST00000269391	T	0.26518	1.73	4.51	1.35	0.21983	.	0.265812	0.37012	N	0.002293	T	0.25606	0.0623	L	0.56769	1.78	0.34791	D	0.735769	P	0.49961	0.93	P	0.44860	0.462	T	0.34304	-0.9834	10	0.72032	D	0.01	-12.7232	7.3917	0.26913	0.154:0.138:0.708:0.0	.	582	Q96PX1	RN157_HUMAN	D	582	ENSP00000269391:A582D	ENSP00000269391:A582D	A	-	2	0	RNF157	71662947	0.979000	0.34478	0.067000	0.19924	0.978000	0.69477	5.107000	0.64603	0.092000	0.17331	0.563000	0.77884	GCT		0.587	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		T	74151352	G	T	74151352	3	4	121	1	0	0	0	0	1	0	0	0	13491	971	34	2	310	2	RNF157	17	74151352	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1019085	74151352	7043858	224	31994										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22804815	22804815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cactgtctgcatgcacaccaCgcagcgaaagcctgtcaggg	11	14	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr18:22804815C>T	ENST00000361524.3	-	4	3215	c.3067G>A	c.(3067-3069)Gtg>Atg	p.V1023M	ZNF521_ENST00000538137.2_Missense_Mutation_p.V1023M|ZNF521_ENST00000584787.1_Missense_Mutation_p.V803M|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1023					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)					ATGCACACCACGCAGCGAAAG	0.517			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0			18											78	66	70					18																	22804815		2203	4300	6503	21058813	SO:0001583	missense	25925			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.3067G>A	18.37:g.22804815C>T	ENSP00000354794:p.Val1023Met		21058813	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.567208	0.28003	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.10288	2.89;2.89	6.17	5.29	0.74685	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.058749	0.64402	D	0.000002	T	0.22859	0.0552	L	0.27053	0.805	0.39314	D	0.965133	D	0.89917	1.0	D	0.91635	0.999	T	0.04991	-1.0913	10	0.48119	T	0.1	-28.1652	17.5212	0.87787	0.0:0.8761:0.1239:0.0	.	1023	Q96K83	ZN521_HUMAN	M	1023;1057;1023	ENSP00000354794:V1023M;ENSP00000382352:V1023M	ENSP00000354794:V1023M	V	-	1	0	ZNF521	21058813	1.000000	0.71417	0.884000	0.34674	0.982000	0.71751	7.487000	0.81328	1.593000	0.50029	0.655000	0.94253	GTG		0.517	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22804815	C	T	22804815	3	4	121	1	0	0	0	0	1	0	0	0	18004	536	19	1	888	1	ZNF521	18	22804815	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10		22804815	55272433	225	31995										
DSG4	147409	hgsc.bcm.edu	37	chr18	28983530	28983530	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gaacattcttatgggtctccGtttactttctgtgttgttga	9	7	3	1	rs142117600		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr18:28983530G>A	ENST00000308128.4	+	11	1704	c.1569G>A	c.(1567-1569)ccG>ccA	p.P523P	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG4_ENST00000359747.4_Silent_p.P523P	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	523					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)	p.P523P(1)		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)			ATGGGTCTCCGTTTACTTTCT	0.383													G|||	1	0.000199681	0	0	5008	,	,		20205	0.001		0	False		,,,				2504	0															1	Substitution - coding silent(1)	central_nervous_system(1)	18											143	131	135					18																	28983530		2203	4300	6503	27237528	SO:0001819	synonymous_variant	147409			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.1569G>A	18.37:g.28983530G>A			27237528	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	37	CCDS11897.1																																																																																				0.383	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		A	28983530	G	A	28983530	2	1	121	1	0	0	0	0	0	0	0	1	4790	1132	40	1		1	DSG4	18	28983530	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	6178715	28983530	49093718	226	31996										
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39576652	39576652	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttacatatgaagaacaagaTcttgtttggaagtttagata	8	4	1	4			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr18:39576652T>C	ENST00000262039.4	+	9	1028	c.942T>C	c.(940-942)gaT>gaC	p.D314D	PIK3C3_ENST00000398870.3_Silent_p.D251D	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	314	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|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)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						AAGAACAAGATCTTGTTTGGA	0.269										TSP Lung(28;0.18)																											NSCLC(37;552 1060 2683 16430 37914)											0			18											78	85	82					18																	39576652		2202	4277	6479	37830650	SO:0001819	synonymous_variant	5289			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.942T>C	18.37:g.39576652T>C			37830650	Q15134	Silent	SNP	ENST00000262039.4	37	CCDS11920.1																																																																																				0.269	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		C	39576652	T	C	39576652	2	2	121	1	0	0	0	0	0	0	0	1	11943	1432	50	4		4	PIK3C3	18	39576652	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	10593122	39576652	38500596	227	31997										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43531068	43531068	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtctatctctgtccccttacCaatttctgcagccagagaag	7	13	3	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr18:43531068C>A	ENST00000282041.5	-	4	1423	c.1389G>T	c.(1387-1389)ttG>ttT	p.L463F		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	463					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						GTCCCCTTACCAATTTCTGCA	0.338																																																0			18											109	97	101					18																	43531068		1846	4097	5943	41785066	SO:0001630	splice_region_variant	57724			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.1389+1G>T	18.37:g.43531068C>A			41785066	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	28.8	4.948722	0.92660	.	.	ENSG00000152223	ENST00000282041	D	0.82711	-1.64	5.33	5.33	0.75918	.	0.769173	0.12869	N	0.432465	D	0.90937	0.7151	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88854	0.3321	9	.	.	.	-10.4395	19.3725	0.94493	0.0:1.0:0.0:0.0	.	463;463	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	F	463	ENSP00000282041:L463F	.	L	-	3	2	EPG5	41785066	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.231000	0.78106	2.650000	0.89964	0.561000	0.74099	TTG		0.338	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	Missense_Mutation	A	43531068	C	A	43531068	5	1	121	1	0	0	0	0	0	0	1	0	8270	608	21	2	6514	2	KIAA1632	18	43531068	Splice_Site	SNP	C	TCGA-G5-6235-01A-11D-1733-10	3954416	43531068	34546180	228	31998										
SMAD2	4087	hgsc.bcm.edu	37	chr18	45391501	45391501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgatatatccaggaggtggcGtttctacaaaagtttaaaac	9	6	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr18:45391501G>A	ENST00000402690.2	-	6	1053	c.659C>T	c.(658-660)aCg>aTg	p.T220M	SMAD2_ENST00000591214.1_Missense_Mutation_p.T190M|SMAD2_ENST00000262160.6_Missense_Mutation_p.T220M|SMAD2_ENST00000586040.1_Missense_Mutation_p.T190M|SMAD2_ENST00000356825.4_Missense_Mutation_p.T190M	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	220					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|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)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.T220M(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						AGGAGGTGGCGTTTCTACAAA	0.368																																																1	Substitution - Missense(1)	central_nervous_system(1)	18											88	74	79					18																	45391501		2203	4300	6503	43645499	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.659C>T	18.37:g.45391501G>A	ENSP00000384449:p.Thr220Met		43645499		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918373	0.92249	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.97209	-4.29;-4.29;-4.29	5.82	5.82	0.92795	SMAD/FHA domain (1);	0.046520	0.85682	D	0.000000	D	0.98052	0.9358	M	0.84948	2.725	0.80722	D	1	D;B;D	0.59357	0.985;0.318;0.985	P;B;P	0.53224	0.721;0.084;0.613	D	0.98254	1.0495	10	0.56958	D	0.05	.	19.7014	0.96054	0.0:0.0:1.0:0.0	.	190;190;220	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	M	220;190;220	ENSP00000262160:T220M;ENSP00000349282:T190M;ENSP00000384449:T220M	ENSP00000262160:T220M	T	-	2	0	SMAD2	43645499	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	9.747000	0.98863	2.755000	0.94549	0.591000	0.81541	ACG		0.368	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		A	45391501	G	A	45391501	3	1	121	1	0	0	0	0	1	0	0	0	14795	1145	40	1	768	1	SMAD2	18	45391501	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	1860433	45391501	32685747	229	31999										
PIGN	23556	hgsc.bcm.edu	37	chr18	59780514	59780514	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgataataggacaatcctttCaatgcaagatgaattagctc	7	7	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr18:59780514C>T	ENST00000357637.5	-	16	1702	c.1287G>A	c.(1285-1287)ttG>ttA	p.L429L	PIGN_ENST00000400334.3_Silent_p.L429L	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	429					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)				ACAATCCTTTCAATGCAAGAT	0.333																																																0			18											96	89	91					18																	59780514		1840	4092	5932	57931494	SO:0001819	synonymous_variant	23556			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.1287G>A	18.37:g.59780514C>T			57931494	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																				0.333	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		T	59780514	C	T	59780514	2	4	121	1	0	0	0	0	0	0	0	1	11924	825	29	3		3	PIGN	18	59780514	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	14389013	59780514	18296734	230	32000										
LMNB2	84823	hgsc.bcm.edu	37	chr19	2432464	2432464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttgggcgtgaacttgtaggCgatctcctccccctccaaga	10	14	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:2432464C>T	ENST00000582871.1	-	9	1566	c.1480G>A	c.(1480-1482)Gcc>Acc	p.A494T	LMNB2_ENST00000475819.1_5'Flank|LMNB2_ENST00000325327.3_Missense_Mutation_p.A514T	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	494	LTD.|Tail.					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)		AACTTGTAGGCGATCTCCTCC	0.627																																																0			19											317	235	263					19																	2432464		2203	4300	6503	2383464	SO:0001583	missense	84823			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.1480G>A	19.37:g.2432464C>T	ENSP00000462730:p.Ala494Thr		2383464	O75292|Q14734|Q96DF6	Missense_Mutation	SNP	ENST00000582871.1	37		.	.	.	.	.	.	.	.	.	.	C	4.770	0.143089	0.09083	.	.	ENSG00000176619	ENST00000325327	.	.	.	4.11	3.04	0.35103	Intermediate filament, C-terminal (1);	0.278905	0.35320	N	0.003288	T	0.23926	0.0579	N	0.03948	-0.315	0.41091	D	0.985594	B	0.09022	0.002	B	0.13407	0.009	T	0.21348	-1.0248	9	0.02654	T	1	.	11.6124	0.51069	0.1799:0.8201:0.0:0.0	.	494	Q03252	LMNB2_HUMAN	T	494	.	ENSP00000327054:A494T	A	-	1	0	LMNB2	2383464	0.438000	0.25602	0.894000	0.35097	0.601000	0.36947	0.740000	0.26188	0.698000	0.31739	0.555000	0.69702	GCC		0.627	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737		T	2432464	C	T	2432464	3	4	121	1	0	0	0	0	1	0	0	0	8874	768	27	1	338	1	LMNB2	19	2432464	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10		2432464	56696519	231	32001										
ZNF77	58492	hgsc.bcm.edu	37	chr19	2933603	2933603	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtgcgttctcacgtgcacacGaagggacgaggaacaactgt	13	10	1	0	rs553602761|rs565530193	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:2933603G>T	ENST00000314531.4	-	4	1614	c.1522C>A	c.(1522-1524)Cgt>Agt	p.R508S		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	508					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)		ACGTGCACACGAAGGGACGAG	0.498																																																0			19											213	176	189					19																	2933603		2203	4300	6503	2884603	SO:0001583	missense	58492			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.1522C>A	19.37:g.2933603G>T	ENSP00000319053:p.Arg508Ser		2884603	Q86XJ3|Q9NPP0	Missense_Mutation	SNP	ENST00000314531.4	37	CCDS12099.1	.	.	.	.	.	.	.	.	.	.	G	8.653	0.898760	0.17686	.	.	ENSG00000175691	ENST00000341064;ENST00000314531	T	0.07567	3.18	2.56	-1.75	0.08031	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03959	0.0111	N	0.22421	0.69	0.09310	N	1	P	0.34662	0.462	B	0.32289	0.143	T	0.42292	-0.9460	9	0.08381	T	0.77	.	5.4716	0.16672	0.0:0.181:0.2699:0.5491	.	508	Q15935	ZNF77_HUMAN	S	302;508	ENSP00000319053:R508S	ENSP00000319053:R508S	R	-	1	0	ZNF77	2884603	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	0.301000	0.19174	-0.017000	0.14103	-0.500000	0.04577	CGT		0.498	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		T	2933603	G	T	2933603	3	4	121	1	0	0	0	0	1	0	0	0	18181	1058	37	2	119	2	ZNF77	19	2933603	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	501139	2933603	56195380	232	32002										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23837046	23837046	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagttctgtcacattcttgaCatttgtagagtttctcacaa	6	8	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:23837046C>T	ENST00000359788.4	-	4	857	c.689G>A	c.(688-690)tGt>tAt	p.C230Y	ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	230					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)				ACATTCTTGACATTTGTAGAG	0.308																																																0			19											51	53	52					19																	23837046		2201	4296	6497	23628886	SO:0001583	missense	171392				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.689G>A	19.37:g.23837046C>T	ENSP00000352836:p.Cys230Tyr		23628886	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	37	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	12.66	2.003977	0.35320	.	.	ENSG00000197372	ENST00000359788	T	0.38560	1.13	0.916	0.916	0.19373	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57548	0.2061	M	0.88570	2.965	0.38238	D	0.941234	P	0.46912	0.886	P	0.52823	0.71	T	0.64084	-0.6490	9	0.66056	D	0.02	.	8.5828	0.33640	0.0:1.0:0.0:0.0	.	230	Q8TD23	ZN675_HUMAN	Y	230	ENSP00000352836:C230Y	ENSP00000352836:C230Y	C	-	2	0	ZNF675	23628886	0.985000	0.35326	0.280000	0.24747	0.278000	0.26855	4.786000	0.62425	0.300000	0.22699	0.305000	0.20034	TGT		0.308	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		T	23837046	C	T	23837046	3	4	121	1	0	0	0	0	1	0	0	0	18121	478	17	3	1021	3	ZNF675	19	23837046	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	20903443	23837046	35291937	233	32003										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40408823	40408823	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggccgttggccagcaccacgGgcagcttcatgtccacaccg	12	16	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:40408823G>T	ENST00000221347.6	-	8	4023	c.4016C>A	c.(4015-4017)cCc>cAc	p.P1339H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1339	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.P1339H(1)		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)			CAGCACCACGGGCAGCTTCAT	0.577																																																1	Substitution - Missense(1)	central_nervous_system(1)	19											23	19	20					19																	40408823		2203	4299	6502	45100663	SO:0001583	missense	8857			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.4016C>A	19.37:g.40408823G>T	ENSP00000221347:p.Pro1339His		45100663	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919525	0.52653	.	.	ENSG00000090920	ENST00000221347	T	0.65916	-0.18	4.95	4.95	0.65309	von Willebrand factor, type D domain (3);	0.000000	0.64402	D	0.000001	D	0.83450	0.5257	M	0.91510	3.215	0.35633	D	0.810356	D	0.89917	1.0	D	0.83275	0.996	D	0.90644	0.4577	10	0.87932	D	0	.	16.9545	0.86254	0.0:0.0:1.0:0.0	.	1339	Q9Y6R7	FCGBP_HUMAN	H	1339	ENSP00000221347:P1339H	ENSP00000221347:P1339H	P	-	2	0	FCGBP	45100663	1.000000	0.71417	0.071000	0.20095	0.035000	0.12851	9.317000	0.96327	2.302000	0.77476	0.650000	0.86243	CCC		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40408823	G	T	40408823	3	4	121	1	0	0	0	0	1	0	0	0	5797	1232	43	2	12317	2	FCGBP	19	40408823	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	16571777	40408823	18720160	234	32004										
PPP1R15A	23645	hgsc.bcm.edu	37	chr19	49377167	49377167	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttgggtgtcttgcccaggggAggaagagaatcaagccacgg	16	8	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:49377167A>T	ENST00000200453.5	+	2	946	c.677A>T	c.(676-678)gAg>gTg	p.E226V		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	226	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		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;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		TGCCCAGGGGAGGAAGAGAAT	0.537																																																0			19											85	95	92					19																	49377167		2203	4300	6503	54068979	SO:0001583	missense	23645			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.677A>T	19.37:g.49377167A>T	ENSP00000200453:p.Glu226Val		54068979	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.780487	0.90195	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.04156	3.69	4.29	4.29	0.51040	.	0.527164	0.17749	N	0.163289	T	0.16471	0.0396	M	0.64997	1.995	0.35384	D	0.790131	D	0.76494	0.999	D	0.76071	0.987	T	0.05818	-1.0862	10	0.62326	D	0.03	-3.959	10.0106	0.41984	1.0:0.0:0.0:0.0	.	226	O75807	PR15A_HUMAN	V	226;66;184	ENSP00000200453:E226V	ENSP00000200453:E226V	E	+	2	0	PPP1R15A	54068979	0.831000	0.29352	0.276000	0.24689	0.632000	0.37999	1.527000	0.35975	1.931000	0.55961	0.459000	0.35465	GAG		0.537	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		T	49377167	A	T	49377167	3	4	121	1	0	0	0	0	1	0	0	0	12397	304	11	5	679	5	PPP1R15A	19	49377167	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	8968344	49377167	9751816	235	32005										
SYT3	84258	hgsc.bcm.edu	37	chr19	51135614	51135614	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	aagcccccaccactggggggCagcaggagcaacccagagcc	13	16	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:51135614C>A	ENST00000338916.4	-	2	1236	c.603G>T	c.(601-603)ctG>ctT	p.L201L	SYT3_ENST00000593901.1_Silent_p.L201L|SYT3_ENST00000544769.1_Silent_p.L201L|SYT3_ENST00000600079.1_Silent_p.L201L	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	201					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)		CACTGGGGGGCAGCAGGAGCA	0.652																																																0			19											43	46	45					19																	51135614		2203	4300	6503	55827426	SO:0001819	synonymous_variant	84258			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.603G>T	19.37:g.51135614C>A			55827426	Q8N5Z1|Q8N640	Silent	SNP	ENST00000338916.4	37	CCDS12798.1																																																																																				0.652	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		A	51135614	C	A	51135614	2	1	121	1	0	0	0	0	0	0	0	1	15514	697	25	2		2	SYT3	19	51135614	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1758447	51135614	7993369	236	32006										
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569529	52569529	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tttgtaaggtttctctccggTatgaattctctgatgtacag	9	7	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:52569529T>G	ENST00000426391.2	-	5	1809	c.1258A>C	c.(1258-1260)Acc>Ccc	p.T420P	ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000594295.1_Missense_Mutation_p.T536P|ZNF841_ENST00000359973.2_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.T536P|CTC-471J1.2_ENST00000569091.1_RNA			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						TTCTCTCCGGTATGAATTCTC	0.398																																																0			19											89	83	85					19																	52569529		692	1591	2283	57261341	SO:0001583	missense	284371			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.1258A>C	19.37:g.52569529T>G	ENSP00000415453:p.Thr420Pro		57261341	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	37		.	.	.	.	.	.	.	.	.	.	T	17.48	3.401170	0.62288	.	.	ENSG00000197608	ENST00000389534;ENST00000426391	T;T	0.25749	1.78;1.78	1.85	1.85	0.25348	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42966	0.1226	M	0.74546	2.27	0.80722	D	1	D;D	0.65815	0.989;0.995	D;D	0.72625	0.978;0.942	T	0.38585	-0.9654	9	0.87932	D	0	.	4.0884	0.09958	0.3152:0.0:0.0:0.6848	.	536;420	Q6ZN19-3;Q6ZN19	.;ZN841_HUMAN	P	536;420	ENSP00000374185:T536P;ENSP00000415453:T420P	ENSP00000374185:T536P	T	-	1	0	ZNF841	57261341	0.001000	0.12720	0.024000	0.17045	0.760000	0.43138	0.267000	0.18552	1.110000	0.41699	0.260000	0.18958	ACC		0.398	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		G	52569529	T	G	52569529	3	3	121	1	0	0	0	0	1	0	0	0	18228	1638	57	4	1172	4	ZNF841	19	52569529	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	1433915	52569529	6559454	237	32007										
ZNF468	90333	hgsc.bcm.edu	37	chr19	53344345	53344345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctccactatgaatcctcctaTgtctttcaaggtgtgatttg	7	10	2	2	rs570708838		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:53344345T>C	ENST00000595646.1	-	4	1322	c.1202A>G	c.(1201-1203)cAt>cGt	p.H401R	ZNF468_ENST00000396409.4_Missense_Mutation_p.H348R|ZNF468_ENST00000390651.4_Missense_Mutation_p.H348R|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000243639.4_3'UTR			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	401					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)		AATCCTCCTATGTCTTTCAAG	0.403																																																0			19											104	104	104					19																	53344345		2203	4300	6503	58036157	SO:0001583	missense	388561			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.1202A>G	19.37:g.53344345T>C	ENSP00000470381:p.His401Arg		58036157	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	.	.	.	.	.	.	.	.	.	.	-	15.22	2.767426	0.49574	.	.	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651;ENST00000393865	D;D	0.86865	-2.18;-2.18	1.88	1.88	0.25563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94876	0.8344	H	0.96889	3.9	0.29191	N	0.87584	D	0.89917	1.0	D	0.91635	0.999	D	0.87966	0.2733	9	0.87932	D	0	.	8.5573	0.33489	0.0:0.0:0.0:1.0	.	401	Q5VIY5	ZN468_HUMAN	R	401;348;348;151	ENSP00000379690:H348R;ENSP00000445669:H348R	ENSP00000243639:H401R	H	-	2	0	ZNF468	58036157	1.000000	0.71417	0.007000	0.13788	0.044000	0.14063	6.312000	0.72840	0.863000	0.35553	0.336000	0.21669	CAT		0.403	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801		C	53344345	T	C	53344345	3	2	121	1	0	0	0	0	1	0	0	0	17967	1464	51	4	370	4	ZNF468	19	53344345	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	774816	53344345	5784638	238	32008										
KIR3DL3	115653	hgsc.bcm.edu	37	chr19	55239242	55239242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cgttggacagctccacgatgCgggttcccaggtcaactatt	11	12	1	0	rs367886097		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:55239242C>T	ENST00000291860.1	+	4	539	c.521C>T	c.(520-522)gCg>gTg	p.A174V	KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	174	Ig-like C2-type 2. {ECO:0000305}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A174V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CTCCACGATGCGGGTTCCCAG	0.547																																																1	Substitution - Missense(1)	ovary(1)	19						C	VAL/ALA	1,3955		0,1,1977	105	88	95		521	-2.8	0	19		95	0,6878		0,0,3439	no	missense	KIR3DL3	NM_153443.3	64	0,1,5416	TT,TC,CC		0.0,0.0253,0.0092	possibly-damaging	174/411	55239242	1,10833	1978	3439	5417	59931054	SO:0001583	missense	115653			AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.521C>T	19.37:g.55239242C>T	ENSP00000291860:p.Ala174Val		59931054	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	.	.	.	.	.	.	.	.	.	.	N	10.75	1.439250	0.25900	2.53E-4	0.0	ENSG00000242019	ENST00000291860	T	0.02787	4.16	1.38	-2.75	0.05914	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02807	0.0084	L	0.31664	0.95	0.09310	N	1	D	0.57571	0.98	P	0.46389	0.515	T	0.36407	-0.9749	9	0.87932	D	0	.	4.6375	0.12531	0.1785:0.2293:0.5921:0.0	.	174	Q8N743	KI3L3_HUMAN	V	174	ENSP00000291860:A174V	ENSP00000291860:A174V	A	+	2	0	KIR3DL3	59931054	0.007000	0.16637	0.000000	0.03702	0.000000	0.00434	-0.073000	0.11468	-0.758000	0.04690	-2.628000	0.00155	GCG		0.547	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443		T	55239242	C	T	55239242	3	4	121	1	0	0	0	0	1	0	0	0	8343	768	27	1	535	1	KIR3DL3	19	55239242	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1894897	55239242	3889741	239	32009										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56329390	56329390	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tggcaacacgttagccagttCttcttttgtcatctgtatca	7	10	5	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:56329390C>T	ENST00000589093.1	-	2	244	c.151G>A	c.(151-153)Gaa>Aaa	p.E51K	NLRP11_ENST00000360133.3_Missense_Mutation_p.E51K|NLRP11_ENST00000443188.1_Missense_Mutation_p.E51K|NLRP11_ENST00000592953.1_Intron|NLRP11_ENST00000589824.2_Missense_Mutation_p.E51K			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	51	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						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)		TTAGCCAGTTCTTCTTTTGTC	0.383																																																0			19											172	159	164					19																	56329390		2203	4300	6503	61021202	SO:0001583	missense	204801			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.151G>A	19.37:g.56329390C>T	ENSP00000466285:p.Glu51Lys		61021202	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.527162	0.27299	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.46063	0.88;0.88	2.84	-0.873	0.10635	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.33904	0.0879	N	0.19112	0.55	0.09310	N	1	B	0.27765	0.188	B	0.43155	0.41	T	0.51044	-0.8755	9	0.52906	T	0.07	.	5.9968	0.19499	0.2063:0.3903:0.4033:0.0	.	51	P59045	NAL11_HUMAN	K	51	ENSP00000409898:E51K;ENSP00000353251:E51K	ENSP00000353251:E51K	E	-	1	0	NLRP11	61021202	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.053000	0.11846	-0.064000	0.13043	-0.155000	0.13514	GAA		0.383	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		T	56329390	C	T	56329390	3	4	121	1	0	0	0	0	1	0	0	0	10504	922	32	3	2986	3	NLRP11	19	56329390	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1090148	56329390	2799593	240	32010										
ZNF749	388567	hgsc.bcm.edu	37	chr19	57955798	57955798	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcaaacataatgttgttcagCatctgaaaattcatactgga	6	7	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:57955798C>T	ENST00000334181.4	+	3	1532	c.1282C>T	c.(1282-1284)Cat>Tat	p.H428Y	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	428					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.H341D(1)		breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		TGTTGTTCAGCATCTGAAAAT	0.438																																																1	Substitution - Missense(1)	ovary(1)	19											90	88	89					19																	57955798		2203	4300	6503	62647610	SO:0001583	missense	388567			AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"Zinc fingers, C2H2-type", "-"	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1282C>T	19.37:g.57955798C>T	ENSP00000333980:p.His428Tyr		62647610		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	C	14.54	2.564731	0.45694	.	.	ENSG00000186230	ENST00000334181	D	0.86769	-2.17	1.96	0.9	0.19278	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.91509	0.7319	M	0.92880	3.355	0.19575	N	0.999965	D	0.63880	0.993	P	0.52514	0.701	D	0.83406	0.0025	9	0.87932	D	0	.	7.9891	0.30229	0.0:0.8592:0.0:0.1408	.	428	O43361	ZN749_HUMAN	Y	428	ENSP00000333980:H428Y	ENSP00000333980:H428Y	H	+	1	0	ZNF749	62647610	0.970000	0.33590	0.002000	0.10522	0.310000	0.27922	6.083000	0.71326	0.388000	0.25054	0.460000	0.39030	CAT		0.438	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561		T	57955798	C	T	57955798	3	4	121	1	0	0	0	0	1	0	0	0	18170	710	25	3	1292	3	ZNF749	19	57955798	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1626408	57955798	1173185	241	32011										
ZNF274	10782	hgsc.bcm.edu	37	chr19	58697120	58697120	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtaacactgggttttaccccGgaagagtggggactgctgga	15	8	0	1	rs567797622	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:58697120G>A	ENST00000326804.4	+	3	534	c.75G>A	c.(73-75)ccG>ccA	p.P25P	ZNF274_ENST00000345813.3_Silent_p.P25P|ZNF274_ENST00000424679.2_Intron|ZNF274_ENST00000597818.1_3'UTR	NM_001278734.1|NM_133502.1	NP_001265663.1|NP_598009.1	Q96GC6	ZN274_HUMAN	zinc finger protein 274	25	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)|skin(1)	21		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		GTTTTACCCCGGAAGAGTGGG	0.512													G|||	2	0.000399361	0	0	5008	,	,		17462	0.001		0	False		,,,				2504	0.001															0			19											94	103	100					19																	58697120		2193	4300	6493	63388932	SO:0001819	synonymous_variant	10782			AB029149	CCDS74473.1, CCDS74474.1, CCDS74475.1, CCDS74476.1	19q13.43	2013-01-09				ENSG00000171606		"Zinc fingers, C2H2-type", "-", "-", "-"	13068	protein-coding gene	gene with protein product		605467				10777669	Standard	NM_133502		Approved	ZKSCAN19, ZSCAN51	uc002qrs.1	Q96GC6		ENST00000326804.4:c.75G>A	19.37:g.58697120G>A			63388932	Q53XU4|Q6MZG1|Q8WY37|Q8WY38|Q92969|Q9UII0|Q9UII1	Silent	SNP	ENST00000326804.4	37																																																																																					0.512	ZNF274-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_133502		A	58697120	G	A	58697120	2	1	121	1	0	0	0	0	0	0	0	1	17848	1103	39	1		1	ZNF274	19	58697120	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	741322	58697120	431863	242	32012										
ZNF544	27300	hgsc.bcm.edu	37	chr19	58773427	58773427	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttagttacacataaaagaacGcacactggagaaaaaccctt	6	9	0	2	rs145233590	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr19:58773427G>A	ENST00000596652.1	+	6	1689	c.1455G>A	c.(1453-1455)acG>acA	p.T485T	ZNF544_ENST00000415203.2_Silent_p.T457T|ZNF544_ENST00000600220.1_Silent_p.T457T|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000600044.1_Silent_p.T457T|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000599953.1_Silent_p.T343T|ZNF544_ENST00000599227.1_3'UTR|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000269829.4_Silent_p.T485T|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000595981.1_Intron			Q6NX49	ZN544_HUMAN	zinc finger protein 544	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)|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)		ATAAAAGAACGCACACTGGAG	0.428																																																0			19						G		0,4406		0,0,2203	83	85	84		1455	-4.7	0	19	dbSNP_134	84	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ZNF544	NM_014480.2		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		485/716	58773427	3,13003	2203	4300	6503	63465239	SO:0001819	synonymous_variant	27300			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.1455G>A	19.37:g.58773427G>A			63465239	A8K6J1|Q9UEX4	Silent	SNP	ENST00000596652.1	37	CCDS12973.1																																																																																				0.428	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		A	58773427	G	A	58773427	2	1	121	1	0	0	0	0	0	0	0	1	18016	1074	38	1		1	ZNF544	19	58773427	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	76307	58773427	355556	243	32013										
TRIB3	57761	hgsc.bcm.edu	37	chr20	377085	377085	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttcggcaagatccgccgcggGgcctacgccttgcctgcagg	14	15	0	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:377085G>A	ENST00000217233.3	+	4	1381	c.828G>A	c.(826-828)ggG>ggA	p.G276G	TRIB3_ENST00000422053.2_Silent_p.G303G	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	276	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)		TCCGCCGCGGGGCCTACGCCT	0.682																																					Melanoma(101;421 2374 19538)											0			20											50	51	50					20																	377085		2203	4299	6502	325085	SO:0001819	synonymous_variant	57761			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.828G>A	20.37:g.377085G>A			325085	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Silent	SNP	ENST00000217233.3	37	CCDS12997.1																																																																																				0.682	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158		A	377085	G	A	377085	2	1	121	1	0	0	0	0	0	0	0	1	16524	1219	43	3		3	TRIB3	20	377085	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10		377085	62648435	244	32014										
PAK7	57144	hgsc.bcm.edu	37	chr20	9561002	9561002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctcctgtcatagtcatccagGctgggtccccattcactttc	7	15	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:9561002G>T	ENST00000378429.3	-	5	1326	c.780C>A	c.(778-780)agC>agA	p.S260R	PAK7_ENST00000353224.5_Missense_Mutation_p.S260R|RP5-986I17.2_ENST00000428769.1_RNA|PAK7_ENST00000378423.1_Missense_Mutation_p.S260R	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	260	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.S260S(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)			AGTCATCCAGGCTGGGTCCCC	0.562																																																1	Substitution - coding silent(1)	ovary(1)	20											100	94	96					20																	9561002		2203	4300	6503	9509002	SO:0001583	missense	57144			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.780C>A	20.37:g.9561002G>T	ENSP00000367686:p.Ser260Arg		9509002	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.867371	0.32977	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.32515	1.45;1.45;1.45	5.11	4.1	0.47936	.	0.591766	0.19576	N	0.110989	T	0.21509	0.0518	L	0.36672	1.1	0.33313	D	0.566291	B;P	0.37864	0.201;0.61	B;B	0.31812	0.029;0.136	T	0.25813	-1.0121	9	.	.	.	.	12.1711	0.54160	0.0:0.0:0.8299:0.1701	.	260;260	B0AZM9;Q9P286	.;PAK7_HUMAN	R	260;260;260;208	ENSP00000367686:S260R;ENSP00000322957:S260R;ENSP00000367679:S260R	.	S	-	3	2	PAK7	9509002	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.117000	0.31234	2.550000	0.86006	0.637000	0.83480	AGC		0.562	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			T	9561002	G	T	9561002	3	4	121	1	0	0	0	0	1	0	0	0	11436	1194	42	2	1407	2	PAK7	20	9561002	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	9183917	9561002	53464518	245	32015										
JAG1	182	hgsc.bcm.edu	37	chr20	10622147	10622147	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttaaaggtaaatgtgatgttCgcacagttatcctggtaata	9	5	0	1	rs142085300		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:10622147C>T	ENST00000254958.5	-	23	3392	c.2877G>A	c.(2875-2877)gcG>gcA	p.A959A	JAG1_ENST00000423891.2_Silent_p.A800A	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	959					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)	p.A959A(1)		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						ATGTGATGTTCGCACAGTTAT	0.463									Alagille Syndrome																																							1	Substitution - coding silent(1)	ovary(1)	20						C		0,4406		0,0,2203	151	147	148		2877	-11.6	0.7	20	dbSNP_134	148	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	JAG1	NM_000214.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		959/1219	10622147	2,13004	2203	4300	6503	10570147	SO:0001819	synonymous_variant	182	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	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.2877G>A	20.37:g.10622147C>T			10570147	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																				0.463	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10622147	C	T	10622147	2	4	121	1	0	0	0	0	0	0	0	1	7955	871	31	1		1	JAG1	20	10622147	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	1061145	10622147	52403373	246	32016										
PCSK2	5126	hgsc.bcm.edu	37	chr20	17437010	17437010	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	caggcaaccacagatttgtaCggcaactgcactctgaggca	10	12	1	2	rs538265087	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:17437010C>T	ENST00000262545.2	+	10	1434	c.1119C>T	c.(1117-1119)taC>taT	p.Y373Y	PCSK2_ENST00000377899.1_Silent_p.Y354Y|PCSK2_ENST00000536609.1_Silent_p.Y338Y	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	373	Peptidase S8.				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)"	CAGATTTGTACGGCAACTGCA	0.507													C|||	2	0.000399361	8e-04	0	5008	,	,		19912	0		0.001	False		,,,				2504	0															0			20											185	186	186					20																	17437010		2203	4300	6503	17385010	SO:0001819	synonymous_variant	5126			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.1119C>T	20.37:g.17437010C>T			17385010	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Silent	SNP	ENST00000262545.2	37	CCDS13125.1																																																																																				0.507	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17437010	C	T	17437010	2	4	121	1	0	0	0	0	0	0	0	1	11632	547	19	1		1	PCSK2	20	17437010	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	6814863	17437010	45588510	247	32017										
BFSP1	631	hgsc.bcm.edu	37	chr20	17475196	17475196	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggagagggctccacctggccGtcataaagcacagagtcttc	12	12	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:17475196G>A	ENST00000377873.3	-	8	1560	c.1521C>T	c.(1519-1521)gaC>gaT	p.D507D	BFSP1_ENST00000544874.1_Silent_p.D368D|BFSP1_ENST00000536626.1_Silent_p.D368D|BFSP1_ENST00000377868.2_Silent_p.D382D	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	507	Tail.				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						CCACCTGGCCGTCATAAAGCA	0.542																																																0			20											62	53	56					20																	17475196		2203	4300	6503	17423196	SO:0001819	synonymous_variant	631			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.1521C>T	20.37:g.17475196G>A			17423196	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	37	CCDS13126.1																																																																																				0.542	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195		A	17475196	G	A	17475196	2	1	121	1	0	0	0	0	0	0	0	1	1416	1136	40	1		1	BFSP1	20	17475196	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10	38186	17475196	45550324	248	32018										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33582119	33582119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gttgcgaggggcgctggctgCggccgaggccaagcgccagg	20	12	0	0	rs369138767		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:33582119C>T	ENST00000262873.7	+	25	2833	c.2741C>T	c.(2740-2742)gCg>gTg	p.A914V		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	872						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)			GCGCTGGCTGCGGCCGAGGCC	0.672																																																0			20						C	VAL/ALA	0,4014		0,0,2007	29	38	35		2741	3.3	0	20		35	2,8314		0,2,4156	no	missense	MYH7B	NM_020884.3	64	0,2,6163	TT,TC,CC		0.0241,0.0,0.0162	benign	914/1984	33582119	2,12328	2007	4158	6165	33045780	SO:0001583	missense	57644			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.2741C>T	20.37:g.33582119C>T	ENSP00000262873:p.Ala914Val		33045780	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.150006	0.57151	0.0	2.41E-4	ENSG00000078814	ENST00000262873	D	0.83163	-1.69	4.32	3.3	0.37823	.	0.425278	0.17358	N	0.177128	T	0.73521	0.3597	L	0.38175	1.15	0.22412	N	0.999123	B	0.23806	0.091	B	0.04013	0.001	T	0.67256	-0.5716	10	0.72032	D	0.01	.	10.038	0.42139	0.4003:0.5997:0.0:0.0	.	872	A7E2Y1	MYH7B_HUMAN	V	914	ENSP00000262873:A914V	ENSP00000262873:A914V	A	+	2	0	MYH7B	33045780	0.867000	0.29959	0.006000	0.13384	0.854000	0.48673	4.412000	0.59787	2.409000	0.81822	0.655000	0.94253	GCG		0.672	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33582119	C	T	33582119	3	4	121	1	0	0	0	0	1	0	0	0	10070	768	27	1	2839	1	MYH7B	20	33582119	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	16106923	33582119	29443401	249	32019										
CHD6	84181	hgsc.bcm.edu	37	chr20	40112055	40112055	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cttagggagtagtttatcaaTcaacacaagctttcctgctg	8	9	2	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:40112055T>A	ENST00000373233.3	-	16	2539	c.2362A>T	c.(2362-2364)Att>Ttt	p.I788F	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	788	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)				AGTTTATCAATCAACACAAGC	0.483																																																0			20											113	104	107					20																	40112055		2203	4300	6503	39545469	SO:0001583	missense	84181			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.2362A>T	20.37:g.40112055T>A	ENSP00000362330:p.Ile788Phe		39545469	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	31	5.104095	0.94245	.	.	ENSG00000124177	ENST00000373233	T	0.77750	-1.12	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000010	T	0.79399	0.4439	N	0.16098	0.37	0.80722	D	1	D	0.67145	0.996	D	0.70487	0.969	D	0.83398	0.0021	10	0.87932	D	0	-14.0533	16.3634	0.83296	0.0:0.0:0.0:1.0	.	788	Q8TD26	CHD6_HUMAN	F	788	ENSP00000362330:I788F	ENSP00000362330:I788F	I	-	1	0	CHD6	39545469	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.970000	0.88000	2.324000	0.78689	0.533000	0.62120	ATT		0.483	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40112055	T	A	40112055	3	1	121	1	0	0	0	0	1	0	0	0	3335	1435	50	5	5873	5	CHD6	20	40112055	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	6529936	40112055	22913465	250	32020										
SGK2	10110	hgsc.bcm.edu	37	chr20	42200775	42200775	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccacattctgtggtacccctGaggtaagcgtaaacatccca	8	13	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:42200775G>T	ENST00000341458.4	+	8	994	c.775G>T	c.(775-777)Gag>Tag	p.E259*	SGK2_ENST00000423407.3_Nonsense_Mutation_p.E199*|SGK2_ENST00000373077.1_Nonsense_Mutation_p.E198*|SGK2_ENST00000373092.3_Nonsense_Mutation_p.E199*|SGK2_ENST00000426287.1_Nonsense_Mutation_p.E225*|SGK2_ENST00000373100.1_Nonsense_Mutation_p.E199*	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> K (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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.E259K(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)			TGGTACCCCTGAGGTAAGCGT	0.547																																																1	Substitution - Missense(1)	lung(1)	20											110	70	84					20																	42200775		2164	4194	6358	41634189	SO:0001587	stop_gained	23678			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.775G>T	20.37:g.42200775G>T	ENSP00000340608:p.Glu259*		41634189	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Nonsense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.018956	0.54576	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	.	.	.	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.6308	0.85032	0.0:0.0:1.0:0.0	.	.	.	.	X	199;199;198;198;199;259;225	.	ENSP00000340608:E259X	E	+	1	0	SGK2	41634189	1.000000	0.71417	0.944000	0.38274	0.134000	0.20937	9.662000	0.98603	2.387000	0.81309	0.563000	0.77884	GAG		0.547	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			T	42200775	G	T	42200775	4	4	121	1	0	0	0	0	0	1	0	0	14246	1291	45	2	805	2	SGK2	20	42200775	Nonsense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	2088720	42200775	20824745	251	32021										
SULF2	55959	hgsc.bcm.edu	37	chr20	46365452	46365452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	cccgtccctgctcacctgtcCggtagccagtgctattgagg	11	15	1	1	rs562017382	byFrequency	TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:46365452C>T	ENST00000359930.4	-	3	1261	c.410G>A	c.(409-411)cGg>cAg	p.R137Q	SULF2_ENST00000478766.1_5'UTR|SULF2_ENST00000467815.1_Missense_Mutation_p.R137Q|SULF2_ENST00000484875.1_Missense_Mutation_p.R137Q|SULF2_ENST00000361612.4_Missense_Mutation_p.R137Q	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	137					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 fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						CTCACCTGTCCGGTAGCCAGT	0.617													C|||	2	0.000399361	0	0.0014	5008	,	,		15068	0		0	False		,,,				2504	0.001															0			20											92	69	77					20																	46365452		2203	4300	6503	45798859	SO:0001583	missense	55959			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.410G>A	20.37:g.46365452C>T	ENSP00000353007:p.Arg137Gln		45798859	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	C	36	5.620982	0.96660	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.98474	-4.95;-4.95;-4.95;-4.95;-4.95	5.24	5.24	0.73138	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.98321	0.9443	L	0.43646	1.37	0.80722	D	1	D;D;D	0.89917	0.967;1.0;1.0	P;D;D	0.91635	0.57;0.999;0.999	D	0.98824	1.0748	10	0.39692	T	0.17	-17.1006	18.8085	0.92048	0.0:1.0:0.0:0.0	.	137;137;137	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	Q	137	ENSP00000353007:R137Q;ENSP00000418290:R137Q;ENSP00000354662:R137Q;ENSP00000418442:R137Q;ENSP00000410026:R137Q	ENSP00000353007:R137Q	R	-	2	0	SULF2	45798859	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	7.814000	0.86154	2.444000	0.82710	0.561000	0.74099	CGG		0.617	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		T	46365452	C	T	46365452	3	4	121	1	0	0	0	0	1	0	0	0	15410	652	23	1	2278	1	SULF2	20	46365452	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	4164677	46365452	16660068	252	32022										
SLCO4A1	28231	hgsc.bcm.edu	37	chr20	61288175	61288175	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gggatgactgtgaatggcttCatcaacacagtcatcacctc	9	11	4	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr20:61288175C>A	ENST00000370507.1	+	1	465	c.369C>A	c.(367-369)ttC>ttA	p.F123L	SLCO4A1_ENST00000217159.1_Missense_Mutation_p.F123L			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	123					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)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TGAATGGCTTCATCAACACAG	0.622																																					Pancreas(168;741 2006 10379 40139 45334)											0			20											51	49	50					20																	61288175		2203	4300	6503	60758620	SO:0001583	missense	28231			AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"Solute carriers"	10953	protein-coding gene	gene with protein product		612436	"solute carrier family 21 (organic anion transporter), member 12"	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.369C>A	20.37:g.61288175C>A	ENSP00000359538:p.Phe123Leu		60758620	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	.	.	.	.	.	.	.	.	.	.	C	0.957	-0.704573	0.03255	.	.	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507;ENST00000342674	T;T	0.35421	1.31;1.31	4.58	1.2	0.21068	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.114616	0.64402	N	0.000014	T	0.18551	0.0445	N	0.21448	0.665	0.47737	D	0.999505	B	0.10296	0.003	B	0.19666	0.026	T	0.11567	-1.0582	10	0.09590	T	0.72	.	6.244	0.20807	0.0:0.5515:0.2878:0.1607	.	123	Q96BD0	SO4A1_HUMAN	L	123	ENSP00000217159:F123L;ENSP00000359538:F123L	ENSP00000217159:F123L	F	+	3	2	SLCO4A1	60758620	1.000000	0.71417	0.905000	0.35620	0.075000	0.17131	1.584000	0.36589	-0.026000	0.13895	0.462000	0.41574	TTC		0.622	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354		A	61288175	C	A	61288175	3	1	121	1	0	0	0	0	1	0	0	0	14766	825	29	2	371	2	SLCO4A1	20	61288175	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	14922723	61288175	1737345	253	32023										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34004045	34004045	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agcaagcagattaaatgacaGatcttcaaatgggtcaatct	8	7	4	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr21:34004045G>A	ENST00000322229.7	-	31	3981	c.3982C>T	c.(3982-3984)Ctg>Ttg	p.L1328L	SYNJ1_ENST00000382491.3_Silent_p.L1281L|SYNJ1_ENST00000357345.3_3'UTR|SYNJ1_ENST00000382499.2_3'UTR|SYNJ1_ENST00000433931.2_Silent_p.L1367L			O43426	SYNJ1_HUMAN	synaptojanin 1	1328	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						TTAAATGACAGATCTTCAAAT	0.413																																																0			21											91	89	90					21																	34004045		2203	4300	6503	32925916	SO:0001819	synonymous_variant	8867			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.3982C>T	21.37:g.34004045G>A			32925916	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	37	CCDS54484.1																																																																																				0.413	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	34004045	G	A	34004045	2	1	121	1	0	0	0	0	0	0	0	1	15491	933	33	3		3	SYNJ1	21	34004045	Silent	SNP	G	TCGA-G5-6235-01A-11D-1733-10		34004045	14125850	254	32024										
RUNX1	861	hgsc.bcm.edu	37	chr21	36231789	36231789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	acttcgaggttctcggggccCatccactgtgattttgatgg	12	10	1	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr21:36231789C>T	ENST00000344691.4	-	3	2091	c.514G>A	c.(514-516)Ggg>Agg	p.G172R	RUNX1_ENST00000358356.5_Missense_Mutation_p.G172R|RUNX1_ENST00000300305.3_Missense_Mutation_p.G199R|RUNX1_ENST00000437180.1_Missense_Mutation_p.G199R|RUNX1_ENST00000399240.1_Missense_Mutation_p.G172R|RUNX1_ENST00000325074.5_Missense_Mutation_p.G187R|RUNX1_ENST00000486278.2_Missense_Mutation_p.G175R	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	172	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.G199R(2)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						TCTCGGGGCCCATCCACTGTG	0.557			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	21											294	256	269					21																	36231789		2203	4300	6503	35153659	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.514G>A	21.37:g.36231789C>T	ENSP00000340690:p.Gly172Arg		35153659	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.698209	0.88830	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278	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	5.12	5.12	0.69794	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99880	0.9943	M	0.91300	3.195	0.80722	D	1	D;D;D;P;P;D;D	0.89917	1.0;1.0;1.0;0.621;0.63;0.998;1.0	D;D;D;B;B;P;D	0.97110	0.996;1.0;0.999;0.367;0.361;0.882;1.0	D	0.96295	0.9217	10	0.87932	D	0	-11.5231	16.0721	0.80941	0.0:1.0:0.0:0.0	.	199;172;172;175;199;187;172	Q2TAM6;Q01196-5;Q01196-3;C9JK12;Q01196-8;Q01196-10;Q01196	.;.;.;.;.;.;RUNX1_HUMAN	R	172;199;199;187;172;175;172;187;175	ENSP00000340690:G172R;ENSP00000300305:G199R;ENSP00000409227:G199R;ENSP00000319459:G187R;ENSP00000382184:G172R;ENSP00000351123:G172R;ENSP00000382182:G187R;ENSP00000438019:G175R	ENSP00000300305:G199R	G	-	1	0	RUNX1	35153659	1.000000	0.71417	0.968000	0.41197	0.987000	0.75469	7.486000	0.81215	2.377000	0.81083	0.655000	0.94253	GGG		0.557	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1			T	36231789	C	T	36231789	3	4	121	1	0	0	0	0	1	0	0	0	13783	594	21	3	896	3	RUNX1	21	36231789	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	2227744	36231789	11898106	255	32025										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40778428	40778428	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttttggtggtagttcttgctCttctttcacaaaaatgtttt	7	6	4	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr21:40778428C>A	ENST00000358268.2	-	10	1921	c.1393G>T	c.(1393-1395)Gag>Tag	p.E465*	LCA5L_ENST00000495240.1_5'UTR|LCA5L_ENST00000288350.3_Nonsense_Mutation_p.E465*|LCA5L_ENST00000380671.2_Nonsense_Mutation_p.E465*|WRB_ENST00000541890.1_Intron			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	465										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)				AGTTCTTGCTCTTCTTTCACA	0.328																																																0			21											108	103	105					21																	40778428		2202	4299	6501	39700298	SO:0001587	stop_gained	150082			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.1393G>T	21.37:g.40778428C>A	ENSP00000351008:p.Glu465*		39700298	D3DSI0|Q3ZCT0	Nonsense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977593	0.92982	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268	.	.	.	4.37	0.305	0.15801	.	0.658236	0.14533	N	0.313724	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-11.9513	1.5455	0.02564	0.1409:0.3487:0.2946:0.2157	.	.	.	.	X	465	.	ENSP00000288350:E465X	E	-	1	0	LCA5L	39700298	0.000000	0.05858	0.001000	0.08648	0.473000	0.32948	-0.265000	0.08644	-0.183000	0.10585	0.467000	0.42956	GAG		0.328	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		A	40778428	C	A	40778428	4	1	121	1	0	0	0	0	0	1	0	0	8679	922	32	2	623	2	LCA5L	21	40778428	Nonsense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	4546639	40778428	7351467	256	32026										
EP300	2033	hgsc.bcm.edu	37	chr22	41572266	41572266	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ttcaggtcttctttgtgatcCgcctcattgctggccctgct	9	13	4	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr22:41572266C>T	ENST00000263253.7	+	30	6014	c.4795C>T	c.(4795-4797)Cgc>Tgc	p.R1599C	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	1599	Binding region for E1A adenovirus.|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						CTTTGTGATCCGCCTCATTGC	0.537			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	0			22											118	115	116					22																	41572266		2203	4300	6503	39902212	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	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.4795C>T	22.37:g.41572266C>T	ENSP00000263253:p.Arg1599Cys		39902212	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405047	0.62288	.	.	ENSG00000100393	ENST00000263253	D	0.93906	-3.31	5.03	5.03	0.67393	.	0.000000	0.49916	D	0.000137	D	0.96932	0.8998	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97424	1.0011	10	0.72032	D	0.01	-9.23	18.7274	0.91718	0.0:1.0:0.0:0.0	.	1599	Q09472	EP300_HUMAN	C	1599	ENSP00000263253:R1599C	ENSP00000263253:R1599C	R	+	1	0	EP300	39902212	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.500000	0.84329	0.650000	0.86243	CGC		0.537	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41572266	C	T	41572266	3	4	121	1	0	0	0	0	1	0	0	0	5161	652	23	1	4913	1	EP300	22	41572266	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10		41572266	9732300	257	32027										
EP300	2033	hgsc.bcm.edu	37	chr22	41574238	41574238	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tgaacatgaaccacaacaccAtgccttcacaattccgagac	5	14	1	3			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr22:41574238A>G	ENST00000263253.7	+	31	7742	c.6523A>G	c.(6523-6525)Atg>Gtg	p.M2175V	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	2175	Interaction with HTLV-1 Tax.|Interaction with NCOA2.				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.M2175L(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						CCACAACACCATGCCTTCACA	0.582			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	22											95	77	83					22																	41574238		2203	4300	6503	39904184	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	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.6523A>G	22.37:g.41574238A>G	ENSP00000263253:p.Met2175Val		39904184	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	5.761	0.324848	0.10900	.	.	ENSG00000100393	ENST00000263253	D	0.82711	-1.64	5.09	5.09	0.68999	.	0.000000	0.56097	D	0.000024	T	0.77164	0.4090	L	0.47716	1.5	0.34005	D	0.650724	B	0.13145	0.007	B	0.09377	0.004	T	0.77104	-0.2711	10	0.21540	T	0.41	-7.3167	14.0417	0.64678	1.0:0.0:0.0:0.0	.	2175	Q09472	EP300_HUMAN	V	2175	ENSP00000263253:M2175V	ENSP00000263253:M2175V	M	+	1	0	EP300	39904184	1.000000	0.71417	0.997000	0.53966	0.703000	0.40648	4.923000	0.63412	1.915000	0.55452	0.459000	0.35465	ATG		0.582	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41574238	A	G	41574238	3	3	121	1	0	0	0	0	1	0	0	0	5161	217	8	4	6645	4	EP300	22	41574238	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	1972	41574238	9730328	258	32028										
EP300	2033	hgsc.bcm.edu	37	chr22	41574377	41574377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccaaggagttggctacccacCacagcagcagcagcggatgc	12	14	0	0	rs28937578		TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr22:41574377C>T	ENST00000263253.7	+	31	7881	c.6662C>T	c.(6661-6663)cCa>cTa	p.P2221L	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	2221	Interaction with NCOA2.		P -> Q (in a colorectal cancer sample; dbSNP:rs28937578). {ECO:0000269|PubMed:10700188}.		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.P2221Q(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						GGCTACCCACCACAGCAGCAG	0.567			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	1	Substitution - Missense(1)	large_intestine(1)	22											58	58	58					22																	41574377		2203	4300	6503	39904323	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	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.6662C>T	22.37:g.41574377C>T	ENSP00000263253:p.Pro2221Leu		39904323	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	1.481	-0.557238	0.03967	.	.	ENSG00000100393	ENST00000263253	D	0.83075	-1.68	5.5	3.21	0.36854	.	0.310466	0.22716	N	0.056503	T	0.72162	0.3426	L	0.29908	0.895	0.24516	N	0.994187	B	0.15141	0.012	B	0.08055	0.003	T	0.62651	-0.6809	10	0.42905	T	0.14	.	11.1262	0.48320	0.2597:0.7403:0.0:0.0	.	2221	Q09472	EP300_HUMAN	L	2221	ENSP00000263253:P2221L	ENSP00000263253:P2221L	P	+	2	0	EP300	39904323	0.933000	0.31639	0.180000	0.23079	0.223000	0.24884	1.193000	0.32162	2.581000	0.87130	0.655000	0.94253	CCA		0.567	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41574377	C	T	41574377	3	4	121	1	0	0	0	0	1	0	0	0	5161	594	21	3	6784	3	EP300	22	41574377	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	139	41574377	9730189	259	32029										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50879368	50879368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggatggcgaccagaaggcagCgagtgccatggatgcggtga	18	8	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chr22:50879368C>T	ENST00000216061.5	+	23	2883	c.2513C>T	c.(2512-2514)gCg>gTg	p.A838V	PPP6R2_ENST00000359139.3_Missense_Mutation_p.A805V|PPP6R2_ENST00000395744.3_Missense_Mutation_p.A804V|PPP6R2_ENST00000395741.3_Missense_Mutation_p.A805V			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	838						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						CAGAAGGCAGCGAGTGCCATG	0.692																																																0			22											40	43	42					22																	50879368		2203	4300	6503	49226234	SO:0001583	missense	0			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.2513C>T	22.37:g.50879368C>T	ENSP00000216061:p.Ala838Val		49226234	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	37		.	.	.	.	.	.	.	.	.	.	C	12.49	1.954248	0.34471	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.74	-0.706	0.11249	.	1.930550	0.04326	N	0.351527	T	0.25901	0.0631	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B;B	0.19935	0.04;0.031;0.018;0.031;0.013;0.031	B;B;B;B;B;B	0.15484	0.013;0.01;0.004;0.004;0.004;0.006	T	0.18524	-1.0334	10	0.34782	T	0.22	-1.3176	2.569	0.04790	0.19:0.4364:0.2248:0.1488	.	364;831;838;805;804;805	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	V	805;805;804;838	ENSP00000352051:A805V;ENSP00000379090:A805V;ENSP00000379093:A804V;ENSP00000216061:A838V	ENSP00000216061:A838V	A	+	2	0	PPP6R2	49226234	0.011000	0.17503	0.001000	0.08648	0.033000	0.12548	0.067000	0.14510	0.322000	0.23283	0.491000	0.48974	GCG		0.692	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		T	50879368	C	T	50879368	3	4	121	1	0	0	0	0	1	0	0	0	13874	768	27	1	2485	1	SAPS2	22	50879368	Missense_Mutation	SNP	C	TCGA-G5-6235-01A-11D-1733-10	9304991	50879368	425198	260	32030										
ATXN3L	92552	hgsc.bcm.edu	37	chrX	13337616	13337616	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gccaagaaatttgcaaggcaTgtatctgatattaattctgg	9	6	2	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:13337616T>C	ENST00000380622.2	-	1	902	c.438A>G	c.(436-438)acA>acG	p.T146T	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	146	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.				protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)	p.T146T(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TTGCAAGGCATGTATCTGATA	0.373																																																1	Substitution - coding silent(1)	ovary(1)	X											65	61	62					X																	13337616		1568	3582	5150	13247537	SO:0001819	synonymous_variant	92552				CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.438A>G	X.37:g.13337616T>C			13247537	B2RNY8	Silent	SNP	ENST00000380622.2	37	CCDS48080.1																																																																																				0.373	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		C	13337616	T	C	13337616	2	2	121	1	0	0	0	0	0	0	0	1	1215	1451	51	4		4	ATXN3L	23	13337616	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10		13337616	141932944	261	32031										
GPR64	10149	hgsc.bcm.edu	37	chrX	19039316	19039316	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gtgaatgtacaatttaatgtGctgtaaggagaaatatacat	9	3	0	2			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:19039316G>A	ENST00000379869.3	-	14	712	c.549C>T	c.(547-549)agC>agT	p.S183S	GPR64_ENST00000379873.2_Splice_Site_p.S183S|GPR64_ENST00000340581.3_Splice_Site_p.S153S|GPR64_ENST00000357544.3_Splice_Site_p.S153S|GPR64_ENST00000356606.4_Splice_Site_p.S169S|GPR64_ENST00000379878.3_Splice_Site_p.S167S|GPR64_ENST00000357991.3_Splice_Site_p.S180S|GPR64_ENST00000379876.1_Splice_Site_p.S159S|GPR64_ENST00000360279.4_Splice_Site_p.S161S|GPR64_ENST00000354791.3_Splice_Site_p.S167S	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	183					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					AATTTAATGTGCTGTAAGGAG	0.338																																																0			X											106	87	93					X																	19039316		2203	4298	6501	18949237	SO:0001630	splice_region_variant	10149			X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"-", "GPCR / Class B : Orphans"	4516	protein-coding gene	gene with protein product	"epididymal protein 6"	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.549-1C>T	X.37:g.19039316G>A			18949237	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Silent	SNP	ENST00000379869.3	37	CCDS43923.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112062	0.37242	.	.	ENSG00000173698	ENST00000397917	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	T	0.72946	0.3524	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75428	-0.3321	5	0.62326	D	0.03	.	12.9938	0.58635	0.0:0.0:1.0:0.0	.	.	.	.	Y	107	.	ENSP00000381013:H107Y	H	-	1	0	GPR64	18949237	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.168000	0.58216	2.466000	0.83321	0.594000	0.82650	CAC		0.338	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2		Silent	A	19039316	G	A	19039316	5	1	121	1	0	0	0	0	0	0	1	0	6725	1333	46	3	2568	3	GPR64	23	19039316	Splice_Site	SNP	G	TCGA-G5-6235-01A-11D-1733-10	5701700	19039316	136231244	262	32032										
ZNF645	158506	hgsc.bcm.edu	37	chrX	22291524	22291524	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	tcatatcaaacgccgccataAgagagctcgaaaacaagtta	7	10	2	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:22291524A>T	ENST00000323684.1	+	1	460	c.416A>T	c.(415-417)aAg>aTg	p.K139M		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	139	HYB domain.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						CGCCGCCATAAGAGAGCTCGA	0.433																																																0			X											62	59	60					X																	22291524		2203	4300	6503	22201445	SO:0001583	missense	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.416A>T	X.37:g.22291524A>T	ENSP00000323348:p.Lys139Met		22201445	A0AV29|A0AV31|E3SBK4|Q6DJY9	Missense_Mutation	SNP	ENST00000323684.1	37	CCDS14205.1	.	.	.	.	.	.	.	.	.	.	A	2.352	-0.348645	0.05208	.	.	ENSG00000175809	ENST00000323684	T	0.27402	1.67	3.52	-3.66	0.04489	Zinc finger, C2H2 (1);	0.402514	0.26571	N	0.023637	T	0.08891	0.0220	N	0.12887	0.27	0.09310	N	1	B	0.33044	0.395	B	0.33042	0.157	T	0.36720	-0.9736	10	0.02654	T	1	.	1.4357	0.02343	0.2231:0.3067:0.318:0.1522	.	139	Q8N7E2	ZN645_HUMAN	M	139	ENSP00000323348:K139M	ENSP00000323348:K139M	K	+	2	0	ZNF645	22201445	1.000000	0.71417	0.000000	0.03702	0.005000	0.04900	1.081000	0.30791	-0.932000	0.03742	0.430000	0.28490	AAG		0.433	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		T	22291524	A	T	22291524	3	4	121	1	0	0	0	0	1	0	0	0	18100	72	3	5	418	5	ZNF645	23	22291524	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	3252208	22291524	132979036	263	32033										
FAM120C	54954	hgsc.bcm.edu	37	chrX	54106713	54106713	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	gatcctctaccagtctgttcTtttccatgcctttagcaagt	6	12	3	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:54106713T>C	ENST00000375180.2	-	15	3044	c.2988A>G	c.(2986-2988)aaA>aaG	p.K996K	FAM120C_ENST00000328235.4_Missense_Mutation_p.K859R	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	996							poly(A) RNA binding (GO:0044822)	p.K996N(1)		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						CAGTCTGTTCTTTTCCATGCC	0.368																																																1	Substitution - Missense(1)	ovary(1)	X											163	137	146					X																	54106713		2203	4300	6503	54123438	SO:0001819	synonymous_variant	54954			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.2988A>G	X.37:g.54106713T>C			54123438	B2RMT7	Silent	SNP	ENST00000375180.2	37	CCDS14356.1	.	.	.	.	.	.	.	.	.	.	T	1.487	-0.555615	0.03967	.	.	ENSG00000184083	ENST00000328235	T	0.32753	1.44	4.89	3.72	0.42706	.	0.503857	0.20488	N	0.091343	T	0.21227	0.0511	.	.	.	0.80722	D	1	B	0.32160	0.358	B	0.33620	0.167	T	0.04537	-1.0944	9	0.27785	T	0.31	-5.3281	7.4002	0.26960	0.0:0.1063:0.0:0.8937	.	859	F8W881	.	R	859	ENSP00000329896:K859R	ENSP00000329896:K859R	K	-	2	0	FAM120C	54123438	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	1.309000	0.33539	1.733000	0.51620	0.412000	0.27726	AAG		0.368	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		C	54106713	T	C	54106713	2	2	121	1	0	0	0	0	0	0	0	1	5434	1606	56	4		4	FAM120C	23	54106713	Silent	SNP	T	TCGA-G5-6235-01A-11D-1733-10	31815189	54106713	101163847	264	32034										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73963171	73963171	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ctgcatggtttatttaaggcAggcttttctccattatcctt	7	9	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:73963171A>G	ENST00000055682.6	-	3	1832	c.1221T>C	c.(1219-1221)ccT>ccC	p.P407P		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	407					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						TATTTAAGGCAGGCTTTTCTC	0.438																																																0			X											253	213	227					X																	73963171		2203	4300	6503	73879896	SO:0001819	synonymous_variant	340533				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.1221T>C	X.37:g.73963171A>G			73879896	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	37	CCDS35337.1																																																																																				0.438	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		G	73963171	A	G	73963171	2	3	121	1	0	0	0	0	0	0	0	1	8290	175	7	4		4	KIAA2022	23	73963171	Silent	SNP	A	TCGA-G5-6235-01A-11D-1733-10	19856458	73963171	81307389	265	32035										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79698263	79698263	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agttacatacttgcaagccaCaatggaatcagctataagga	8	8	1	0			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:79698263C>T	ENST00000308293.5	+	3	464	c.225C>T	c.(223-225)caC>caT	p.H75H	FAM46D_ENST00000538312.1_Silent_p.H75H	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	75										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						TTGCAAGCCACAATGGAATCA	0.388																																																0			X											114	101	105					X																	79698263		2203	4300	6503	79584919	SO:0001819	synonymous_variant	169966			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.225C>T	X.37:g.79698263C>T			79584919	B2R9Q6|Q7Z3F6|Q8NHU1	Silent	SNP	ENST00000308293.5	37	CCDS14446.1																																																																																				0.388	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		T	79698263	C	T	79698263	2	4	121	1	0	0	0	0	0	0	0	1	5587	477	17	3		3	FAM46D	23	79698263	Silent	SNP	C	TCGA-G5-6235-01A-11D-1733-10	5735092	79698263	75572297	266	32036										
BEX2	84707	hgsc.bcm.edu	37	chrX	102564882	102564882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ccacgatgagattgtttaacGctcgttcctctttggactcc	8	12	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:102564882G>A	ENST00000372677.3	-	3	290	c.23C>T	c.(22-24)gCg>gTg	p.A8V	BEX2_ENST00000536889.1_Missense_Mutation_p.A40V|BEX2_ENST00000372674.1_Missense_Mutation_p.A8V	NM_032621.3	NP_116010.1	Q9BXY8	BEX2_HUMAN	brain expressed X-linked 2	8					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|lung(1)|ovary(1)	3						ATTGTTTAACGCTCGTTCCTC	0.463																																																0			X											60	55	57					X																	102564882		2203	4300	6503	102451538	SO:0001583	missense	84707			BC015522	CCDS14505.1, CCDS55467.1	Xq22	2014-03-21			ENSG00000133134	ENSG00000133134			30933	protein-coding gene	gene with protein product		300691				16221301	Standard	NM_001168399		Approved	DJ79P11.1	uc004eka.3	Q9BXY8	OTTHUMG00000022095	ENST00000372677.3:c.23C>T	X.37:g.102564882G>A	ENSP00000361762:p.Ala8Val		102451538	B2R574|D3DXA2|F5H7H5|Q5JVV9	Missense_Mutation	SNP	ENST00000372677.3	37	CCDS14505.1	.	.	.	.	.	.	.	.	.	.	G	2.069	-0.413461	0.04799	.	.	ENSG00000133134	ENST00000372677;ENST00000536889;ENST00000372674;ENST00000449185	T;T;T;T	0.10960	2.92;2.9;2.92;2.82	4.19	-8.39	0.00969	.	1.658220	0.03767	N	0.259209	T	0.06690	0.0171	N	0.25485	0.75	0.09310	N	1	B;B	0.24368	0.003;0.102	B;B	0.17979	0.002;0.02	T	0.16541	-1.0399	10	0.17369	T	0.5	.	9.3608	0.38195	0.6779:0.0:0.1343:0.1878	.	8;40	Q9BXY8;F5H7H5	BEX2_HUMAN;.	V	8;40;8;8	ENSP00000361762:A8V;ENSP00000442521:A40V;ENSP00000361759:A8V;ENSP00000394915:A8V	ENSP00000361759:A8V	A	-	2	0	BEX2	102451538	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	-1.344000	0.02639	-3.614000	0.00132	-0.340000	0.08031	GCG		0.463	BEX2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057702.1	NM_032621		A	102564882	G	A	102564882	3	1	121	1	0	0	0	0	1	0	0	0	1412	1087	38	1	367	1	BEX2	23	102564882	Missense_Mutation	SNP	G	TCGA-G5-6235-01A-11D-1733-10	22866619	102564882	52705678	267	32037										
TMSB15B	286527	hgsc.bcm.edu	37	chrX	103219130	103219130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	agacttgtcggaagtggagaAgtttgacaggtcaaaactga	13	5	1	4			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:103219130A>G	ENST00000436583.1	+	2	1678	c.35A>G	c.(34-36)aAg>aGg	p.K12R	TMSB15B_ENST00000569577.1_Missense_Mutation_p.K12R|TMSB15B_ENST00000540220.1_Missense_Mutation_p.K12R|TMSB15B_ENST00000567181.1_Missense_Mutation_p.K12R|TMSB15B_ENST00000563257.1_Missense_Mutation_p.K12R|TMSB15B_ENST00000419165.1_Missense_Mutation_p.K12R			P0CG35	TB15B_HUMAN	thymosin beta 15B	12					actin cytoskeleton organization (GO:0030036)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				skin(1)	1						GAAGTGGAGAAGTTTGACAGG	0.358																																																0			X											106	87	93					X																	103219130		1568	3582	5150	103105786	SO:0001583	missense	286527				CCDS59172.1	Xq22.2	2009-01-12			ENSG00000158427	ENSG00000158427			28612	protein-coding gene	gene with protein product						17567946	Standard	NM_194324		Approved	MGC39900	uc010noz.3	P0CG35	OTTHUMG00000022117	ENST00000436583.1:c.35A>G	X.37:g.103219130A>G	ENSP00000455771:p.Lys12Arg		103105786	A8K614|Q99406	Missense_Mutation	SNP	ENST00000436583.1	37	CCDS59172.1																																																																																				0.358	TMSB15B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057752.2	NM_194324		G	103219130	A	G	103219130	3	3	121	1	0	0	0	0	1	0	0	0	16295	72	3	4	37	4	TMSB15B	23	103219130	Missense_Mutation	SNP	A	TCGA-G5-6235-01A-11D-1733-10	654248	103219130	52051430	268	32038										
PDZD4	57595	hgsc.bcm.edu	37	chrX	153070578	153070578	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0261194029850746	7	1	0.354517396184063	0	0.365342354846172	0.00890091190715127	0.0920060331825037	0	ggcagggggtgatttcagttTacgagcacgcagctccccct	13	12	1	1			TCGA-G5-6235-01A-11D-1733-10	TCGA-G5-6235-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	e4a584c8-cdab-4cf2-ac96-fd3ace3b9fd8	4f521799-7126-4cc3-a9d9-d254a6d2f0d6	g.chrX:153070578T>C	ENST00000164640.4	-	7	927	c.736A>G	c.(736-738)Aaa>Gaa	p.K246E	PDZD4_ENST00000393758.2_Missense_Mutation_p.K171E|PDZD4_ENST00000544474.1_Missense_Mutation_p.K137E|PDZD4_ENST00000475140.1_5'UTR	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	246						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)					GATTTCAGTTTACGAGCACGC	0.612																																																0			X											131	111	118					X																	153070578		2203	4300	6503	152723772	SO:0001583	missense	57595			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.736A>G	X.37:g.153070578T>C	ENSP00000164640:p.Lys246Glu		152723772	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Missense_Mutation	SNP	ENST00000164640.4	37	CCDS14732.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.765803	0.00651	.	.	ENSG00000067840	ENST00000164640;ENST00000393758;ENST00000537633;ENST00000544474	T;T;T	0.04275	3.66;3.66;3.87	5.03	5.03	0.67393	.	0.357432	0.31721	N	0.007177	T	0.02571	0.0078	N	0.14661	0.345	0.33652	D	0.60855	B;B;B;B;B	0.29716	0.027;0.013;0.005;0.255;0.007	B;B;B;B;B	0.24394	0.016;0.01;0.006;0.053;0.01	T	0.22800	-1.0206	10	0.06365	T	0.9	-44.5132	9.5459	0.39279	0.0:0.0:0.1744:0.8255	.	137;252;246;171;150	B7ZKY3;Q17RL8;Q76G19;D3DWW0;B3KVR9	.;.;PDZD4_HUMAN;.;.	E	246;171;150;137	ENSP00000164640:K246E;ENSP00000377355:K171E;ENSP00000442033:K137E	ENSP00000164640:K246E	K	-	1	0	PDZD4	152723772	0.997000	0.39634	0.761000	0.31378	0.011000	0.07611	4.641000	0.61375	1.667000	0.50832	0.486000	0.48141	AAA		0.612	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512		C	153070578	T	C	153070578	3	2	121	1	0	0	0	0	1	0	0	0	11734	1763	61	4	1581	4	PDZD4	23	153070578	Missense_Mutation	SNP	T	TCGA-G5-6235-01A-11D-1733-10	49851448	153070578	2199982	269	32039										
DMBX1	127343	hgsc.bcm.edu	37	chr1	46977882	46977882	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	actactcgtccttcgaagtaGggggtccggcccctgctgct	12	14	0	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:46977882G>A	ENST00000360032.3	+	4	864	c.850G>A	c.(850-852)Ggg>Agg	p.G284R	DMBX1_ENST00000371956.4_Missense_Mutation_p.G289R	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)					CTTCGAAGTAGGGGGTCCGGC	0.647																																																0			1											35	37	36					1																	46977882		2203	4299	6502	46750469	SO:0001583	missense	127343			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.850G>A	1.37:g.46977882G>A	ENSP00000353132:p.Gly284Arg		46750469		Missense_Mutation	SNP	ENST00000360032.3	37	CCDS536.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870597	0.72065	.	.	ENSG00000197587	ENST00000371956;ENST00000360032	D;D	0.93712	-3.18;-3.27	5.46	4.54	0.55810	.	0.476895	0.22990	N	0.053201	D	0.92541	0.7631	L	0.34521	1.04	0.42064	D	0.991176	P;D	0.54964	0.948;0.969	P;P	0.54499	0.572;0.754	D	0.91903	0.5533	10	0.38643	T	0.18	.	14.9902	0.71381	0.0:0.0:0.8564:0.1436	.	289;284	Q8NFW5;Q8NFW5-2	DMBX1_HUMAN;.	R	289;284	ENSP00000361024:G289R;ENSP00000353132:G284R	ENSP00000353132:G284R	G	+	1	0	DMBX1	46750469	1.000000	0.71417	0.988000	0.46212	0.493000	0.33554	6.048000	0.71046	1.416000	0.47057	0.655000	0.94253	GGG		0.647	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1			A	46977882	G	A	46977882	3	1	122	1	0	0	0	0	1	0	0	0	4589	1000	35	3	879	3	DMBX1	1	46977882	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10		46977882	202272739	1	32040										
KANK4	163782	hgsc.bcm.edu	37	chr1	62737156	62737156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	caagcgatgcttacccaccgTtaaccccaacaaactgaagg	7	14	0	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:62737156T>C	ENST00000371153.4	-	4	2384	c.2006A>G	c.(2005-2007)aAc>aGc	p.N669S	KANK4_ENST00000354381.3_Missense_Mutation_p.N41S|KANK4_ENST00000371150.1_Missense_Mutation_p.N25S	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	669						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						TTACCCACCGTTAACCCCAAC	0.478																																																0			1											197	182	187					1																	62737156		2203	4300	6503	62509744	SO:0001583	missense	163782			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.2006A>G	1.37:g.62737156T>C	ENSP00000360195:p.Asn669Ser		62509744	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.720979	0.89205	.	.	ENSG00000132854	ENST00000371153;ENST00000354381;ENST00000371150	T;T;T	0.73575	-0.76;-0.11;-0.74	5.67	5.67	0.87782	.	0.000000	0.43110	D	0.000603	D	0.87954	0.6308	M	0.86953	2.85	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.89824	0.3991	10	0.66056	D	0.02	-36.7437	15.924	0.79597	0.0:0.0:0.0:1.0	.	41;669	Q5T7N3-2;Q5T7N3	.;KANK4_HUMAN	S	669;41;25	ENSP00000360195:N669S;ENSP00000346352:N41S;ENSP00000360192:N25S	ENSP00000346352:N41S	N	-	2	0	KANK4	62509744	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.532000	0.81985	2.163000	0.67991	0.459000	0.35465	AAC		0.478	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		C	62737156	T	C	62737156	3	2	122	1	0	0	0	0	1	0	0	0	8000	1725	60	4	1009	4	KANK4	1	62737156	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	15759274	62737156	186513465	2	32041										
HRNR	388697	hgsc.bcm.edu	37	chr1	152193158	152193158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cgtggctggaggagtgccccGaaccggacccatgtcggacg	16	13	0	0	rs201797889		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:152193158G>A	ENST00000368801.2	-	3	1022	c.947C>T	c.(946-948)tCg>tTg	p.S316L	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	316					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)			GGAGTGCCCCGAACCGGACCC	0.607																																																0			1						G	LEU/SER	0,4406		0,0,2203	82	92	89		947	-0.9	0	1		89	2,8598	2.2+/-6.3	0,2,4298	yes	missense	HRNR	NM_001009931.1	145	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	316/2851	152193158	2,13004	2203	4300	6503	150459782	SO:0001583	missense	388697			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.947C>T	1.37:g.152193158G>A	ENSP00000357791:p.Ser316Leu		150459782	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	9.470	1.095297	0.20471	0.0	2.33E-4	ENSG00000197915	ENST00000368801	T	0.01804	4.63	4.04	-0.89	0.10577	.	.	.	.	.	T	0.00300	0.0009	N	0.14661	0.345	0.09310	N	1	P	0.37864	0.61	B	0.21917	0.037	T	0.42275	-0.9461	9	0.27082	T	0.32	.	4.0184	0.09654	0.2066:0.0:0.4864:0.307	.	316	Q86YZ3	HORN_HUMAN	L	316	ENSP00000357791:S316L	ENSP00000357791:S316L	S	-	2	0	HRNR	150459782	0.056000	0.20664	0.000000	0.03702	0.001000	0.01503	0.903000	0.28475	-0.381000	0.07882	0.644000	0.83932	TCG		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152193158	G	A	152193158	3	1	122	1	0	0	0	0	1	0	0	0	7380	1059	37	1	7609	1	HRNR	1	152193158	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	89456002	152193158	97057463	3	32042										
FLG	2312	hgsc.bcm.edu	37	chr1	152282997	152282997	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtgctgggtgcagtctgtccGtgtgtggactcagactgttc	15	9	2	1	rs142950612		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:152282997G>A	ENST00000368799.1	-	3	4400	c.4365C>T	c.(4363-4365)caC>caT	p.H1455H	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1455	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)			CAGTCTGTCCGTGTGTGGACT	0.572									Ichthyosis				g|||	1	0.000199681	8e-04	0	5008	,	,		19930	0		0	False		,,,				2504	0															0			1						G		2,4404	4.2+/-10.8	0,2,2201	221	212	215		4365	-7.9	0	1	dbSNP_134	215	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FLG	NM_002016.1		0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231		1455/4062	152282997	3,13003	2203	4300	6503	150549621	SO:0001819	synonymous_variant	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	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.4365C>T	1.37:g.152282997G>A			150549621	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152282997	G	A	152282997	2	1	122	1	0	0	0	0	0	0	0	1	5941	1136	40	1		1	FLG	1	152282997	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10	89839	152282997	96967624	4	32043										
GON4L	54856	hgsc.bcm.edu	37	chr1	155823441	155823441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gatcccaggatagtgacaccGaactcaagtccttaacctgg	9	12	1	1	rs141714959		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:155823441G>A	ENST00000368331.1	-	2	179	c.131C>T	c.(130-132)tCg>tTg	p.S44L	GON4L_ENST00000361040.5_Missense_Mutation_p.S44L|GON4L_ENST00000271883.5_Missense_Mutation_p.S44L|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Missense_Mutation_p.S44L	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	44					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)					TAGTGACACCGAACTCAAGTC	0.468																																																0			1						G	LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	187	164	171		131,131	4.4	0	1	dbSNP_134	171	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GON4L	NM_001037533.1,NM_032292.4	145,145	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	44/2241,44/1530	155823441	2,13004	2203	4300	6503	154090065	SO:0001583	missense	54856			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.131C>T	1.37:g.155823441G>A	ENSP00000357315:p.Ser44Leu		154090065	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	G	13.84	2.358093	0.41801	2.27E-4	1.16E-4	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040	T;T;T;T	0.18016	2.41;2.41;2.41;2.24	4.38	4.38	0.52667	.	0.221046	0.23340	N	0.049245	T	0.17109	0.0411	L	0.34521	1.04	0.09310	N	1	P;D;D	0.71674	0.938;0.997;0.998	B;D;D	0.75484	0.285;0.968;0.986	T	0.03043	-1.1079	10	0.45353	T	0.12	.	12.3015	0.54876	0.0:0.0:1.0:0.0	.	44;44;44	Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;GON4L_HUMAN;.	L	44	ENSP00000396117:S44L;ENSP00000357315:S44L;ENSP00000271883:S44L;ENSP00000354322:S44L	ENSP00000271883:S44L	S	-	2	0	GON4L	154090065	0.057000	0.20700	0.018000	0.16275	0.170000	0.22686	2.751000	0.47508	2.251000	0.74343	0.561000	0.74099	TCG		0.468	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155823441	G	A	155823441	3	1	122	1	0	0	0	0	1	0	0	0	6592	1059	37	1	6832	1	GON4L	1	155823441	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	3540444	155823441	93427180	5	32044										
KIF14	9928	hgsc.bcm.edu	37	chr1	200522807	200522807	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tagctgccaacagaagtagaAggcacactgaagtcactgta	10	9	1	3	rs529988099		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:200522807A>G	ENST00000367350.4	-	30	5094	c.4656T>C	c.(4654-4656)ccT>ccC	p.P1552P		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1552	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						CAGAAGTAGAAGGCACACTGA	0.403													A|||	1	0.000199681	8e-04	0	5008	,	,		20000	0		0	False		,,,				2504	0															0			1											99	95	96					1																	200522807		2203	4300	6503	198789430	SO:0001819	synonymous_variant	9928			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.4656T>C	1.37:g.200522807A>G			198789430	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																				0.403	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		G	200522807	A	G	200522807	2	3	122	1	0	0	0	0	0	0	0	1	8297	59	3	4		4	KIF14	1	200522807	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10	44699366	200522807	48727814	6	32045										
RYR2	6262	hgsc.bcm.edu	37	chr1	237580424	237580424	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ctagagacgctaagagttgcGtaagtagaacttctaaacac	9	8	1	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:237580424G>A	ENST00000366574.2	+	11	1165		c.e11+1		RYR2_ENST00000542537.1_Splice_Site|RYR2_ENST00000360064.6_Splice_Site	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)						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.?(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)			TAAGAGTTGCGTAAGTAGAAC	0.448																																																1	Unknown(1)	lung(1)	1											111	109	110					1																	237580424		2054	4221	6275	235647047	SO:0001630	splice_region_variant	6262			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.848+1G>A	1.37:g.237580424G>A			235647047	Q15411|Q546N8|Q5T3P2	Splice_Site	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	32	5.139705	0.94560	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4581	0.99154	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RYR2	235647047	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.740000	0.98839	2.835000	0.97688	0.650000	0.86243	.		0.448	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Intron	A	237580424	G	A	237580424	5	1	122	1	0	0	0	0	0	0	1	0	13806	1159	40	1	891	1	RYR2	1	237580424	Splice_Site	SNP	G	TCGA-G5-6641-01A-11D-1826-10	37057617	237580424	11670197	7	32046										
ADSS	159	hgsc.bcm.edu	37	chr1	244582174	244582174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tacccaaaccagtacaaacaCctccaacagtacaatttgaa	3	13	0	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:244582174C>T	ENST00000366535.3	-	9	1149	c.833G>A	c.(832-834)gGt>gAt	p.G278D	ADSS_ENST00000462358.1_5'Flank	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)			AGTACAAACACCTCCAACAGT	0.363																																																0			1											81	75	77					1																	244582174		2203	4300	6503	242648797	SO:0001583	missense	159			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.833G>A	1.37:g.244582174C>T	ENSP00000355493:p.Gly278Asp		242648797		Missense_Mutation	SNP	ENST00000366535.3	37	CCDS1624.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046908	0.93740	.	.	ENSG00000035687	ENST00000366535;ENST00000449326	T	0.49432	0.78	5.98	5.07	0.68467	.	0.044145	0.85682	D	0.000000	T	0.79269	0.4417	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86775	0.1975	10	0.87932	D	0	-13.7219	15.3276	0.74179	0.0:0.933:0.0:0.067	.	278	P30520	PURA2_HUMAN	D	278;257	ENSP00000355493:G278D	ENSP00000355493:G278D	G	-	2	0	ADSS	242648797	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	1.541000	0.49316	0.591000	0.81541	GGT		0.363	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126		T	244582174	C	T	244582174	3	4	122	1	0	0	0	0	1	0	0	0	347	507	18	3	557	3	ADSS	1	244582174	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	7001750	244582174	4668447	8	32047										
OR2B11	127623	hgsc.bcm.edu	37	chr1	247614573	247614573	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cgtcccaaaggccttgtgtcGtcccttggaggactggatcc	12	13	0	0	rs145019591	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:247614573G>A	ENST00000318749.6	-	1	735	c.712C>T	c.(712-714)Cga>Tga	p.R238*		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R238*(2)		endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	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;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GCCTTGTGTCGTCCCTTGGAG	0.562																																																2	Substitution - Nonsense(2)	prostate(1)|endometrium(1)	1						G	stop/ARG	2,4404	4.2+/-10.8	0,2,2201	122	117	119		712	3.2	0	1	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	OR2B11	NM_001004492.1		0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231		238/318	247614573	3,13003	2203	4300	6503	245681196	SO:0001587	stop_gained	127623				CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"GPCR / Class A : Olfactory receptors"	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.712C>T	1.37:g.247614573G>A	ENSP00000325682:p.Arg238*		245681196	B2RP03	Nonsense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.169584	0.78452	4.54E-4	1.16E-4	ENSG00000177535	ENST00000318749	.	.	.	5.09	3.15	0.36227	.	0.514615	0.16116	N	0.228849	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2879	0.49232	0.0:0.0:0.4885:0.5115	.	.	.	.	X	238	.	ENSP00000325682:R238X	R	-	1	2	OR2B11	245681196	0.000000	0.05858	0.011000	0.14972	0.763000	0.43281	-0.194000	0.09559	0.783000	0.33636	0.643000	0.83706	CGA		0.562	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492		A	247614573	G	A	247614573	4	1	122	1	0	0	0	0	0	1	0	0	11019	1153	40	1	244	1	OR2B11	1	247614573	Nonsense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	3032399	247614573	1636048	9	32048										
OR2M4	26245	hgsc.bcm.edu	37	chr1	248403031	248403031	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agaccagcttctaaacatacGccagaccaggacaagatggt	9	11	1	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:248403031G>A	ENST00000306687.1	+	1	801	c.801G>A	c.(799-801)acG>acA	p.T267T		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	267					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(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	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)			CTAAACATACGCCAGACCAGG	0.517																																																0			1											130	111	118					1																	248403031		2203	4300	6503	246469654	SO:0001819	synonymous_variant	26245			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"GPCR / Class A : Olfactory receptors"	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.801G>A	1.37:g.248403031G>A			246469654	Q15611|Q8NG82	Silent	SNP	ENST00000306687.1	37	CCDS31108.1																																																																																				0.517	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504		A	248403031	G	A	248403031	2	1	122	1	0	0	0	0	0	0	0	1	11043	1074	38	1		1	OR2M4	1	248403031	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10	788458	248403031	847590	10	32049										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525428	248525428	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ctgtcatcaggctgctggttCctgggctcagtggatggctt	14	10	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr1:248525428C>A	ENST00000366475.1	+	1	546	c.546C>A	c.(544-546)ttC>ttA	p.F182L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	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(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)			GCTGCTGGTTCCTGGGCTCAG	0.547																																																0			1											262	228	239					1																	248525428		2203	4300	6503	246592051	SO:0001583	missense	127074			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.546C>A	1.37:g.248525428C>A	ENSP00000355431:p.Phe182Leu		246592051	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	0.659	-0.806383	0.02819	.	.	ENSG00000196944	ENST00000366475	T	0.32023	1.47	3.61	-3.39	0.04868	GPCR, rhodopsin-like superfamily (1);	0.441477	0.19272	N	0.118381	T	0.06462	0.0166	N	0.01289	-0.905	0.09310	N	1	B	0.11235	0.004	B	0.17979	0.02	T	0.30416	-0.9979	10	0.05525	T	0.97	.	4.9023	0.13781	0.0:0.3919:0.2685:0.3395	.	182	Q8NH00	OR2T4_HUMAN	L	182	ENSP00000355431:F182L	ENSP00000355431:F182L	F	+	3	2	OR2T4	246592051	0.000000	0.05858	0.496000	0.27539	0.372000	0.29890	-5.874000	0.00093	-0.783000	0.04534	-0.234000	0.12200	TTC		0.547	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		A	248525428	C	A	248525428	3	1	122	1	0	0	0	0	1	0	0	0	11058	854	30	2	548	2	OR2T4	1	248525428	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	122397	248525428	725193	11	32050										
USP34	9736	hgsc.bcm.edu	37	chr2	61522383	61522383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atacaatagcttgtgggcgcTcttaattttgagaagttctt	9	6	2	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr2:61522383T>C	ENST00000398571.2	-	31	4373	c.4297A>G	c.(4297-4299)Agc>Ggc	p.S1433G		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1433					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)			TTGTGGGCGCTCTTAATTTTG	0.343																																																0			2											106	99	101					2																	61522383		1809	4069	5878	61375887	SO:0001583	missense	9736			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.4297A>G	2.37:g.61522383T>C	ENSP00000381577:p.Ser1433Gly		61375887	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	19.32	3.804917	0.70682	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.03951	3.75	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.14356	0.0347	L	0.55990	1.75	0.58432	D	0.999997	P	0.49447	0.924	P	0.57776	0.827	T	0.00254	-1.1874	10	0.72032	D	0.01	.	14.0369	0.64651	0.0:0.0:0.0:1.0	.	1433	Q70CQ2	UBP34_HUMAN	G	1281;1281;1433	ENSP00000381577:S1433G	ENSP00000263989:S1281G	S	-	1	0	USP34	61375887	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.174000	0.71943	1.906000	0.55180	0.533000	0.62120	AGC		0.343	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61522383	T	C	61522383	3	2	122	1	0	0	0	0	1	0	0	0	17105	1551	54	4	6543	4	USP34	2	61522383	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10		61522383	181676990	12	32051										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166848033	166848033	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	acgctgaataatgacagcagAtacttcctcttgttttcgtt	7	9	1	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr2:166848033A>G	ENST00000303395.4	-	26	5751	c.5752T>C	c.(5752-5754)Tct>Cct	p.S1918P	SCN1A_ENST00000423058.2_Missense_Mutation_p.S1918P|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.S1907P|SCN1A_ENST00000409050.1_Missense_Mutation_p.S1890P			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1918	IQ.				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)	ATGACAGCAGATACTTCCTCT	0.408																																																0			2											104	98	100					2																	166848033		2203	4300	6503	166556279	SO:0001583	missense	6323			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.5752T>C	2.37:g.166848033A>G	ENSP00000303540:p.Ser1918Pro		166556279	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	16.12	3.031739	0.54790	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96685	-4.09;-4.09;-4.05;-4.04	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000008	D	0.98394	0.9466	M	0.89601	3.045	0.58432	D	0.999992	D	0.89917	1.0	D	0.79784	0.993	D	0.99445	1.0939	10	0.72032	D	0.01	.	16.0863	0.81056	1.0:0.0:0.0:0.0	.	1907	P35498-2	.	P	1918;1918;1907;1890	ENSP00000407030:S1918P;ENSP00000303540:S1918P;ENSP00000364554:S1907P;ENSP00000386312:S1890P	ENSP00000303540:S1918P	S	-	1	0	SCN1A	166556279	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.253000	0.78320	2.197000	0.70478	0.454000	0.30748	TCT		0.408	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166848033	A	G	166848033	3	3	122	1	0	0	0	0	1	0	0	0	13951	333	12	4	281	4	SCN1A	2	166848033	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	105325650	166848033	76351340	13	32052										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100111	168100111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aaagaagtataaaatgtttcGaaactcaaccattatatgtt	5	5	1	1	rs201995517		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr2:168100111G>A	ENST00000409195.1	+	9	2298	c.2209G>A	c.(2209-2211)Gaa>Aaa	p.E737K	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.E737K|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.E515K|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	562					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						AAAATGTTTCGAAACTCAACC	0.373																																																0			2						G	LYS/GLU,LYS/GLU,,,	1,3701		0,1,1850	58	55	56		1543,2209,,,	5.9	1	2		56	4,8172		0,4,4084	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	56,56,,,	0,5,5934	AA,AG,GG		0.0489,0.027,0.0421	probably-damaging,probably-damaging,,,	515/3328,737/3550,,,	168100111	5,11873	1851	4088	5939	167808357	SO:0001583	missense	129446			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.2209G>A	2.37:g.168100111G>A	ENSP00000386840:p.Glu737Lys		167808357	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	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390983	0.82902	2.7E-4	4.89E-4	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03330	3.97;3.97;3.97	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.23611	0.0571	M	0.84683	2.71	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.993;0.993	T	0.00180	-1.1949	10	0.66056	D	0.02	-23.554	19.9164	0.97064	0.0:0.0:1.0:0.0	.	562;562;515	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	K	737;737;515	ENSP00000386840:E737K;ENSP00000295237:E737K;ENSP00000387255:E515K	ENSP00000295237:E737K	E	+	1	0	XIRP2	167808357	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.380000	0.66202	2.810000	0.96702	0.650000	0.86243	GAA		0.373	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168100111	G	A	168100111	3	1	122	1	0	0	0	0	1	0	0	0	17470	1059	37	1	2239	1	XIRP2	2	168100111	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	1252078	168100111	75099262	14	32053										
TTN	7273	hgsc.bcm.edu	37	chr2	179414890	179414890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cactccatctttgaaccaagTtactcgaggcactggtcttc	7	13	2	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr2:179414890T>C	ENST00000591111.1	-	287	86976	c.86752A>G	c.(86752-86754)Act>Gct	p.T28918A	TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T21494A|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T21686A|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T21619A|TTN_ENST00000342992.6_Missense_Mutation_p.T27991A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T30559A|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28918	Ig-like 133.				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.T21494S(1)|p.T27989S(1)		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)			TTGAACCAAGTTACTCGAGGC	0.428																																																2	Substitution - Missense(2)	ovary(2)	2											204	200	201					2																	179414890		1869	4109	5978	179123136	SO:0001583	missense	7273			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.86752A>G	2.37:g.179414890T>C	ENSP00000465570:p.Thr28918Ala		179123136	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		.	.	.	.	.	.	.	.	.	.	T	16.03	3.007683	0.54361	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.74	5.74	0.90152	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	0.69967	0.3170	M	0.80982	2.52	0.33697	D	0.614028	P;P;P;P	0.38617	0.454;0.454;0.454;0.64	B;B;B;B	0.40602	0.266;0.266;0.266;0.334	T	0.81846	-0.0745	9	0.87932	D	0	.	10.6581	0.45686	0.0:0.0714:0.0:0.9286	.	21494;21619;21686;28918	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	27991;21494;21686;21619;21491	ENSP00000343764:T27991A;ENSP00000434586:T21494A;ENSP00000340554:T21686A;ENSP00000352154:T21619A	ENSP00000340554:T21686A	T	-	1	0	TTN	179123136	0.921000	0.31238	1.000000	0.80357	0.987000	0.75469	1.254000	0.32897	2.317000	0.78254	0.460000	0.39030	ACT		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179414890	T	C	179414890	3	2	122	1	0	0	0	0	1	0	0	0	16775	1725	60	4	16408	4	TTN	2	179414890	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	11314779	179414890	63784483	15	32054										
TTN	7273	hgsc.bcm.edu	37	chr2	179425005	179425005	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	acacgatattcatattcacaTccttcccgaagtcctgttga	5	12	2	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr2:179425005T>C	ENST00000591111.1	-	276	81155	c.80931A>G	c.(80929-80931)ggA>ggG	p.G26977G	TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Silent_p.G19553G|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.G19745G|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Silent_p.G19678G|TTN_ENST00000342992.6_Silent_p.G26050G|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.G28618G|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26977	Fibronectin type-III 96. {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)	p.G26048G(1)|p.G19553G(1)		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)			CATATTCACATCCTTCCCGAA	0.398																																																2	Substitution - coding silent(2)	ovary(2)	2											103	101	102					2																	179425005		1912	4125	6037	179133251	SO:0001819	synonymous_variant	7273			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.80931A>G	2.37:g.179425005T>C			179133251	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	37																																																																																					0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179425005	T	C	179425005	2	2	122	1	0	0	0	0	0	0	0	1	16775	1422	50	4		4	TTN	2	179425005	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10	10115	179425005	63774368	16	32055										
RAD18	56852	hgsc.bcm.edu	37	chr3	8923064	8923064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	attcctattacgcttgtttcTtggttcaatctcagcacttt	5	10	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:8923064T>C	ENST00000264926.2	-	13	1581	c.1465A>G	c.(1465-1467)Aga>Gga	p.R489G		NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	489					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		CGCTTGTTTCTTGGTTCAATC	0.383								Rad6 pathway																																								0			3											176	167	170					3																	8923064		2203	4300	6503	8898064	SO:0001583	missense	56852				CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.1465A>G	3.37:g.8923064T>C	ENSP00000264926:p.Arg489Gly		8898064	Q58F55|Q9NRT6	Missense_Mutation	SNP	ENST00000264926.2	37	CCDS2571.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.557167	0.45590	.	.	ENSG00000070950	ENST00000264926	T	0.38560	1.13	4.54	3.39	0.38822	.	0.098347	0.44097	D	0.000486	T	0.26919	0.0659	L	0.27053	0.805	0.36553	D	0.871951	B	0.32573	0.376	B	0.30401	0.115	T	0.27571	-1.0070	10	0.87932	D	0	-17.4904	6.8781	0.24158	0.0:0.1039:0.0:0.8961	.	489	Q9NS91	RAD18_HUMAN	G	489	ENSP00000264926:R489G	ENSP00000264926:R489G	R	-	1	2	RAD18	8898064	0.998000	0.40836	0.986000	0.45419	0.878000	0.50629	3.248000	0.51430	0.890000	0.36211	-0.250000	0.11733	AGA		0.383	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165		C	8923064	T	C	8923064	3	2	122	1	0	0	0	0	1	0	0	0	13017	1617	56	4	26	4	RAD18	3	8923064	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10		8923064	189099366	17	32056										
VHL	7428	hgsc.bcm.edu	37	chr3	10191649	10191649	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	catcaacggatgggagattgAagatttctgttgaaacttac	10	6	2	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:10191649A>G	ENST00000256474.2	+	3	1482	c.642A>G	c.(640-642)tgA>tgG	p.*214W	VHL_ENST00000345392.2_Nonstop_Mutation_p.*173W|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	0					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.*214CRFLLKLTLFHLSF*(2)|p.D213fs(1)|p.?(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)		TGGGAGATTGAAGATTTCTGT	0.458		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	4	Nonstop extension(2)|Unknown(1)|Complex - frameshift(1)	adrenal_gland(2)|kidney(2)	3											52	44	47					3																	10191649		2203	4300	6503	10166649	SO:0001578	stop_lost	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	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.642A>G	3.37:g.10191649A>G	ENSP00000256474:p.*214Trpext*14		10166649	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	8.497	0.863338	0.17250	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	.	.	.	4.68	2.31	0.28768	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.9942	0.19485	0.795:0.0:0.205:0.0	.	.	.	.	W	214;173;132	.	.	X	+	3	0	VHL	10166649	0.181000	0.23161	0.016000	0.15963	0.011000	0.07611	2.874000	0.48483	0.323000	0.23307	0.533000	0.62120	TGA		0.458	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10191649	A	G	10191649	4	3	122	1	0	0	0	0	0	0	0	0	17202	259	9	4	652	4	VHL	3	10191649	Nonstop_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	1268585	10191649	187830781	18	32057										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15711978	15711978	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gatgataaaggactacttgaTgagacaggcatcatggtggc	13	6	1	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:15711978T>C	ENST00000399451.2	-	28	3328	c.2961A>G	c.(2959-2961)tcA>tcG	p.S987S	ANKRD28_ENST00000383777.1_Silent_p.S1020S|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	987						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						GACTACTTGATGAGACAGGCA	0.438																																																0			3											171	167	168					3																	15711978		1978	4163	6141	15686982	SO:0001819	synonymous_variant	23243			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.2961A>G	3.37:g.15711978T>C			15686982	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Silent	SNP	ENST00000399451.2	37	CCDS46769.1																																																																																				0.438	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		C	15711978	T	C	15711978	2	2	122	1	0	0	0	0	0	0	0	1	656	1451	51	4		4	ANKRD28	3	15711978	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10	5520329	15711978	182310452	19	32058										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33725898	33725898	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agatccatcctcactttttcTcccacatgtctataaatctc	2	14	4	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:33725898T>C	ENST00000468888.2	-	6	643	c.597A>G	c.(595-597)ggA>ggG	p.G199G	CLASP2_ENST00000399362.4_Silent_p.G199G|CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000359576.5_Silent_p.G199G			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1252					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						TCACTTTTTCTCCCACATGTC	0.318																																																0			3											138	139	139					3																	33725898		1815	4079	5894	33700902	SO:0001819	synonymous_variant	23122			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.597A>G	3.37:g.33725898T>C			33700902	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																					0.318	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		C	33725898	T	C	33725898	2	2	122	1	0	0	0	0	0	0	0	1	3461	1538	54	4		4	CLASP2	3	33725898	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10	18013920	33725898	164296532	20	32059										
FLNB	2317	hgsc.bcm.edu	37	chr3	58094230	58094230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agaaatctggatgcattgtcAacaacctggccgagttcact	9	10	3	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:58094230A>G	ENST00000295956.4	+	13	2152	c.1987A>G	c.(1987-1989)Aac>Gac	p.N663D	FLNB_ENST00000429972.2_Missense_Mutation_p.N663D|FLNB_ENST00000357272.4_Missense_Mutation_p.N663D|FLNB_ENST00000493452.1_Missense_Mutation_p.N494D|FLNB_ENST00000419752.2_Missense_Mutation_p.N494D|FLNB_ENST00000490882.1_Missense_Mutation_p.N663D|FLNB_ENST00000358537.3_Missense_Mutation_p.N663D|FLNB_ENST00000348383.5_Missense_Mutation_p.N663D	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	663			N -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)		ATGCATTGTCAACAACCTGGC	0.473																																																0			3											86	82	83					3																	58094230		2203	4300	6503	58069270	SO:0001583	missense	2317			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.1987A>G	3.37:g.58094230A>G	ENSP00000295956:p.Asn663Asp		58069270	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	10.28	1.305862	0.23736	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	T;T;T;T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71	5.56	5.56	0.83823	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.119241	0.85682	D	0.000000	T	0.64305	0.2586	L	0.48260	1.515	0.33560	D	0.597227	B;B;B;B;B;B	0.20052	0.018;0.04;0.041;0.003;0.023;0.023	B;B;B;B;B;B	0.22880	0.024;0.042;0.042;0.02;0.042;0.042	T	0.66280	-0.5963	10	0.15952	T	0.53	.	16.002	0.80301	1.0:0.0:0.0:0.0	.	663;663;494;494;663;663	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	D	663;663;663;663;663;663;494;494	ENSP00000295956:N663D;ENSP00000420213:N663D;ENSP00000351339:N663D;ENSP00000415599:N663D;ENSP00000232447:N663D;ENSP00000349819:N663D;ENSP00000418510:N494D;ENSP00000414532:N494D	ENSP00000295956:N663D	N	+	1	0	FLNB	58069270	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	4.264000	0.58859	2.241000	0.73720	0.533000	0.62120	AAC		0.473	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58094230	A	G	58094230	3	3	122	1	0	0	0	0	1	0	0	0	5953	130	5	4	2037	4	FLNB	3	58094230	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	24368332	58094230	139928200	21	32060										
TMF1	7110	hgsc.bcm.edu	37	chr3	69096730	69096730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttcatttacttcttcagattTtccttcagcagattcaactg	4	10	5	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:69096730T>C	ENST00000398559.2	-	2	1342	c.1126A>G	c.(1126-1128)Aaa>Gaa	p.K376E	CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.K376E|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	376					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)		TCTTCAGATTTTCCTTCAGCA	0.378																																																0			3											108	101	103					3																	69096730		1860	4093	5953	69179420	SO:0001583	missense	7110				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.1126A>G	3.37:g.69096730T>C	ENSP00000381567:p.Lys376Glu		69179420	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	37	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490825	0.26774	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248;ENST00000438636	T;T	0.76060	-0.99;-0.99	5.86	5.86	0.93980	.	0.232088	0.51477	D	0.000084	T	0.64940	0.2644	L	0.34521	1.04	0.40351	D	0.979138	B;B	0.15930	0.015;0.009	B;B	0.17979	0.02;0.009	T	0.60546	-0.7242	10	0.15499	T	0.54	-15.672	16.5602	0.84551	0.0:0.0:0.0:1.0	.	376;376	P82094-2;P82094	.;TMF1_HUMAN	E	376;376;289;376	ENSP00000381567:K376E;ENSP00000438706:K376E	ENSP00000348582:K289E	K	-	1	0	TMF1	69179420	1.000000	0.71417	0.967000	0.41034	0.195000	0.23768	3.633000	0.54295	2.367000	0.80283	0.528000	0.53228	AAA		0.378	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69096730	T	C	69096730	3	2	122	1	0	0	0	0	1	0	0	0	16267	1850	64	4	2219	4	TMF1	3	69096730	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	11002500	69096730	128925700	22	32061										
ZIC4	84107	hgsc.bcm.edu	37	chr3	147114001	147114001	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aagcgccaggaccgtggggcGcagcgaggttcaccgtcagg	17	12	2	0	rs375753545		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:147114001G>T	ENST00000383075.3	-	3	838	c.326C>A	c.(325-327)gCg>gAg	p.A109E	ZIC4_ENST00000473123.1_Missense_Mutation_p.A109E|ZIC4_ENST00000491672.1_Intron|ZIC4_ENST00000425731.3_Missense_Mutation_p.A147E|ZIC4_ENST00000484399.1_Missense_Mutation_p.A109E|ZIC4_ENST00000525172.2_Missense_Mutation_p.A159E	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	109						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						ACCGTGGGGCGCAGCGAGGTT	0.706													G|||	1	0.000199681	8e-04	0	5008	,	,		14536	0		0	False		,,,				2504	0															0			3						G	GLU/ALA,GLU/ALA,GLU/ALA	1,4383		0,1,2191	25	30	28		476,440,326	4.1	1	3		28	0,8590		0,0,4295	no	missense,missense,missense	ZIC4	NM_001168378.1,NM_001168379.1,NM_032153.5	107,107,107	0,1,6486	TT,TG,GG		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	159/385,147/373,109/335	147114001	1,12973	2192	4295	6487	148596691	SO:0001583	missense	84107			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.326C>A	3.37:g.147114001G>T	ENSP00000372553:p.Ala109Glu		148596691	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	37	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.510507	0.85389	2.28E-4	0.0	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000462748	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	4.98	4.1	0.47936	.	0.306081	0.22881	N	0.054502	T	0.51991	0.1707	M	0.65975	2.015	0.80722	D	1	P;P	0.52061	0.95;0.884	P;B	0.46543	0.52;0.406	T	0.56535	-0.7963	10	0.54805	T	0.06	.	13.2973	0.60305	0.077:0.0:0.923:0.0	.	159;109	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	E	109;147;159;109;109;109	ENSP00000372553:A109E;ENSP00000397695:A147E;ENSP00000435509:A159E;ENSP00000417855:A109E;ENSP00000420775:A109E;ENSP00000420627:A109E	ENSP00000372553:A109E	A	-	2	0	ZIC4	148596691	1.000000	0.71417	0.956000	0.39512	0.949000	0.60115	7.644000	0.83416	1.085000	0.41206	0.561000	0.74099	GCG		0.706	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			T	147114001	G	T	147114001	3	4	122	1	0	0	0	0	1	0	0	0	17720	1087	38	2	690	2	ZIC4	3	147114001	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	78017271	147114001	50908429	23	32062										
DHX36	170506	hgsc.bcm.edu	37	chr3	154022661	154022661	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tattactttcaagtcagatcGaaaattgagaaggtctttaa	7	5	3	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:154022661G>A	ENST00000496811.1	-	8	1149	c.1069C>T	c.(1069-1071)Cga>Tga	p.R357*	DHX36_ENST00000544526.1_Nonsense_Mutation_p.R357*|DHX36_ENST00000329463.5_Nonsense_Mutation_p.R357*|DHX36_ENST00000308361.6_Nonsense_Mutation_p.R357*	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	357	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AAGTCAGATCGAAAATTGAGA	0.308																																																0			3											42	42	42					3																	154022661		2203	4298	6501	155505355	SO:0001587	stop_gained	170506			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"DEAH-boxes"	14410	protein-coding gene	gene with protein product		612767	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.1069C>T	3.37:g.154022661G>A	ENSP00000417078:p.Arg357*		155505355	B2RB00|Q70JU3|Q8IYE5|Q9P240	Nonsense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	G	40	7.916949	0.98560	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	.	.	.	5.9	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3314	0.83015	0.0:0.0:0.8667:0.1333	.	.	.	.	X	357;357;357;357;271	.	ENSP00000309296:R357X	R	-	1	2	DHX36	155505355	1.000000	0.71417	0.838000	0.33150	0.955000	0.61496	7.543000	0.82106	1.474000	0.48178	0.655000	0.94253	CGA		0.308	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		A	154022661	G	A	154022661	4	1	122	1	0	0	0	0	0	1	0	0	4520	1066	37	1	2029	1	DHX36	3	154022661	Nonsense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	6908660	154022661	43999769	24	32063										
ARL14	80117	hgsc.bcm.edu	37	chr3	160395155	160395155	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atgggttcgctgggttctaaAaatccgcaaaccaaacaagc	9	10	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:160395155A>G	ENST00000320767.2	+	1	208	c.21A>G	c.(19-21)aaA>aaG	p.K7K		NM_025047.2	NP_079323.1	Q8N4G2	ARL14_HUMAN	ADP-ribosylation factor-like 14	7					small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	GTP binding (GO:0005525)			lung(6)	6			Lung(72;7.02e-05)|LUSC - Lung squamous cell carcinoma(72;7.23e-05)			TGGGTTCTAAAAATCCGCAAA	0.383																																																0			3											45	45	45					3																	160395155		2203	4300	6503	161877849	SO:0001819	synonymous_variant	80117			AK026248	CCDS3192.1	3q25.33	2014-05-09	2005-11-03	2005-11-03	ENSG00000179674	ENSG00000179674		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	22974	protein-coding gene	gene with protein product		614439	"ADP-ribosylation factor 7"	ARF7		15367757	Standard	NM_025047		Approved	FLJ22595	uc003fdq.3	Q8N4G2	OTTHUMG00000159031	ENST00000320767.2:c.21A>G	3.37:g.160395155A>G			161877849	Q9H655	Silent	SNP	ENST00000320767.2	37	CCDS3192.1																																																																																				0.383	ARL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352958.1	NM_025047		G	160395155	A	G	160395155	2	3	122	1	0	0	0	0	0	0	0	1	930	11	1	4		4	ARL14	3	160395155	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10	6372494	160395155	37627275	25	32064										
BCHE	590	hgsc.bcm.edu	37	chr3	165547891	165547891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtttactgacaaaggagtccCataggggacaacaaatgctt	10	8	0	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:165547891C>T	ENST00000264381.3	-	2	1097	c.931G>A	c.(931-933)Ggg>Agg	p.G311R	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	311					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)	AAAGGAGTCCCATAGGGGACA	0.393																																																0			3											45	49	48					3																	165547891		2202	4295	6497	167030585	SO:0001583	missense	590			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.931G>A	3.37:g.165547891C>T	ENSP00000264381:p.Gly311Arg		167030585	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	37	CCDS3198.1	.	.	.	.	.	.	.	.	.	.	C	0.077	-1.190568	0.01607	.	.	ENSG00000114200	ENST00000264381	D	0.95238	-3.65	5.42	4.54	0.55810	Carboxylesterase, type B (1);	0.752409	0.13633	N	0.373588	D	0.84710	0.5532	N	0.04387	-0.21	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.73081	-0.4095	10	0.23302	T	0.38	.	7.6275	0.28220	0.2946:0.6292:0.0:0.0762	.	311	P06276	CHLE_HUMAN	R	311	ENSP00000264381:G311R	ENSP00000264381:G311R	G	-	1	0	BCHE	167030585	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.052000	0.11865	1.269000	0.44280	-0.182000	0.12963	GGG		0.393	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			T	165547891	C	T	165547891	3	4	122	1	0	0	0	0	1	0	0	0	1359	594	21	3	889	3	BCHE	3	165547891	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	5152736	165547891	32474539	26	32065										
FXR1	8087	hgsc.bcm.edu	37	chr3	180680830	180680830	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tacaaggttctaggtcttatAgcggaagaggcagaggtcgt	14	6	2	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr3:180680830A>G	ENST00000357559.4	+	13	1534	c.1150A>G	c.(1150-1152)Agc>Ggc	p.S384G	FXR1_ENST00000480918.1_Missense_Mutation_p.S371G|FXR1_ENST00000305586.7_Missense_Mutation_p.S299G|FXR1_ENST00000468861.1_Missense_Mutation_p.S299G|FXR1_ENST00000445140.2_Missense_Mutation_p.S384G|FXR1_ENST00000491062.1_Missense_Mutation_p.S335G	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	384					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)			TAGGTCTTATAGCGGAAGAGG	0.388																																																0			3											152	155	154					3																	180680830		2203	4300	6503	182163524	SO:0001583	missense	8087			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.1150A>G	3.37:g.180680830A>G	ENSP00000350170:p.Ser384Gly		182163524	A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	ENST00000357559.4	37	CCDS3238.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.412543	0.42817	.	.	ENSG00000114416	ENST00000357559;ENST00000305586;ENST00000491062;ENST00000468861;ENST00000445140;ENST00000480918	T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55	5.22	5.22	0.72569	.	0.041544	0.85682	D	0.000000	T	0.18676	0.0448	N	0.04880	-0.145	0.43846	D	0.996432	B;B;B;B;B;B	0.29909	0.002;0.001;0.002;0.261;0.001;0.126	B;B;B;B;B;B	0.35073	0.005;0.01;0.01;0.195;0.005;0.096	T	0.14337	-1.0476	10	0.18710	T	0.47	-8.6699	15.3902	0.74739	1.0:0.0:0.0:0.0	.	371;335;299;328;384;384	B4DXZ6;E9PFF5;E7EU85;E7ERF5;P51114-2;P51114	.;.;.;.;.;FXR1_HUMAN	G	384;299;335;299;384;371	ENSP00000350170:S384G;ENSP00000307633:S299G;ENSP00000420643:S335G;ENSP00000420515:S299G;ENSP00000388828:S384G;ENSP00000418097:S371G	ENSP00000307633:S299G	S	+	1	0	FXR1	182163524	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.177000	0.65032	2.098000	0.63641	0.383000	0.25322	AGC		0.388	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			G	180680830	A	G	180680830	3	3	122	1	0	0	0	0	1	0	0	0	6134	420	15	4	1200	4	FXR1	3	180680830	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	15132939	180680830	17341600	27	32066										
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tggagtgccacctgctcacaCacgtgcccatgtggagtgcc					rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr4:1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENST00000324803.4	+	1	3255_3283	c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	c.(295-324)cacgtgcccatgtggagtgcccgcctgctcfs	p.HVPMWSARLL99fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	99					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACGTGCCCA	0.655																																																1	Substitution - Missense(1)	pancreas(1)	4																																								1378622	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	4.37:g.1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENSP00000323978:p.His99fs		1378594	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.655	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1388622	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	1388594	7	5	122	1	0	1	0	1	0	0	0	0	3883	478	17	0	297	0	CRIPAK	4	1388594	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	TCGA-G5-6641-01A-11D-1826-10		1388594	189765682	28	32067										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7398082	7398082	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tctggaaagttctctgtggcGgtaagtcagcccgatggcag	14	9	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr4:7398082G>A	ENST00000507866.2	+	2	657	c.548G>A	c.(547-549)cGg>cAg	p.R183Q	SORCS2_ENST00000511199.1_3'UTR|SORCS2_ENST00000329016.9_Splice_Site_p.R11Q	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	183					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						TCTCTGTGGCGGTAAGTCAGC	0.522																																																0			4											111	113	112					4																	7398082		2060	4194	6254	7448983	SO:0001630	splice_region_variant	57537			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.548+1G>A	4.37:g.7398082G>A			7448983	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	37	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	G	33	5.242627	0.95272	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.37584	1.19;1.19	5.64	5.64	0.86602	VPS10 (1);	0.193290	0.30142	N	0.010305	T	0.52677	0.1749	M	0.70595	2.14	0.41663	D	0.98919	D;D	0.69078	0.99;0.997	P;P	0.53035	0.716;0.716	T	0.57213	-0.7850	10	0.72032	D	0.01	.	17.187	0.86869	0.0:0.0:1.0:0.0	.	11;183	B5MED8;Q96PQ0	.;SORC2_HUMAN	Q	183;11	ENSP00000422185:R183Q;ENSP00000329124:R11Q	ENSP00000329124:R11Q	R	+	2	0	SORCS2	7448983	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	4.767000	0.62286	2.661000	0.90470	0.655000	0.94253	CGG		0.522	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	Missense_Mutation	A	7398082	G	A	7398082	5	1	122	1	0	0	0	0	0	0	1	0	14968	1130	39	1	554	1	SORCS2	4	7398082	Splice_Site	SNP	G	TCGA-G5-6641-01A-11D-1826-10	6009488	7398082	183756194	29	32068										
AFM	173	hgsc.bcm.edu	37	chr4	74354468	74354468	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gggatgttgtgcagtgcatcCgtgacacggtgaatattctc	13	8	1	2	rs368606268		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr4:74354468C>T	ENST00000226355.3	+	7	928	c.835C>T	c.(835-837)Cgt>Tgt	p.R279C		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	279	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)			GCAGTGCATCCGTGACACGGT	0.363													C|||	1	0.000199681	8e-04	0	5008	,	,		16210	0		0	False		,,,				2504	0															0			4						C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	142	142	142		835	3.5	0.1	4		142	1,8599	1.2+/-3.3	0,1,4299	no	missense	AFM	NM_001133.2	180	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	279/600	74354468	2,13004	2203	4300	6503	74573332	SO:0001583	missense	173			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	ENST00000226355.3:c.835C>T	4.37:g.74354468C>T	ENSP00000226355:p.Arg279Cys		74573332	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	37	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693772	0.48202	2.27E-4	1.16E-4	ENSG00000079557	ENST00000226355	T	0.74315	-0.83	5.27	3.53	0.40419	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.769783	0.12691	N	0.447209	D	0.83166	0.5195	M	0.76574	2.34	0.20074	N	0.999934	D	0.89917	1.0	D	0.65773	0.938	T	0.70894	-0.4748	10	0.87932	D	0	.	8.3628	0.32369	0.0:0.8161:0.0:0.1839	.	279	P43652	AFAM_HUMAN	C	279	ENSP00000226355:R279C	ENSP00000226355:R279C	R	+	1	0	AFM	74573332	0.000000	0.05858	0.082000	0.20525	0.013000	0.08279	0.315000	0.19451	0.599000	0.29845	0.655000	0.94253	CGT		0.363	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			T	74354468	C	T	74354468	3	4	122	1	0	0	0	0	1	0	0	0	361	652	23	1	861	1	AFM	4	74354468	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	66956386	74354468	116799808	30	32069										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186544776	186544776	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggacacaaccccgtcctggtCgctgtcggaaaactccacgt	10	15	0	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr4:186544776C>T	ENST00000284776.7	-	13	2304	c.1795G>A	c.(1795-1797)Gac>Aac	p.D599N	SORBS2_ENST00000431808.1_Missense_Mutation_p.D599N|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000355634.5_Missense_Mutation_p.D699N|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.D503N|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000393528.3_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	599					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)		CCGTCCTGGTCGCTGTCGGAA	0.567																																					Esophageal Squamous(153;41 2433 9491 36028)											0			4											59	56	57					4																	186544776		2203	4300	6503	186781770	SO:0001583	missense	8470				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.1795G>A	4.37:g.186544776C>T	ENSP00000284776:p.Asp599Asn		186781770	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.926424	0.73327	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.37915	1.29;1.29;1.17;1.28	5.88	5.88	0.94601	.	0.133309	0.64402	D	0.000002	T	0.57095	0.2030	L	0.51422	1.61	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.99;0.993	T	0.49153	-0.8969	10	0.42905	T	0.14	-35.233	20.2405	0.98372	0.0:1.0:0.0:0.0	.	503;699;599	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	N	599;599;503;699	ENSP00000284776:D599N;ENSP00000411764:D599N;ENSP00000397482:D503N;ENSP00000347852:D699N	ENSP00000284776:D599N	D	-	1	0	SORBS2	186781770	1.000000	0.71417	0.979000	0.43373	0.546000	0.35178	7.818000	0.86416	2.797000	0.96272	0.561000	0.74099	GAC		0.567	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186544776	C	T	186544776	3	4	122	1	0	0	0	0	1	0	0	0	14965	884	31	1	1543	1	SORBS2	4	186544776	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	112190308	186544776	4609500	31	32070										
CDH18	1016	hgsc.bcm.edu	37	chr5	19473693	19473693	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gattcctcaaggctgtgatgTcaaaggcctctgtgtcttcc	10	11	4	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:19473693T>A	ENST00000507958.1	-	15	3005	c.2015A>T	c.(2014-2016)gAc>gTc	p.D672V	CDH18_ENST00000274170.4_Missense_Mutation_p.D672V|CDH18_ENST00000506372.1_3'UTR|CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000382275.1_Missense_Mutation_p.D672V|CDH18_ENST00000502796.1_3'UTR			Q13634	CAD18_HUMAN	cadherin 18, type 2	672					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)					GGCTGTGATGTCAAAGGCCTC	0.507																																																0			5											153	145	148					5																	19473693		2203	4300	6503	19509450	SO:0001583	missense	1016			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.2015A>T	5.37:g.19473693T>A	ENSP00000425093:p.Asp672Val		19509450	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.641053	0.87859	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	D;D;D	0.83837	-1.77;-1.77;-1.77	6.16	6.16	0.99307	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.93442	0.7908	H	0.95004	3.61	0.80722	D	1	D	0.63046	0.992	D	0.70487	0.969	D	0.94923	0.8075	9	.	.	.	.	15.6301	0.76899	0.0:0.0:0.0:1.0	.	672	Q13634	CAD18_HUMAN	V	672	ENSP00000371710:D672V;ENSP00000425093:D672V;ENSP00000274170:D672V	.	D	-	2	0	CDH18	19509450	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.035000	0.88872	2.367000	0.80283	0.528000	0.53228	GAC		0.507	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19473693	T	A	19473693	3	1	122	1	0	0	0	0	1	0	0	0	3109	1667	58	5	361	5	CDH18	5	19473693	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10		19473693	161441567	32	32071										
ACTBL2	345651	hgsc.bcm.edu	37	chr5	56778092	56778092	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ccatcacgatgcctgtggtcCgtcctgaggcatagagggac	13	12	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:56778092C>T	ENST00000423391.1	-	1	544	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	AC025470.1_ENST00000584598.1_RNA|CTD-2023N9.1_ENST00000506106.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	148						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)		GCCTGTGGTCCGTCCTGAGGC	0.537																																																0			5											106	91	96					5																	56778092		2203	4300	6503	56813849	SO:0001583	missense	345651				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.443G>A	5.37:g.56778092C>T	ENSP00000416706:p.Arg148Gln		56813849	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434339	0.62955	.	.	ENSG00000169067	ENST00000423391	D	0.94613	-3.47	4.7	4.7	0.59300	.	0.000000	0.64402	D	0.000008	D	0.98027	0.9350	H	0.96398	3.815	0.50313	D	0.999862	D	0.76494	0.999	D	0.71184	0.972	D	0.99123	1.0850	10	0.87932	D	0	.	15.1626	0.72795	0.0:1.0:0.0:0.0	.	148	Q562R1	ACTBL_HUMAN	Q	148	ENSP00000416706:R148Q	ENSP00000416706:R148Q	R	-	2	0	ACTBL2	56813849	1.000000	0.71417	0.992000	0.48379	0.911000	0.54048	5.895000	0.69814	2.416000	0.81992	0.655000	0.94253	CGG		0.537	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992		T	56778092	C	T	56778092	3	4	122	1	0	0	0	0	1	0	0	0	194	652	23	1	691	1	ACTBL2	5	56778092	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	37304399	56778092	124137168	33	32072										
APC	324	hgsc.bcm.edu	37	chr5	112175752	112175752	+	Frame_Shift_Del	DEL	T	T	-													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gttcttccagatgctgatacTttattacattttgccacgga							TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:112175752delT	ENST00000457016.1	+	16	4841	c.4461delT	c.(4459-4461)actfs	p.T1487fs	APC_ENST00000257430.4_Frame_Shift_Del_p.T1487fs|APC_ENST00000508376.2_Frame_Shift_Del_p.T1487fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1487	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.T1487fs*17(10)|p.L1488fs*19(7)|p.L1488fs*26(5)|p.L1488fs*18(1)|p.?(1)|p.K1454fs*3(1)|p.T1487fs*25(1)|p.T1487T(1)|p.K1192fs*3(1)|p.T1487fs*23(1)|p.L1488fs*20(1)|p.L1488fs*21(1)|p.L1488fs*23(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)		ATGCTGATACTTTATTACATT	0.443		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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	32	Deletion - Frameshift(21)|Insertion - Frameshift(7)|Complex - frameshift(2)|Unknown(1)|Substitution - coding silent(1)	large_intestine(29)|thyroid(1)|soft_tissue(1)|skin(1)	5											69	70	70					5																	112175752		2202	4300	6502	112203651	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.4461delT	5.37:g.112175752delT	ENSP00000413133:p.Thr1487fs		112203651	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		-	112175752	T	-	112175752	7	5	122	1	0	1	0	1	0	0	0	0	763	1596	56	0	4519	0	APC	5	112175752	Frame_Shift_Del	DEL	T	TCGA-G5-6641-01A-11D-1826-10	55397660	112175752	68739508	34	32073	58	2								
APC	324	hgsc.bcm.edu	37	chr5	112175754	112175755	+	Missense_Mutation	DNP	TA	TA	AT													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tcttccagatgctgatacttTattacattttgccacggaaa							TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T|A	T|A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:112175754_112175755TA>AT	ENST00000457016.1	+	16	4843_4844	c.4463_4464TA>AT	c.(4462-4464)tTA>tAT	p.L1488Y	APC_ENST00000257430.4_Missense_Mutation_p.L1488Y|APC_ENST00000508376.2_Missense_Mutation_p.L1488Y|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1488	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.L1488fs*18(18)|p.L1488fs*19(12)|p.T1487fs*17(10)|p.L1488*(3)|p.L1488fs*23(3)|p.L1488fs*25(2)|p.L1489fs*19(2)|p.?(1)|p.K1454fs*3(1)|p.L1488F(1)|p.T1487fs*25(1)|p.L1488fs*13(1)|p.K1192fs*3(1)|p.T1487fs*23(1)|p.L1488fs*20(1)|p.L1488fs*22(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)		GCTGATACTTTATTACATTTTG	0.441		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)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	59	Deletion - Frameshift(49)|Insertion - Frameshift(3)|Substitution - Nonsense(3)|Complex - frameshift(2)|Unknown(1)|Substitution - Missense(1)	large_intestine(54)|thyroid(1)|soft_tissue(1)|small_intestine(1)|lung(1)|skin(1)	5	GRCh37	CI002198	APC	I																																				112203653|112203654	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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	5.37:g.112175754_112175755delinsAT	ENSP00000413133:p.Leu1488Tyr		112203653|112203654	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.441	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		AT	112175755	TA	AT	112175754	3	1	122	1	0	0	0	0	1	0	0	0	763	1764	61	5	4521	5	APC	5	112175754	Missense_Mutation	DNP	TA	TCGA-G5-6641-01A-11D-1826-10	2	112175754	68739506	35	32074	58	2								
APC	324	hgsc.bcm.edu	37	chr5	112176817	112176817	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggaagttttgcttttgattcAcctcatcattacacgcctat	6	10	3	1	rs577725739		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:112176817A>G	ENST00000457016.1	+	16	5906	c.5526A>G	c.(5524-5526)tcA>tcG	p.S1842S	APC_ENST00000257430.4_Silent_p.S1842S|APC_ENST00000508376.2_Silent_p.S1842S|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1842	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.K1192fs*3(1)|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)		CTTTTGATTCACCTCATCATT	0.338		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)			A|||	1	0.000199681	0	0	5008	,	,		19615	0.001		0	False		,,,				2504	0				NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											96	88	91					5																	112176817		2202	4300	6502	112204716	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.5526A>G	5.37:g.112176817A>G			112204716	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.338	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112176817	A	G	112176817	2	3	122	1	0	0	0	0	0	0	0	1	763	146	6	4		4	APC	5	112176817	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10	1063	112176817	68738443	36	32075										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114469836	114469836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttcctcattgatctctggcaCgtctatgcctgaaagaatta	7	10	3	3	rs147215007	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:114469836C>T	ENST00000282369.3	-	8	1376	c.1255G>A	c.(1255-1257)Gtg>Atg	p.V419M	TRIM36_ENST00000514154.1_Missense_Mutation_p.V264M|TRIM36_ENST00000513154.1_Missense_Mutation_p.V407M	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	419	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		ATCTCTGGCACGTCTATGCCT	0.313													C|||	7	0.00139776	0	0.0014	5008	,	,		15064	0		0.004	False		,,,				2504	0.002															0			5						C	MET/VAL	1,4403	2.1+/-5.4	0,1,2201	70	65	67		1255	3.1	1	5	dbSNP_134	67	24,8576	17.3+/-56.4	0,24,4276	yes	missense	TRIM36	NM_018700.3	21	0,25,6477	TT,TC,CC		0.2791,0.0227,0.1922	benign	419/729	114469836	25,12979	2202	4300	6502	114497735	SO:0001583	missense	55521			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.1255G>A	5.37:g.114469836C>T	ENSP00000282369:p.Val419Met		114497735	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	CCDS4115.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	10.77	1.443597	0.25987	2.27E-4	0.002791	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.64618	0.57;0.69;-0.11	5.28	3.11	0.35812	Fibronectin, type III (3);	0.387682	0.31507	N	0.007529	T	0.40546	0.1121	L	0.44542	1.39	0.80722	D	1	B;B	0.16396	0.017;0.013	B;B	0.09377	0.003;0.004	T	0.44019	-0.9355	10	0.49607	T	0.09	.	5.969	0.19340	0.0:0.5732:0.0:0.4268	.	407;419	E9PFI8;Q9NQ86	.;TRI36_HUMAN	M	419;407;264	ENSP00000282369:V419M;ENSP00000423934:V407M;ENSP00000424259:V264M	ENSP00000282369:V419M	V	-	1	0	TRIM36	114497735	0.999000	0.42202	0.999000	0.59377	0.765000	0.43378	0.761000	0.26489	1.199000	0.43173	0.563000	0.77884	GTG		0.313	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		T	114469836	C	T	114469836	3	4	122	1	0	0	0	0	1	0	0	0	16550	536	19	1	943	1	TRIM36	5	114469836	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	2293019	114469836	66445424	37	32076										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129070664	129070664	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aaggaatgcagtcccgtgtaAtccaatgcatgcataagatc	9	9	0	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:129070664A>G	ENST00000274487.4	+	22	3479	c.3334A>G	c.(3334-3336)Atc>Gtc	p.I1112V	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	1112	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.I1112F(1)		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)		GTCCCGTGTAATCCAATGCAT	0.378																																																1	Substitution - Missense(1)	ovary(1)	5											102	101	101					5																	129070664		2203	4300	6503	129098563	SO:0001583	missense	171019			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.3334A>G	5.37:g.129070664A>G	ENSP00000274487:p.Ile1112Val		129098563		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.471483	0.43942	.	.	ENSG00000145808	ENST00000274487	T	0.50813	0.73	4.26	3.1	0.35709	.	0.280714	0.28001	N	0.016983	T	0.13200	0.0320	N	0.00170	-1.935	0.41443	D	0.987939	B	0.24651	0.108	B	0.32090	0.14	T	0.10543	-1.0625	9	.	.	.	.	10.1071	0.42539	0.9192:0.0:0.0808:0.0	.	1112	Q8TE59	ATS19_HUMAN	V	1112	ENSP00000274487:I1112V	.	I	+	1	0	ADAMTS19	129098563	0.998000	0.40836	1.000000	0.80357	0.932000	0.56968	2.244000	0.43124	0.978000	0.38470	0.477000	0.44152	ATC		0.378	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	129070664	A	G	129070664	3	3	122	1	0	0	0	0	1	0	0	0	264	101	4	4	3420	4	ADAMTS19	5	129070664	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	14600828	129070664	51844596	38	32077										
EGR1	1958	hgsc.bcm.edu	37	chr5	137802688	137802688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cagcggcctcctccgcctccGcctcccagagcccacccctg	8	24	0	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:137802688G>A	ENST00000239938.4	+	2	822	c.550G>A	c.(550-552)Gcc>Acc	p.A184T		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	184					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|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)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CTCCGCCTCCGCCTCCCAGAG	0.642																																																0			5											110	114	112					5																	137802688		2203	4300	6503	137830587	SO:0001583	missense	1958			M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"Zinc fingers, C2H2-type"	3238	protein-coding gene	gene with protein product	"nerve growth factor-induced protein A", "transcription factor ETR103", "zinc finger protein 225", "early growth response protein 1"	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.550G>A	5.37:g.137802688G>A	ENSP00000239938:p.Ala184Thr		137830587		Missense_Mutation	SNP	ENST00000239938.4	37	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.568852	0.45798	.	.	ENSG00000120738	ENST00000535792;ENST00000239938	T	0.21361	2.01	3.91	2.95	0.34219	.	0.290655	0.33127	N	0.005249	T	0.11281	0.0275	N	0.14661	0.345	0.30296	N	0.789931	B	0.19331	0.035	B	0.17098	0.017	T	0.05468	-1.0883	10	0.48119	T	0.1	-25.2608	8.1917	0.31372	0.0:0.0:0.7614:0.2386	.	184	P18146	EGR1_HUMAN	T	184	ENSP00000239938:A184T	ENSP00000239938:A184T	A	+	1	0	EGR1	137830587	1.000000	0.71417	0.935000	0.37517	0.799000	0.45148	3.749000	0.55150	2.186000	0.69663	0.313000	0.20887	GCC		0.642	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		A	137802688	G	A	137802688	3	1	122	1	0	0	0	0	1	0	0	0	4982	1087	38	1	556	1	EGR1	5	137802688	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	8732024	137802688	43112572	39	32078										
CCDC99	54908	hgsc.bcm.edu	37	chr5	169025559	169025559	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cacctattatacagatttacTtcagatgaagctggataact	6	8	1	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr5:169025559T>C	ENST00000265295.4	+	9	1391	c.1112T>C	c.(1111-1113)cTt>cCt	p.L371P		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		ACAGATTTACTTCAGATGAAG	0.363																																																0			5											150	156	154					5																	169025559		2203	4300	6503	168958137	SO:0001583	missense	54908			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.1112T>C	5.37:g.169025559T>C	ENSP00000265295:p.Leu371Pro		168958137		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384589	0.82792	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.57595	0.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.72317	0.3445	M	0.72894	2.215	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	0.75249	-0.3384	10	0.72032	D	0.01	-11.0546	16.2332	0.82358	0.0:0.0:0.0:1.0	.	293;272;371	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	P	371;272	ENSP00000265295:L371P	ENSP00000265295:L371P	L	+	2	0	CCDC99	168958137	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.656000	0.74396	2.233000	0.73108	0.523000	0.50628	CTT		0.363	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		C	169025559	T	C	169025559	3	2	122	1	0	0	0	0	1	0	0	0	2882	1609	56	4	1142	4	CCDC99	5	169025559	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	31222871	169025559	11889701	40	32079										
CDKAL1	54901	hgsc.bcm.edu	37	chr6	21065366	21065366	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	caagaaacagtgaaacttgtTgaagagtacaaattcccaag	8	7	0	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:21065366T>C	ENST00000378610.1	+	10	1153	c.1143T>C	c.(1141-1143)gtT>gtC	p.V381V	CDKAL1_ENST00000274695.4_Silent_p.V381V|CDKAL1_ENST00000378624.4_Silent_p.V311V			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	381					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TGAAACTTGTTGAAGAGTACA	0.373																																																0			6											103	102	102					6																	21065366		2203	4300	6503	21173345	SO:0001819	synonymous_variant	54901			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1143T>C	6.37:g.21065366T>C			21173345	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Silent	SNP	ENST00000378610.1	37	CCDS4546.1																																																																																				0.373	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		C	21065366	T	C	21065366	2	2	122	1	0	0	0	0	0	0	0	1	3158	1799	63	4		4	CDKAL1	6	21065366	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10		21065366	150049701	41	32080										
TDP2	51567	hgsc.bcm.edu	37	chr6	24667006	24667006	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gaccgaggcaaactccacacAcagaagtcgccgctttttca	8	14	1	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:24667006A>T	ENST00000378198.4	-	1	255	c.85T>A	c.(85-87)Tgt>Agt	p.C29S	ACOT13_ENST00000537591.1_5'Flank|ACOT13_ENST00000230048.4_5'Flank|TDP2_ENST00000341060.3_5'Flank|TDP2_ENST00000545995.1_Missense_Mutation_p.C59S			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	29					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						AACTCCACACACAGAAGTCGC	0.632								Direct reversal of damage																																								0			6											182	199	193					6																	24667006		2203	4300	6503	24774985	SO:0001583	missense	0			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.85T>A	6.37:g.24667006A>T	ENSP00000367440:p.Cys29Ser		24774985	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	37	CCDS4557.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.235767	0.58886	.	.	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780	T;T	0.26518	1.79;1.73	5.09	5.09	0.68999	UBA-like (1);	0.045010	0.85682	N	0.000000	T	0.16811	0.0404	L	0.58810	1.83	0.47862	D	0.99953	P;P	0.46512	0.879;0.59	B;B	0.41571	0.36;0.197	T	0.02144	-1.1206	10	0.46703	T	0.11	-16.5107	12.8785	0.58003	1.0:0.0:0.0:0.0	.	59;29	O95551-2;O95551	.;TYDP2_HUMAN	S	29;59;29	ENSP00000367440:C29S;ENSP00000437637:C59S	ENSP00000367440:C29S	C	-	1	0	TDP2	24774985	0.998000	0.40836	0.089000	0.20774	0.653000	0.38743	5.821000	0.69257	2.129000	0.65627	0.533000	0.62120	TGT		0.632	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			T	24667006	A	T	24667006	3	4	122	1	0	0	0	0	1	0	0	0	15768	159	6	5	1031	5	TDP2	6	24667006	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	3601640	24667006	146448061	42	32081										
MRPS18B	28973	hgsc.bcm.edu	37	chr6	30585650	30585650	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggcgtacgtcaagatggcggCgtctgtattaaacaccgtgc	13	10	2	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:30585650C>G	ENST00000259873.4	+	1	165	c.8C>G	c.(7-9)gCg>gGg	p.A3G	AL662800.1_ENST00000410962.1_RNA|MRPS18B_ENST00000472229.1_3'UTR|PPP1R10_ENST00000484449.1_5'Flank|MRPS18B_ENST00000506373.2_Missense_Mutation_p.A3G|PPP1R10_ENST00000376511.2_5'Flank	NM_014046.3	NP_054765.1	Q9Y676	RT18B_HUMAN	mitochondrial ribosomal protein S18B	3					translation (GO:0006412)	cell junction (GO:0030054)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(2)	13						AAGATGGCGGCGTCTGTATTA	0.532																																																0			6											180	154	163					6																	30585650		2203	4300	6503	30693629	SO:0001583	missense	28973			AF100761	CCDS4682.1	6p21	2012-09-13			ENSG00000204568	ENSG00000204568		"Mitochondrial ribosomal proteins / small subunits"	14516	protein-coding gene	gene with protein product		611982				11279123	Standard	NM_014046		Approved	MRPS18-2, PTD017, C6orf14, HSPC183	uc003nqo.2	Q9Y676	OTTHUMG00000031268	ENST00000259873.4:c.8C>G	6.37:g.30585650C>G	ENSP00000259873:p.Ala3Gly		30693629	A6NDQ0|Q659G4|Q9BS27	Missense_Mutation	SNP	ENST00000259873.4	37	CCDS4682.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769223	0.69992	.	.	ENSG00000204568	ENST00000259873;ENST00000506373;ENST00000376508	T	0.52057	0.68	5.35	5.35	0.76521	.	0.060205	0.64402	D	0.000004	T	0.33962	0.0881	M	0.63843	1.955	0.28840	N	0.896656	P;P;P	0.42620	0.647;0.785;0.732	B;B;B	0.39465	0.3;0.3;0.217	T	0.39482	-0.9612	10	0.87932	D	0	.	14.4323	0.67259	0.0:1.0:0.0:0.0	.	3;3;3	B4DFG6;Q5STN0;Q9Y676	.;.;RT18B_HUMAN	G	3	ENSP00000259873:A3G	ENSP00000259873:A3G	A	+	2	0	MRPS18B	30693629	0.908000	0.30866	0.922000	0.36590	0.198000	0.23893	3.347000	0.52200	2.780000	0.95670	0.655000	0.94253	GCG		0.532	MRPS18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076584.2			G	30585650	C	G	30585650	3	3	122	1	0	0	0	0	1	0	0	0	9859	768	27	5	10	5	MRPS18B	6	30585650	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	5918644	30585650	140529417	43	32082										
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35987297	35987297	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gaaagattggacacacgcacCggcactggacgtggtgtctg	14	10	1	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:35987297C>T	ENST00000490799.1	-	2	541	c.188G>A	c.(187-189)cGc>cAc	p.R63H	SLC26A8_ENST00000394602.2_Splice_Site_p.R63H|SLC26A8_ENST00000355574.2_Splice_Site_p.R63H	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8									p.R63P(1)		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						ACACACGCACCGGCACTGGAC	0.517																																																1	Substitution - Missense(1)	ovary(1)	6											201	151	168					6																	35987297		2203	4300	6503	36095275	SO:0001630	splice_region_variant	116369			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.188+1G>A	6.37:g.35987297C>T			36095275		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.759331	0.69763	.	.	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574;ENST00000480663	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	4.79	3.0	0.34707	.	0.596683	0.14408	N	0.321455	T	0.15696	0.0378	L	0.32530	0.975	0.31928	N	0.612576	D;B	0.71674	0.998;0.251	P;B	0.57324	0.818;0.047	T	0.04635	-1.0937	9	.	.	.	.	7.2081	0.25919	0.0:0.7988:0.0:0.2012	.	63;63	Q96RN1;Q96RN1-2	S26A8_HUMAN;.	H	63;63;63;149	ENSP00000417638:R63H;ENSP00000378100:R63H;ENSP00000347778:R63H;ENSP00000420488:R149H	.	R	-	2	0	SLC26A8	36095275	0.986000	0.35501	0.975000	0.42487	0.752000	0.42762	0.717000	0.25851	0.736000	0.32559	0.650000	0.86243	CGC		0.517	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		Missense_Mutation	T	35987297	C	T	35987297	5	4	122	1	0	0	0	0	0	0	1	0	14560	666	23	1	2800	1	SLC26A8	6	35987297	Splice_Site	SNP	C	TCGA-G5-6641-01A-11D-1826-10	5401647	35987297	135127770	44	32083										
PRIM2	5558	hgsc.bcm.edu	37	chr6	57472371	57472371	+	3'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gttgtcagggtgcccattccGtcacagtgatccagagctgc	12	12	2	2	rs112546318	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:57472371G>A	ENST00000389488.2	+	0	1247				PRIM2_ENST00000607273.1_3'UTR			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)						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)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TGCCCATTCCGTCACAGTGAT	0.453													G|||	3	0.000599042	0.0023	0	5008	,	,		33942	0		0	False		,,,				2504	0															0			6						G	HIS/ARG	8,4040		0,8,2016	191	175	180		1160	3	1	6	dbSNP_132	180	1,8385		0,1,4192	no	missense	PRIM2	XM_003403439.1	29	0,9,6208	AA,AG,GG		0.0119,0.1976,0.0724	probably-damaging	387/510	57472371	9,12425	2024	4193	6217	57580330	SO:0001624	3_prime_UTR_variant	5558				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.*1244G>A	6.37:g.57472371G>A			57580330	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Missense_Mutation	SNP	ENST00000389488.2	37																																																																																					0.453	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000043468.3	NM_000947		A	57472371	G	A	57472371	1	1	122	0	1	0	0	0	0	0	0	0	12525	1145	40	1		1	PRIM2	6	57472371	3'UTR	SNP	G	TCGA-G5-6641-01A-11D-1826-10	21485074	57472371	113642696	45	32084										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76731907	76731907	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggtgtcatcaggagtgagagGgaaaggcccaagtgagacgt	17	6	2	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:76731907G>A	ENST00000369950.3	-	6	781	c.592C>T	c.(592-594)Cct>Tct	p.P198S	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)				GGAGTGAGAGGGAAAGGCCCA	0.388																																					Pancreas(37;839 1141 2599 26037)											0			6											160	142	148					6																	76731907		2203	4300	6503	76788627	SO:0001583	missense	3617			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.592C>T	6.37:g.76731907G>A	ENSP00000358966:p.Pro198Ser		76788627		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	0.189	-1.054949	0.01965	.	.	ENSG00000112706	ENST00000369950	T	0.20332	2.08	4.96	2.91	0.33838	.	0.822085	0.10672	N	0.647433	T	0.03608	0.0103	N	0.21583	0.68	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.40001	-0.9586	10	0.06625	T	0.88	.	10.1634	0.42866	0.0:0.2172:0.6029:0.1799	.	198	Q17R60	IMPG1_HUMAN	S	198	ENSP00000358966:P198S	ENSP00000358966:P198S	P	-	1	0	IMPG1	76788627	0.126000	0.22350	0.014000	0.15608	0.026000	0.11368	1.741000	0.38238	1.052000	0.40392	0.650000	0.86243	CCT		0.388	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76731907	G	A	76731907	3	1	122	1	0	0	0	0	1	0	0	0	7749	1232	43	3	1849	3	IMPG1	6	76731907	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	19259536	76731907	94383160	46	32085										
AHI1	54806	hgsc.bcm.edu	37	chr6	135787317	135787317	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tggggcaccgtctttatcacCtttttatttggctttccttg	8	10	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:135787317C>T	ENST00000367800.4	-	5	600	c.384G>A	c.(382-384)aaG>aaA	p.K128K	AHI1_ENST00000327035.6_Silent_p.K128K|AHI1_ENST00000457866.2_Silent_p.K128K	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	128					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)		TCTTTATCACCTTTTTATTTG	0.408																																																0			6											220	201	207					6																	135787317		1934	4127	6061	135829010	SO:0001819	synonymous_variant	54806			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.384G>A	6.37:g.135787317C>T			135829010	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Silent	SNP	ENST00000367800.4	37	CCDS47483.1																																																																																				0.408	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		T	135787317	C	T	135787317	2	4	122	1	0	0	0	0	0	0	0	1	413	680	24	3		3	AHI1	6	135787317	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	59055410	135787317	35327750	47	32086										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136597485	136597485	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ccccttctgaatcattaaacTtttgttttccagactcttta	3	11	3	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:136597485T>A	ENST00000531224.1	-	5	1430	c.1178A>T	c.(1177-1179)aAg>aTg	p.K393M	BCLAF1_ENST00000527536.1_Missense_Mutation_p.K393M|BCLAF1_ENST00000353331.4_Missense_Mutation_p.K391M|BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000527759.1_Missense_Mutation_p.K391M|BCLAF1_ENST00000392348.2_Missense_Mutation_p.K391M	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	393					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)		ATCATTAAACTTTTGTTTTCC	0.433																																					Colon(142;1534 1789 5427 7063 28491)											0			6											306	321	316					6																	136597485		2203	4300	6503	136639178	SO:0001583	missense	9774			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.1178A>T	6.37:g.136597485T>A	ENSP00000435210:p.Lys393Met		136639178	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.124616	0.56613	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42;2.42	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000002	T	0.11665	0.0284	N	0.08118	0	0.80722	D	1	D;D;D	0.64830	0.987;0.994;0.987	P;P;P	0.59012	0.753;0.85;0.753	T	0.28427	-1.0044	10	0.44086	T	0.13	-8.8214	15.9539	0.79865	0.0:0.0:0.0:1.0	.	391;391;393	Q9NYF8-2;Q9NYF8-3;Q9NYF8	.;.;BCLF1_HUMAN	M	393;391;393;391;391;393	ENSP00000435210:K393M;ENSP00000229446:K391M;ENSP00000435441:K393M;ENSP00000434826:K391M;ENSP00000376159:K391M;ENSP00000431734:K393M	ENSP00000229446:K391M	K	-	2	0	BCLAF1	136639178	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.700000	0.61803	2.240000	0.73641	0.528000	0.53228	AAG		0.433	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136597485	T	A	136597485	3	1	122	1	0	0	0	0	1	0	0	0	1384	1609	56	5	1620	5	BCLAF1	6	136597485	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	810168	136597485	34517582	48	32087										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200292	138200292	+	Silent	SNP	C	C	T													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aagtcagatccctcgcggctCgtccggagcccctccccgca					rs542739083		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:138200292C>T	ENST00000237289.4	+	7	1776	c.1710C>T	c.(1708-1710)ctC>ctT	p.L570L		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	570	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)		CCTCGCGGCTCGTCCGGAGCC	0.632			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"								C|||	1	0.000199681	0	0	5008	,	,		15802	0		0	False		,,,				2504	0.001				GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	6											57	63	61					6																	138200292		2203	4300	6503	138241985	SO:0001819	synonymous_variant	7128			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.1710C>T	6.37:g.138200292C>T			138241985	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	37	CCDS5187.1																																																																																				0.632	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			T	138200292	C	T	138200292	2	4	122	1	0	0	0	0	0	0	0	1	16313	871	31	1		1	TNFAIP3	6	138200292	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	1602807	138200292	32914775	49	32088	59	2								
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200296	138200296	+	Silent	SNP	C	C	A													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cagatccctcgcggctcgtcCggagcccctccccgcattct							TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:138200296C>A	ENST00000237289.4	+	7	1780	c.1714C>A	c.(1714-1716)Cgg>Agg	p.R572R		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	572	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)		GCGGCTCGTCCGGAGCCCCTC	0.637			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	6											54	60	58					6																	138200296		2203	4300	6503	138241989	SO:0001819	synonymous_variant	7128			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.1714C>A	6.37:g.138200296C>A			138241989	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	37	CCDS5187.1																																																																																				0.637	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			A	138200296	C	A	138200296	2	1	122	1	0	0	0	0	0	0	0	1	16313	643	23	2		2	TNFAIP3	6	138200296	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	4	138200296	32914771	50	32089	59	2								
MYCT1	80177	hgsc.bcm.edu	37	chr6	153042915	153042915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tcactgtatccatggcaatcGggctggtacttggaggattt	12	8	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr6:153042915G>A	ENST00000367245.5	+	2	243	c.235G>A	c.(235-237)Ggg>Agg	p.G79R	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	79						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)		CATGGCAATCGGGCTGGTACT	0.408																																																0			6											156	140	145					6																	153042915		2203	4300	6503	153084608	SO:0001583	missense	80177			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.235G>A	6.37:g.153042915G>A	ENSP00000356214:p.Gly79Arg		153084608	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	37	CCDS5239.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898475	0.91962	.	.	ENSG00000120279	ENST00000367245	T	0.63913	-0.07	5.77	5.77	0.91146	.	0.100261	0.64402	D	0.000002	T	0.74574	0.3734	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.67725	0.953;0.923	T	0.75777	-0.3198	10	0.72032	D	0.01	-5.4393	19.99	0.97362	0.0:0.0:1.0:0.0	.	31;79	D6Q1S4;Q8N699	.;MYCT1_HUMAN	R	79	ENSP00000356214:G79R	ENSP00000356214:G79R	G	+	1	0	MYCT1	153084608	1.000000	0.71417	0.060000	0.19600	0.943000	0.58893	8.091000	0.89528	2.723000	0.93209	0.573000	0.79308	GGG		0.408	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107		A	153042915	G	A	153042915	3	1	122	1	0	0	0	0	1	0	0	0	10052	1116	39	1	241	1	MYCT1	6	153042915	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	14842619	153042915	18072152	51	32090										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21654801	21654801	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aatctactcgtctttttgaaGtggctcttccagagtacaaa	7	9	3	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr7:21654801G>A	ENST00000409508.3	+	21	3953	c.3922G>A	c.(3922-3924)Gtg>Atg	p.V1308M	DNAH11_ENST00000328843.6_Missense_Mutation_p.V1308M	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1308	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)			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						TCTTTTTGAAGTGGCTCTTCC	0.393									Kartagener syndrome																																							0			7											127	120	122					7																	21654801		1849	4096	5945	21621326	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	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.3922G>A	7.37:g.21654801G>A	ENSP00000475939:p.Val1308Met		21621326	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	23.0	4.357546	0.82243	.	.	ENSG00000105877	ENST00000328843	T	0.25250	1.81	5.37	5.37	0.77165	.	0.559829	0.18755	N	0.132066	T	0.36826	0.0981	.	.	.	0.54753	D	0.999987	P	0.52577	0.954	P	0.50708	0.648	T	0.04537	-1.0944	9	0.49607	T	0.09	.	13.7695	0.63015	0.0764:0.0:0.9236:0.0	.	1308	Q96DT5	DYH11_HUMAN	M	1308	ENSP00000330671:V1308M	ENSP00000330671:V1308M	V	+	1	0	DNAH11	21621326	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.903000	0.87398	2.659000	0.90383	0.655000	0.94253	GTG		0.393	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21654801	G	A	21654801	3	1	122	1	0	0	0	0	1	0	0	0	4610	1029	36	3	4004	3	DNAH11	7	21654801	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10		21654801	137483862	52	32091										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77885428	77885428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtcaagtatttgtttcacccGctgtcctgtaggactgtcgg	11	10	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr7:77885428G>A	ENST00000354212.4	-	10	2132	c.1879C>T	c.(1879-1881)Cgg>Tgg	p.R627W	MAGI2_ENST00000419488.1_Missense_Mutation_p.R627W|MAGI2_ENST00000522391.1_Missense_Mutation_p.R627W|MAGI2_ENST00000535697.1_Missense_Mutation_p.R464W|MAGI2_ENST00000536571.1_Missense_Mutation_p.R459W	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	627	PDZ 3. {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)				TGTTTCACCCGCTGTCCTGTA	0.517																																																0			7											71	61	64					7																	77885428		2203	4300	6503	77723364	SO:0001583	missense	9863			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.1879C>T	7.37:g.77885428G>A	ENSP00000346151:p.Arg627Trp		77723364	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245718	0.59103	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66	5.74	3.76	0.43208	PDZ/DHR/GLGF (4);	0.000000	0.33457	U	0.004881	T	0.56232	0.1971	M	0.81802	2.56	0.58432	D	0.999998	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	0.992;0.988;1.0;1.0;0.994;0.998	T	0.63427	-0.6640	10	0.87932	D	0	.	13.0805	0.59112	0.0:0.0:0.6243:0.3757	.	464;459;627;627;627;627	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	W	627;627;627;627;459;464	ENSP00000405766:R627W;ENSP00000346151:R627W;ENSP00000428389:R627W;ENSP00000441584:R459W;ENSP00000441603:R464W	ENSP00000346151:R627W	R	-	1	2	MAGI2	77723364	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.393000	0.34497	1.407000	0.46875	0.561000	0.74099	CGG		0.517	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77885428	G	A	77885428	3	1	122	1	0	0	0	0	1	0	0	0	9221	1086	38	1	2540	1	MAGI2	7	77885428	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	56230627	77885428	81253235	53	32092										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92731562	92731562	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gcctcttcattttgcttaatAttgttcctgggttttagcag	8	8	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr7:92731562A>G	ENST00000379958.2	-	3	4118	c.3849T>C	c.(3847-3849)aaT>aaC	p.N1283N		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1283						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)			TTTGCTTAATATTGTTCCTGG	0.289																																																0			7											53	61	58					7																	92731562		2199	4293	6492	92569498	SO:0001819	synonymous_variant	54809			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.3849T>C	7.37:g.92731562A>G			92569498	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																				0.289	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		G	92731562	A	G	92731562	2	3	122	1	0	0	0	0	0	0	0	1	13863	446	16	4		4	SAMD9	7	92731562	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10	14846134	92731562	66407101	54	32093										
PARP12	64761	hgsc.bcm.edu	37	chr7	139727183	139727183	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cagaccttctgatactcttcCgaggaagaactaagggtgat	10	9	2	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr7:139727183C>T	ENST00000263549.3	-	10	2394	c.1521G>A	c.(1519-1521)tcG>tcA	p.S507S		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	507	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)					GATACTCTTCCGAGGAAGAAC	0.453																																																0			7											109	106	107					7																	139727183		2203	4300	6503	139373652	SO:0001819	synonymous_variant	64761			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.1521G>A	7.37:g.139727183C>T			139373652	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																				0.453	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750		T	139727183	C	T	139727183	2	4	122	1	0	0	0	0	0	0	0	1	11488	639	23	1		1	PARP12	7	139727183	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	46995621	139727183	19411480	55	32094										
SSPO	23145	hgsc.bcm.edu	37	chr7	149498993	149498993	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtgtctgtctgctgagcggcGctgtgacctgcggcctgact	15	12	2	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr7:149498993G>A	ENST00000378016.2	+	0	7445							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)			GCTGAGCGGCGCTGTGACCTG	0.672																																																0			7											28	31	30					7																	149498993		2154	4245	6399	149129926			23145			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		7.37:g.149498993G>A			149129926	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																					0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149498993	G	A	149498993	1	1	122	0	1	0	0	0	0	0	0	0	15228	1087	38	1		1	SSPO	7	149498993	RNA	SNP	G	TCGA-G5-6641-01A-11D-1826-10	9771810	149498993	9639670	56	32095										
NEFL	4747	hgsc.bcm.edu	37	chr8	24813787	24813787	+	RNA	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtgcggatggacttgaggtcGttgctgatggcggctacctg	17	8	0	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr8:24813787G>A	ENST00000221169.5	-	0	837				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		ACTTGAGGTCGTTGCTGATGG	0.627																																																0			8											30	34	32					8																	24813787		2169	4274	6443	24869704			4747				CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24813787G>A			24869704	B9ZVN2|Q16154|Q8IU72	Silent	SNP	ENST00000221169.5	37																																																																																					0.627	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24813787	G	A	24813787	1	1	122	0	1	0	0	0	0	0	0	0	10346	1136	40	1		1	NEFL	8	24813787	RNA	SNP	G	TCGA-G5-6641-01A-11D-1826-10		24813787	121550235	57	32096										
PLAG1	5324	hgsc.bcm.edu	37	chr8	57079935	57079935	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtagttcttgccacattcttCgcacttaaacgtctctttgt	6	11	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr8:57079935C>T	ENST00000316981.3	-	5	849	c.370G>A	c.(370-372)Gaa>Aaa	p.E124K	PLAG1_ENST00000429357.2_Missense_Mutation_p.E124K|PLAG1_ENST00000423799.2_Missense_Mutation_p.E42K	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	124	Decreased nuclear import with localization in the nucleus but also in the cytoplasm.				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)		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)			CCACATTCTTCGCACTTAAAC	0.428			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	0			8											158	116	130					8																	57079935		2202	4300	6502	57242489	SO:0001583	missense	5324			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.370G>A	8.37:g.57079935C>T	ENSP00000325546:p.Glu124Lys		57242489	B4DLC2|Q59GH8|Q9Y4L2	Missense_Mutation	SNP	ENST00000316981.3	37	CCDS6165.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225010	0.58668	.	.	ENSG00000181690	ENST00000316981;ENST00000423799;ENST00000429357	T;T;T	0.50813	0.73;0.73;0.73	5.55	5.55	0.83447	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.218976	0.48286	D	0.000190	T	0.37237	0.0996	L	0.33093	0.98	0.47778	D	0.999513	P	0.44627	0.839	B	0.33568	0.166	T	0.28106	-1.0054	10	0.41790	T	0.15	-21.0199	19.5003	0.95091	0.0:1.0:0.0:0.0	.	124	Q6DJT9	PLAG1_HUMAN	K	124;42;124	ENSP00000325546:E124K;ENSP00000404067:E42K;ENSP00000416537:E124K	ENSP00000325546:E124K	E	-	1	0	PLAG1	57242489	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	2.926000	0.48892	2.594000	0.87642	0.585000	0.79938	GAA		0.428	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		T	57079935	C	T	57079935	3	4	122	1	0	0	0	0	1	0	0	0	12049	893	31	1	1136	1	PLAG1	8	57079935	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	32266148	57079935	89284087	58	32097										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113267537	113267537	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atctgcttgacatattctggTgcttgatcccactaatatga	7	9	2	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr8:113267537T>C	ENST00000297405.5	-	62	10226	c.9982A>G	c.(9982-9984)Acc>Gcc	p.T3328A	CSMD3_ENST00000352409.3_Missense_Mutation_p.T3258A|CSMD3_ENST00000455883.2_Missense_Mutation_p.T3159A|CSMD3_ENST00000343508.3_Missense_Mutation_p.T3288A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3328	Sushi 26. {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						CATATTCTGGTGCTTGATCCC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											133	120	124					8																	113267537		2203	4300	6503	113336713	SO:0001583	missense	114788			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.9982A>G	8.37:g.113267537T>C	ENSP00000297405:p.Thr3328Ala		113336713	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.380700	0.61845	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.19	4.03	0.46877	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.69531	0.3121	L	0.60012	1.86	0.40164	D	0.977093	D;D;B	0.69078	0.996;0.997;0.376	D;D;B	0.71870	0.957;0.975;0.233	T	0.67237	-0.5721	10	0.07990	T	0.79	.	11.5802	0.50887	0.1335:0.0:0.0:0.8664	.	3159;3328;3288	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	3288;3328;2598;3159;3258	ENSP00000345799:T3288A;ENSP00000297405:T3328A;ENSP00000341558:T2598A;ENSP00000412263:T3159A;ENSP00000343124:T3258A	ENSP00000297405:T3328A	T	-	1	0	CSMD3	113336713	1.000000	0.71417	0.997000	0.53966	0.849000	0.48306	5.909000	0.69923	0.982000	0.38575	-0.336000	0.08194	ACC		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113267537	T	C	113267537	3	2	122	1	0	0	0	0	1	0	0	0	3952	1696	59	4	1181	4	CSMD3	8	113267537	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	56187602	113267537	33096485	59	32098										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113303837	113303837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	caggattgcagtcatagaatAccacagtgccgtaagtaaaa	9	8	1	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr8:113303837A>G	ENST00000297405.5	-	56	9120	c.8876T>C	c.(8875-8877)gTa>gCa	p.V2959A	CSMD3_ENST00000352409.3_Missense_Mutation_p.V2889A|CSMD3_ENST00000455883.2_Missense_Mutation_p.V2790A|CSMD3_ENST00000343508.3_Missense_Mutation_p.V2919A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2959	Sushi 20. {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						GTCATAGAATACCACAGTGCC	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						0			8											125	124	124					8																	113303837		2203	4298	6501	113373013	SO:0001583	missense	114788			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.8876T>C	8.37:g.113303837A>G	ENSP00000297405:p.Val2959Ala		113373013	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220516	0.79464	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48	5.35	5.35	0.76521	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000012	D	0.83562	0.5281	M	0.78916	2.43	0.58432	D	0.999991	D;D;D	0.76494	0.994;0.999;0.961	D;D;P	0.87578	0.986;0.998;0.774	T	0.83229	-0.0064	10	0.35671	T	0.21	.	15.6317	0.76917	1.0:0.0:0.0:0.0	.	2790;2959;2919	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	2919;2959;2229;2790;2889	ENSP00000345799:V2919A;ENSP00000297405:V2959A;ENSP00000341558:V2229A;ENSP00000412263:V2790A;ENSP00000343124:V2889A	ENSP00000297405:V2959A	V	-	2	0	CSMD3	113373013	1.000000	0.71417	0.996000	0.52242	0.883000	0.51084	9.255000	0.95524	2.146000	0.66826	0.482000	0.46254	GTA		0.353	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113303837	A	G	113303837	3	3	122	1	0	0	0	0	1	0	0	0	3952	391	14	4	2311	4	CSMD3	8	113303837	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	36300	113303837	33060185	60	32099										
PAX5	5079	hgsc.bcm.edu	37	chr9	37015164	37015164	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttggatcctccaattaccccAggcttgatgcttcctgtctc	7	14	1	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr9:37015164A>G	ENST00000358127.4	-	3	314	c.240T>C	c.(238-240)ccT>ccC	p.P80P	PAX5_ENST00000520154.1_Silent_p.P80P|PAX5_ENST00000520281.1_Silent_p.P80P|PAX5_ENST00000414447.1_Silent_p.P80P|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000377853.2_Silent_p.P80P|PAX5_ENST00000377852.2_Silent_p.P80P|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000446742.1_Intron|PAX5_ENST00000377847.2_Silent_p.P80P|PAX5_ENST00000523241.1_Silent_p.P80P	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	80	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.		P -> R. {ECO:0000269|PubMed:24013638}.		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|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)	p.?(42)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		CAATTACCCCAGGCTTGATGC	0.458			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	42	Unknown(42)	haematopoietic_and_lymphoid_tissue(42)	9											197	203	201					9																	37015164		2203	4300	6503	37005164	SO:0001819	synonymous_variant	5079				CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"Paired boxes", "Homeoboxes / PRD class"	8619	protein-coding gene	gene with protein product	"B-cell lineage specific activator"	167414	"paired box gene 5 (B-cell lineage specific activator protein)", "paired box gene 5 (B-cell lineage specific activator)"			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.240T>C	9.37:g.37015164A>G			37005164	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Silent	SNP	ENST00000358127.4	37	CCDS6607.1																																																																																				0.458	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			G	37015164	A	G	37015164	2	3	122	1	0	0	0	0	0	0	0	1	11513	175	7	4		4	PAX5	9	37015164	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10		37015164	104198267	61	32100										
ERP44	23071	hgsc.bcm.edu	37	chr9	102768907	102768907	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tgtctaaatttgtcacaatcGgcatgtaaaaagtttattgt	7	5	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr9:102768907G>A	ENST00000262455.6	-	10	1096	c.897C>T	c.(895-897)gcC>gcT	p.A299A		NM_015051.1	NP_055866.1	Q9BS26	ERP44_HUMAN	endoplasmic reticulum protein 44	299					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						TGTCACAATCGGCATGTAAAA	0.318																																																0			9											88	90	90					9																	102768907		2203	4300	6503	101808728	SO:0001819	synonymous_variant	23071			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.897C>T	9.37:g.102768907G>A			101808728	O60319|Q4VXC1|Q5VWZ7|Q6UW14|Q8WX67	Silent	SNP	ENST00000262455.6	37	CCDS35082.1																																																																																				0.318	ERP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053402.1	XM_088476		A	102768907	G	A	102768907	2	1	122	1	0	0	0	0	0	0	0	1	5256	1103	39	1		1	ERP44	9	102768907	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10	65753743	102768907	38444524	62	32101										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113341377	113341377	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tcttggaggagcagcgcgcaCttgtgctggcgcgcgcggcg	18	12	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr9:113341377C>T	ENST00000401783.2	-	1	783	c.447G>A	c.(445-447)aaG>aaA	p.K149K	SVEP1_ENST00000302728.8_Silent_p.K149K|SVEP1_ENST00000374469.1_Silent_p.K126K|SVEP1_ENST00000374461.1_Silent_p.K126K	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	149	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						GCAGCGCGCACTTGTGCTGGC	0.682																																																0			9											6	8	7					9																	113341377		1867	3982	5849	112381198	SO:0001819	synonymous_variant	79987			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.447G>A	9.37:g.113341377C>T			112381198	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																				0.682	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113341377	C	T	113341377	2	4	122	1	0	0	0	0	0	0	0	1	15459	564	20	3		3	SVEP1	9	113341377	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	10572470	113341377	27872054	63	32102										
OR1N1	138883	hgsc.bcm.edu	37	chr9	125288888	125288888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggccttgcccaccccaccacGggttcggaccctcaggatag	11	17	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr9:125288888G>A	ENST00000304880.2	-	1	684	c.685C>T	c.(685-687)Cgt>Tgt	p.R229C		NM_012363.1	NP_036495.1	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N, member 1	229						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)|large_intestine(2)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						ACCCCACCACGGGTTCGGACC	0.547																																																0			9											87	74	78					9																	125288888		2203	4300	6503	124328709	SO:0001583	missense	138883			U86216	CCDS6844.1	9q34.11	2012-08-09			ENSG00000171505	ENSG00000171505		"GPCR / Class A : Olfactory receptors"	8221	protein-coding gene	gene with protein product				OR1N3		9500546	Standard	NM_012363		Approved	OR1-26	uc004bmn.1	Q8NGS0	OTTHUMG00000020608	ENST00000304880.2:c.685C>T	9.37:g.125288888G>A	ENSP00000306974:p.Arg229Cys		124328709	A3KFM1|O43870|Q6IF16|Q96R93	Missense_Mutation	SNP	ENST00000304880.2	37	CCDS6844.1	.	.	.	.	.	.	.	.	.	.	G	9.934	1.215749	0.22373	.	.	ENSG00000171505	ENST00000304880	T	0.00137	8.68	3.75	-4.13	0.03904	GPCR, rhodopsin-like superfamily (1);	1.158660	0.07121	U	0.843857	T	0.00073	0.0002	N	0.12569	0.235	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09662	-1.0664	10	0.72032	D	0.01	.	7.354	0.26709	0.2477:0.4455:0.3069:0.0	.	229	Q8NGS0	OR1N1_HUMAN	C	229	ENSP00000306974:R229C	ENSP00000306974:R229C	R	-	1	0	OR1N1	124328709	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.952000	0.01528	-0.669000	0.05289	-0.300000	0.09419	CGT		0.547	OR1N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053938.1			A	125288888	G	A	125288888	3	1	122	1	0	0	0	0	1	0	0	0	11000	1116	39	1	254	1	OR1N1	9	125288888	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	11947511	125288888	15924543	64	32103										
COBRA1	25920	hgsc.bcm.edu	37	chr9	140160820	140160820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gctgctgctccggctgctggCgctgggccagggagcctggg	19	13	0	0	rs150102832		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr9:140160820C>T	ENST00000343053.4	+	8	1374	c.1037C>T	c.(1036-1038)gCg>gTg	p.A346V		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	346					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)											CGGCTGCTGGCGCTGGGCCAG	0.662																																																0			9						C	VAL/ALA	0,4380		0,0,2190	32	31	31		1037	5.4	1	9	dbSNP_134	31	1,8559		0,1,4279	no	missense	COBRA1	NM_015456.3	64	0,1,6469	TT,TC,CC		0.0117,0.0,0.0077	benign	346/581	140160820	1,12939	2190	4280	6470	139280641	SO:0001583	missense	25920			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.1037C>T	9.37:g.140160820C>T	ENSP00000339495:p.Ala346Val		139280641	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	37	CCDS7040.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.796228	0.70567	0.0	1.17E-4	ENSG00000188986	ENST00000343053	.	.	.	5.36	5.36	0.76844	.	0.102696	0.64402	D	0.000002	T	0.44540	0.1298	N	0.12961	0.28	0.51012	D	0.999909	B	0.31611	0.331	B	0.31337	0.128	T	0.49597	-0.8923	9	0.66056	D	0.02	-41.6393	17.637	0.88125	0.0:1.0:0.0:0.0	.	346	Q8WX92	NELFB_HUMAN	V	346	.	ENSP00000339495:A346V	A	+	2	0	COBRA1	139280641	1.000000	0.71417	0.955000	0.39395	0.957000	0.61999	4.709000	0.61867	2.506000	0.84524	0.491000	0.48974	GCG		0.662	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		T	140160820	C	T	140160820	3	4	122	1	0	0	0	0	1	0	0	0	3661	768	27	1	1067	1	COBRA1	9	140160820	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	14871932	140160820	1052611	65	32104										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140707887	140707887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ccatcccctgtgtcaacgccGtggacagcgagccatgcccc	10	18	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr9:140707887G>A	ENST00000460843.1	+	21	3112	c.3085G>A	c.(3085-3087)Gtg>Atg	p.V1029M		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1029					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)		TGTCAACGCCGTGGACAGCGA	0.587																																																0			9											143	83	103					9																	140707887		2203	4300	6503	139827708	SO:0001583	missense	79813			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.3085G>A	9.37:g.140707887G>A	ENSP00000417980:p.Val1029Met		139827708	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	G	17.28	3.350199	0.61183	.	.	ENSG00000181090	ENST00000371400;ENST00000460843	D	0.90676	-2.71	4.99	4.09	0.47781	Pre-SET zinc-binding sub-group (1);Pre-SET domain (1);	0.121948	0.56097	D	0.000031	D	0.95790	0.8630	M	0.94021	3.485	0.80722	D	1	P	0.50819	0.939	P	0.60789	0.879	D	0.96247	0.9180	10	0.72032	D	0.01	.	13.3558	0.60627	0.0764:0.0:0.9236:0.0	.	1029	Q9H9B1	EHMT1_HUMAN	M	998;1029	ENSP00000417980:V1029M	ENSP00000360453:V998M	V	+	1	0	EHMT1	139827708	1.000000	0.71417	0.702000	0.30337	0.081000	0.17604	6.624000	0.74243	1.089000	0.41292	0.655000	0.94253	GTG		0.587	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		A	140707887	G	A	140707887	3	1	122	1	0	0	0	0	1	0	0	0	4994	1145	40	1	3216	1	EHMT1	9	140707887	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	547067	140707887	505544	66	32105										
KIN	22944	hgsc.bcm.edu	37	chr10	7822037	7822037	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	accttctctgcccagccactTagtaaaatcagtcagagttt	6	12	3	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr10:7822037T>C	ENST00000379562.4	-	4	405	c.358A>G	c.(358-360)Aag>Gag	p.K120E	KIN_ENST00000543003.1_Missense_Mutation_p.K14E|KIN_ENST00000535925.1_Missense_Mutation_p.K120E	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						CCCAGCCACTTAGTAAAATCA	0.403																																																0			10											169	150	156					10																	7822037		2203	4300	6503	7862043	SO:0001583	missense	22944			AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.358A>G	10.37:g.7822037T>C	ENSP00000368881:p.Lys120Glu		7862043		Missense_Mutation	SNP	ENST00000379562.4	37	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252724	0.59212	.	.	ENSG00000151657	ENST00000535925;ENST00000379562;ENST00000543003	.	.	.	5.74	5.74	0.90152	DNA/RNA-binding protein Kin17, conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.80879	0.4708	M	0.85542	2.76	0.80722	D	1	P;D;D	0.58970	0.75;0.984;0.984	B;D;D	0.75484	0.111;0.986;0.986	T	0.83127	-0.0115	9	0.54805	T	0.06	-27.9075	14.6061	0.68481	0.0:0.0:0.0:1.0	.	14;120;120	F5GXB3;B4DX32;O60870	.;.;KIN17_HUMAN	E	120;120;14	.	ENSP00000368881:K120E	K	-	1	0	KIN	7862043	1.000000	0.71417	0.926000	0.36857	0.730000	0.41778	7.649000	0.83500	2.186000	0.69663	0.533000	0.62120	AAG		0.403	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311		C	7822037	T	C	7822037	3	2	122	1	0	0	0	0	1	0	0	0	8336	1763	61	4	863	4	KIN	10	7822037	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10		7822037	127712710	67	32106										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26359311	26359311	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tgctcatcttttagttcagcAgctgacagtgcttggaaagg	11	8	3	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr10:26359311A>G	ENST00000265944.5	+	14	1506	c.1340A>G	c.(1339-1341)cAg>cGg	p.Q447R	MYO3A_ENST00000543632.1_Missense_Mutation_p.Q447R	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	447	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						TTAGTTCAGCAGCTGACAGTG	0.313																																																0			10											93	92	92					10																	26359311		2203	4299	6502	26399317	SO:0001583	missense	53904			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.1340A>G	10.37:g.26359311A>G	ENSP00000265944:p.Gln447Arg		26399317	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.700463	0.88924	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	D;D	0.87103	-2.21;-2.21	5.79	5.79	0.91817	Myosin head, motor domain (3);	0.051914	0.85682	D	0.000000	D	0.92446	0.7602	M	0.81341	2.54	0.80722	D	1	P;P;D	0.57257	0.554;0.608;0.979	B;B;P	0.59825	0.248;0.342;0.864	D	0.92133	0.5714	10	0.40728	T	0.16	.	16.1223	0.81369	1.0:0.0:0.0:0.0	.	447;447;447	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	R	447	ENSP00000265944:Q447R;ENSP00000445909:Q447R	ENSP00000265944:Q447R	Q	+	2	0	MYO3A	26399317	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.988000	0.93501	2.201000	0.70794	0.528000	0.53228	CAG		0.313	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26359311	A	G	26359311	3	3	122	1	0	0	0	0	1	0	0	0	10106	188	7	4	1386	4	MYO3A	10	26359311	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	18537274	26359311	109175436	68	32107										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31809758	31809758	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	taaaaaaagaaaatccagtcGctacaaacagttgtaaaagt	6	6	0	1	rs139511659		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr10:31809758G>T	ENST00000320985.10	+	7	1605	c.1495G>T	c.(1495-1497)Gct>Tct	p.A499S	ZEB1_ENST00000361642.5_Missense_Mutation_p.A500S|ZEB1_ENST00000446923.2_Missense_Mutation_p.A483S|ZEB1_ENST00000560721.2_Missense_Mutation_p.A479S|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Missense_Mutation_p.A432S			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	499					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)				AAATCCAGTCGCTACAAACAG	0.373																																					Ovarian(40;423 959 14296 36701 49589)											0			10											53	62	59					10																	31809758		2203	4300	6503	31849764	SO:0001583	missense	6935			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.1495G>T	10.37:g.31809758G>T	ENSP00000319248:p.Ala499Ser		31849764	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	G	3.578	-0.086146	0.07097	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000541037;ENST00000543514;ENST00000446923	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	5.45	4.54	0.55810	.	0.186906	0.38436	N	0.001691	T	0.53610	0.1807	N	0.08118	0	0.24075	N	0.995965	B;B;B;B;B;B;B;B	0.28933	0.006;0.047;0.228;0.004;0.028;0.005;0.068;0.004	B;B;B;B;B;B;B;B	0.26517	0.002;0.034;0.07;0.0;0.015;0.002;0.025;0.0	T	0.28964	-1.0027	10	0.10636	T	0.68	-6.672	16.624	0.84937	0.0:0.8678:0.1321:0.0	.	432;499;483;499;499;479;500;499	F5H4I8;F5H1R1;E9PCM7;B2RBI8;A0JLS9;Q5VZ84;Q2KJ05;P37275	.;.;.;.;.;.;.;ZEB1_HUMAN	S	281;499;500;499;432;499;479;358;390;483	ENSP00000444282:A281S;ENSP00000354487:A500S;ENSP00000444891:A432S;ENSP00000319248:A499S;ENSP00000391612:A483S	ENSP00000319248:A499S	A	+	1	0	ZEB1	31849764	0.770000	0.28543	0.979000	0.43373	0.912000	0.54170	1.551000	0.36233	1.442000	0.47568	-0.147000	0.13772	GCT		0.373	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		T	31809758	G	T	31809758	3	4	122	1	0	0	0	0	1	0	0	0	17662	1087	38	2	1535	2	ZEB1	10	31809758	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	5450447	31809758	103724989	69	32108										
RET	5979	hgsc.bcm.edu	37	chr10	43610157	43610157	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ctggactccatggagaaccaGgtctccgtggatgccttcaa	11	12	2	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr10:43610157G>C	ENST00000355710.3	+	11	2341	c.2109G>C	c.(2107-2109)caG>caC	p.Q703H	RET_ENST00000340058.5_Missense_Mutation_p.Q703H	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	703					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)	TGGAGAACCAGGTCTCCGTGG	0.682		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																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	0			10											31	31	31					10																	43610157		2203	4300	6503	42930163	SO:0001583	missense	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	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.2109G>C	10.37:g.43610157G>C	ENSP00000347942:p.Gln703His		42930163	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364016	0.61513	.	.	ENSG00000165731	ENST00000355710;ENST00000340058	D;D	0.89123	-2.47;-2.47	4.88	3.02	0.34903	.	0.000000	0.85682	D	0.000000	D	0.87446	0.6179	N	0.24115	0.695	0.48288	D	0.99962	P;D;D	0.63046	0.918;0.986;0.992	B;P;D	0.64144	0.429;0.838;0.922	T	0.82868	-0.0244	10	0.21540	T	0.41	.	11.1557	0.48486	0.1501:0.0:0.8499:0.0	.	449;703;703	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	H	703	ENSP00000347942:Q703H;ENSP00000344798:Q703H	ENSP00000344798:Q703H	Q	+	3	2	RET	42930163	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.875000	0.48491	0.659000	0.30945	-0.291000	0.09656	CAG		0.682	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		C	43610157	G	C	43610157	3	2	122	1	0	0	0	0	1	0	0	0	13272	991	35	5	2151	5	RET	10	43610157	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	11800399	43610157	91924590	70	32109										
CHAT	1103	hgsc.bcm.edu	37	chr10	50822317	50822317	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agggaggaggtacaagaggaAggagagaagtgcggccagct	19	5	0	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr10:50822317A>C	ENST00000337653.2	+	1	235	c.82A>C	c.(82-84)Agg>Cgg	p.R28R	CHAT_ENST00000339797.1_Intron|CHAT_ENST00000395562.2_5'UTR|CHAT_ENST00000351556.3_Intron|CHAT_ENST00000455728.2_5'Flank|CHAT_ENST00000460699.1_Intron|CHAT_ENST00000395559.2_Intron	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	28					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)			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)	tacaagaggaaggagagAAGT	0.687																																																0			10											9	11	10					10																	50822317		1943	3766	5709	50492323	SO:0001819	synonymous_variant	10044			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.82A>C	10.37:g.50822317A>C			50492323	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	37	CCDS7232.1																																																																																				0.687	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		C	50822317	A	C	50822317	2	2	122	1	0	0	0	0	0	0	0	1	3319	63	3	4		4	CHAT	10	50822317	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10	7212160	50822317	84712430	71	32110										
OR10A4	283297	hgsc.bcm.edu	37	chr11	6898122	6898122	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	acttggtcattgtgcccaagAtgctggggaccctgatcatt	11	10	2	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:6898122A>G	ENST00000379829.2	+	1	267	c.244A>G	c.(244-246)Atg>Gtg	p.M82V		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	82					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)	p.M82L(1)		kidney(1)|large_intestine(2)|liver(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGTGCCCAAGATGCTGGGGAC	0.468																																																1	Substitution - Missense(1)	ovary(1)	11											149	135	140					11																	6898122		2201	4296	6497	6854698	SO:0001583	missense	283297			AF209506	CCDS7774.1	11p15.4	2012-08-09	2002-11-13	2004-03-10	ENSG00000170782	ENSG00000170782		"GPCR / Class A : Olfactory receptors"	15130	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily A, member 4 pseudogene"	OR10A4P			Standard	NM_207186		Approved		uc010rat.2	Q9H209	OTTHUMG00000165740	ENST00000379829.2:c.244A>G	11.37:g.6898122A>G	ENSP00000369157:p.Met82Val		6854698	B2RNP5|B9EH36|Q96R20	Missense_Mutation	SNP	ENST00000379829.2	37	CCDS7774.1	.	.	.	.	.	.	.	.	.	.	a	10.71	1.426793	0.25726	.	.	ENSG00000170782	ENST00000379829	T	0.05580	3.42	4.91	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000042	T	0.09774	0.0240	M	0.72479	2.2	0.26251	N	0.978723	B	0.10296	0.003	B	0.12837	0.008	T	0.12268	-1.0554	10	0.59425	D	0.04	.	10.3455	0.43903	0.8349:0.1651:0.0:0.0	.	82	Q9H209	O10A4_HUMAN	V	82	ENSP00000369157:M82V	ENSP00000369157:M82V	M	+	1	0	OR10A4	6854698	0.005000	0.15991	1.000000	0.80357	0.943000	0.58893	0.216000	0.17585	0.989000	0.38761	0.533000	0.62120	ATG		0.468	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186		G	6898122	A	G	6898122	3	3	122	1	0	0	0	0	1	0	0	0	10923	333	12	4	246	4	OR10A4	11	6898122	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10		6898122	128108394	72	32111										
STK33	65975	hgsc.bcm.edu	37	chr11	8486291	8486291	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttttttaattgcccacttcgTttctgtttccttgtctgtcg	6	10	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:8486291T>C	ENST00000447869.1	-	3	1336	c.418A>G	c.(418-420)Acg>Gcg	p.T140A	STK33_ENST00000358872.3_5'UTR|STK33_ENST00000315204.1_Missense_Mutation_p.T140A|STK33_ENST00000396672.1_Missense_Mutation_p.T140A|STK33_ENST00000396673.1_Missense_Mutation_p.T140A|STK33_ENST00000534493.1_Missense_Mutation_p.T99A			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	140	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)		GCCCACTTCGTTTCTGTTTCC	0.413																																																0			11											344	280	302					11																	8486291		2201	4295	6496	8442867	SO:0001583	missense	65975			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.418A>G	11.37:g.8486291T>C	ENSP00000416750:p.Thr140Ala		8442867	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	.	.	.	.	.	.	.	.	.	.	T	10.71	1.427937	0.25726	.	.	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000396673;ENST00000534493;ENST00000418597;ENST00000422559;ENST00000457885	T;T;T;T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.13	6.02	2.19	0.27852	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.264388	0.41823	N	0.000810	T	0.37598	0.1009	N	0.11789	0.175	0.09310	N	0.999992	B	0.12013	0.005	B	0.19666	0.026	T	0.16247	-1.0409	10	0.17832	T	0.49	.	7.937	0.29935	0.0:0.0708:0.2301:0.6991	.	140	Q9BYT3	STK33_HUMAN	A	140;140;140;140;99;99;99;140	ENSP00000416750:T140A;ENSP00000320754:T140A;ENSP00000379905:T140A;ENSP00000379906:T140A;ENSP00000436418:T99A;ENSP00000391362:T99A;ENSP00000411510:T99A;ENSP00000403599:T140A	ENSP00000320754:T140A	T	-	1	0	STK33	8442867	0.620000	0.27068	0.988000	0.46212	0.621000	0.37620	2.457000	0.45005	1.112000	0.41740	0.528000	0.53228	ACG		0.413	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906		C	8486291	T	C	8486291	3	2	122	1	0	0	0	0	1	0	0	0	15339	1725	60	4	1166	4	STK33	11	8486291	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	1588169	8486291	126520225	73	32112										
USP47	55031	hgsc.bcm.edu	37	chr11	11941795	11941795	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aagaagaagtgtgatgcacgGaaggtaaatgccatgtagag	14	4	0	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:11941795G>A	ENST00000399455.2	+	10	1242	c.1122G>A	c.(1120-1122)cgG>cgA	p.R374R	USP47_ENST00000527733.1_Silent_p.R354R|USP47_ENST00000339865.5_Silent_p.R286R|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	374	USP.				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)		GTGATGCACGGAAGGTAAATG	0.378																																																0			11											117	108	111					11																	11941795		1840	4074	5914	11898371	SO:0001819	synonymous_variant	55031			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.1122G>A	11.37:g.11941795G>A			11898371	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	37																																																																																					0.378	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		A	11941795	G	A	11941795	2	1	122	1	0	0	0	0	0	0	0	1	17118	1161	41	3		3	USP47	11	11941795	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10	3455504	11941795	123064721	74	32113										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33374957	33374957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cagtggcatagttcaccaagTcccagtgggcttaaatcccc	9	13	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:33374957T>C	ENST00000303296.4	+	17	3796	c.3491T>C	c.(3490-3492)gTc>gCc	p.V1164A	HIPK3_ENST00000379016.3_Missense_Mutation_p.V1143A|HIPK3_ENST00000456517.1_Missense_Mutation_p.V1143A|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000525975.1_Missense_Mutation_p.V1143A	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	1164					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						GTTCACCAAGTCCCAGTGGGC	0.488																																																0			11											174	148	157					11																	33374957		2202	4298	6500	33331533	SO:0001583	missense	10114			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.3491T>C	11.37:g.33374957T>C	ENSP00000304226:p.Val1164Ala		33331533	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	37	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.663408	0.88251	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	6.16	6.16	0.99307	.	0.000000	0.53938	D	0.000052	T	0.77130	0.4085	L	0.55481	1.735	0.80722	D	1	D;D	0.58268	0.982;0.969	P;P	0.60886	0.88;0.763	T	0.78445	-0.2201	10	0.66056	D	0.02	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	1143;1164	Q9H422-2;Q9H422	.;HIPK3_HUMAN	A	1143;1164;1143;1143	ENSP00000431710:V1143A;ENSP00000304226:V1164A;ENSP00000368301:V1143A;ENSP00000398241:V1143A	ENSP00000304226:V1164A	V	+	2	0	HIPK3	33331533	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.499000	0.81566	2.367000	0.80283	0.528000	0.53228	GTC		0.488	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33374957	T	C	33374957	3	2	122	1	0	0	0	0	1	0	0	0	7139	1667	58	4	3553	4	HIPK3	11	33374957	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	21433162	33374957	101631559	75	32114										
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974225	49974242	+	In_Frame_Del	DEL	TCTATGAAAACAAGACTA	TCTATGAAAACAAGACTA	-													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	taagctgatcacagattcacTctatgaaaacaagactatct					rs555352141		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	TCTATGAAAACAAGACTA	TCTATGAAAACAAGACTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:49974225_49974242delTCTATGAAAACAAGACTA	ENST00000555099.1	+	1	283_300	c.251_268delTCTATGAAAACAAGACTA	c.(250-270)ctctatgaaaacaagactatc>ctc	p.YENKTI85del		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L84L(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						ACAGATTCACTCTATGAAAACAAGACTATCTTATTCAA	0.417																																																1	Substitution - coding silent(1)	large_intestine(1)	11																																								49930818	SO:0001651	inframe_deletion	283092			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.251_268delTCTATGAAAACAAGACTA	11.37:g.49974225_49974242delTCTATGAAAACAAGACTA	ENSP00000452277:p.Tyr85_Ile90del		49930801	A6NJJ3|B9EH30|Q6IF48|Q96R68	In_Frame_Del	DEL	ENST00000555099.1	37	CCDS31495.1																																																																																				0.417	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		-	49974242	TCTATGAAAACAAGACTA	-	49974225	7	5	122	1	0	1	0	1	0	0	0	0	11078	1551	54	0	253	0	OR4C13	11	49974225	In_Frame_Del	DEL	TCTATGAAAACAAGACTA	TCGA-G5-6641-01A-11D-1826-10	16599268	49974225	85032291	76	32115										
OR8H3	390152	hgsc.bcm.edu	37	chr11	55890364	55890364	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttgcatttctgtgactcaaaCataattcatcactttttctg	4	9	5	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:55890364C>T	ENST00000313472.3	+	1	516	c.516C>T	c.(514-516)aaC>aaT	p.N172N		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	172						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(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					GTGACTCAAACATAATTCATC	0.438																																																0			11											254	227	236					11																	55890364		2201	4296	6497	55646940	SO:0001819	synonymous_variant	390152			AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"GPCR / Class A : Olfactory receptors"	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.516C>T	11.37:g.55890364C>T			55646940	Q6IFB7	Silent	SNP	ENST00000313472.3	37	CCDS31519.1																																																																																				0.438	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		T	55890364	C	T	55890364	2	4	122	1	0	0	0	0	0	0	0	1	11270	477	17	3		3	OR8H3	11	55890364	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	5916139	55890364	79116152	77	32116										
PGA5	5222	hgsc.bcm.edu	37	chr11	61017285	61017285	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agcgagaactcagatggcgaCgtgagtccagccccgactgc	13	13	1	3	rs202236720		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:61017285C>T	ENST00000312403.5	+	7	1103	c.918C>T	c.(916-918)gaC>gaT	p.D306D	CTD-2331C18.5_ENST00000537594.1_RNA|PGA5_ENST00000451616.2_Splice_Site_p.D152D|PGA4_ENST00000422676.2_Splice_Site_p.D306D|PGA5_ENST00000541528.1_Splice_Site_p.D46D	NM_014224.2	NP_055039.1	P0DJD9	PEPA5_HUMAN	pepsinogen 5, group I (pepsinogen A)	306					digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			large_intestine(1)|skin(1)	2						CAGATGGCGACGTGAGTCCAG	0.577																																																0			11						C		0,4404		0,0,2202	166	168	167		918	-0.4	0	11		167	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous-near-splice	PGA5	NM_014224.2		0,2,6499	TT,TC,CC		0.0233,0.0,0.0154		306/389	61017285	2,13000	2202	4299	6501	60773861	SO:0001630	splice_region_variant	5222			BC029055	CCDS8001.1	11q13	2012-10-02			ENSG00000256713	ENSG00000256713	3.4.23.1		8887	protein-coding gene	gene with protein product		169730					Standard	NM_014224		Approved		uc001nqz.3	P0DJD9	OTTHUMG00000168075	ENST00000312403.5:c.918+1C>T	11.37:g.61017285C>T			60773861	A8K749|B7ZW62|B7ZW75|P00790|Q7M4R0|Q8N1E3	Silent	SNP	ENST00000312403.5	37	CCDS8001.1																																																																																				0.577	PGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397972.1	NM_014224	Silent	T	61017285	C	T	61017285	5	4	122	1	0	0	0	0	0	0	1	0	11803	550	19	1	944	1	PGA5	11	61017285	Splice_Site	SNP	C	TCGA-G5-6641-01A-11D-1826-10	5126921	61017285	73989231	78	32117										
EHD1	10938	hgsc.bcm.edu	37	chr11	64622144	64622144	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ccctcgccgtagccgtgcccGaacggcccgttcatggtgcc	12	18	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:64622144G>T	ENST00000320631.3	-	5	1520	c.1266C>A	c.(1264-1266)ttC>ttA	p.F422L	EHD1_ENST00000488711.1_5'UTR|EHD1_ENST00000359393.2_Missense_Mutation_p.F422L	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	422					blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						AGCCGTGCCCGAACGGCCCGT	0.662																																																0			11											115	104	108					11																	64622144		2201	4296	6497	64378720	SO:0001583	missense	10938			AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"EF-hand domain containing"	3242	protein-coding gene	gene with protein product	"testilin"	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.1266C>A	11.37:g.64622144G>T	ENSP00000320516:p.Phe422Leu		64378720	O14611|Q2M3Q4|Q9UNR3	Missense_Mutation	SNP	ENST00000320631.3	37	CCDS8084.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.198652	0.38806	.	.	ENSG00000110047	ENST00000320631;ENST00000359393;ENST00000541001;ENST00000421510	T;T;T	0.57436	2.18;2.18;0.4	4.38	-8.75	0.00834	EF-hand-like domain (1);	0.048927	0.85682	D	0.000000	T	0.68421	0.2999	M	0.89534	3.04	0.49798	D	0.999827	D;D	0.76494	0.999;0.999	D;D	0.65773	0.938;0.938	T	0.82468	-0.0442	10	0.34782	T	0.22	.	15.8734	0.79141	0.4383:0.0:0.5617:0.0	.	422;422	B2R5U3;Q9H4M9	.;EHD1_HUMAN	L	422;422;398;286	ENSP00000320516:F422L;ENSP00000352354:F422L;ENSP00000391429:F286L	ENSP00000320516:F422L	F	-	3	2	EHD1	64378720	0.000000	0.05858	0.628000	0.29241	0.283000	0.27025	-1.936000	0.01549	-2.334000	0.00630	-2.434000	0.00213	TTC		0.662	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795		T	64622144	G	T	64622144	3	4	122	1	0	0	0	0	1	0	0	0	4988	1049	37	2	342	2	EHD1	11	64622144	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	3604859	64622144	70384372	79	32118										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76924066	76924066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agtatggggtcagcctcatcGatcccaaaacgaaggtgagc	12	10	2	1	rs1132036	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:76924066G>A	ENST00000409709.3	+	47	6696	c.6424G>A	c.(6424-6426)Gat>Aat	p.D2142N	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.D2093N|MYO7A_ENST00000458637.2_Missense_Mutation_p.D2102N	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2142	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.		D -> N (in dbSNP:rs1132036).		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						CAGCCTCATCGATCCCAAAAC	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		20348	0		0.001	False		,,,				2504	0															0			11						G	ASN/ASP,ASN/ASP	312,3634		18,276,1679	61	55	57	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6424,6304	3.8	0.9	11	dbSNP_86	57	2,8300		0,2,4149	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	23,23	18,278,5828	AA,AG,GG		0.0241,7.9067,2.5637	benign,benign	2142/2216,2102/2176	76924066	314,11934	1973	4151	6124	76601714	SO:0001583	missense	4647			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.6424G>A	11.37:g.76924066G>A	ENSP00000386331:p.Asp2142Asn		76601714	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	57	0.0260989010989011	52	0.10569105691056911	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.65	2.300715	0.40694	0.079067	2.41E-4	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	4.74	3.83	0.44106	FERM domain (1);Pleckstrin homology-type (1);	0.201491	0.49916	D	0.000122	T	0.02649	0.0080	N	0.20328	0.56	0.58432	D	0.999998	B;B	0.31485	0.068;0.325	B;B	0.20384	0.014;0.029	T	0.05146	-1.0903	10	0.24483	T	0.36	.	13.242	0.60002	0.0776:0.0:0.9224:0.0	rs1132036;rs3192425;rs7117511;rs11546951;rs17417614;rs52822228;rs1132036	2102;2142	F8VUN5;Q13402	.;MYO7A_HUMAN	N	2142;2102;2093;1315;2141;2111;2018;1284	ENSP00000386331:D2142N;ENSP00000392185:D2102N;ENSP00000386635:D2093N;ENSP00000417017:D1284N	ENSP00000345075:D2018N	D	+	1	0	MYO7A	76601714	1.000000	0.71417	0.932000	0.37286	0.858000	0.48976	5.057000	0.64294	1.117000	0.41842	0.585000	0.79938	GAT		0.532	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76924066	G	A	76924066	3	1	122	1	0	0	0	0	1	0	0	0	10112	1058	37	1	6640	1	MYO7A	11	76924066	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	12301922	76924066	58082450	80	32119										
ATM	472	hgsc.bcm.edu	37	chr11	108178712	108178712	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tacatgagaagacaaaagagGtaatgtaatgagtgttgctt	11	3	0	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:108178712G>T	ENST00000452508.2	+	39	5951		c.e39+1		ATM_ENST00000278616.4_Splice_Site			Q13315	ATM_HUMAN	ATM serine/threonine kinase						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)	GACAAAAGAGGTAATGTAATG	0.358			"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)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	0			11											148	136	140					11																	108178712		2201	4298	6499	107683922	SO:0001630	splice_region_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	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.5762+1G>T	11.37:g.108178712G>T			107683922	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Splice_Site	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.859105	0.71834	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3396	0.90300	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATM	107683922	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.311000	0.65786	2.854000	0.98071	0.655000	0.94253	.		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	Intron	T	108178712	G	T	108178712	5	4	122	1	0	0	0	0	0	0	1	0	1110	1275	44	2	5909	2	ATM	11	108178712	Splice_Site	SNP	G	TCGA-G5-6641-01A-11D-1826-10	31254646	108178712	26827804	81	32120										
ATM	472	hgsc.bcm.edu	37	chr11	108196879	108196880	+	Frame_Shift_Ins	INS	-	-	A													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gaagcacaagtattctgggcINSaaaaaaggagcagagtcttg							TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr11:108196879_108196880insA	ENST00000452508.2	+	48	7091_7092	c.6902_6903insA	c.(6901-6906)gcaaaafs	p.AK2301fs	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Frame_Shift_Ins_p.AK2301fs			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2301	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				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)	p.E2304fs*69(1)		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)	GTATTCTGGGCAAAAAAGGAGC	0.426			"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)																												yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	1	Insertion - Frameshift(1)	central_nervous_system(1)	11																																								107702090	SO:0001589	frameshift_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	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.6908dupA	11.37:g.108196885_108196885dupA	ENSP00000388058:p.Ala2301fs		107702089	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Frame_Shift_Ins	INS	ENST00000452508.2	37	CCDS31669.1																																																																																				0.426	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108196880	-	A	108196879	7	5	122	1	0	1	1	0	0	0	0	0	1110	710	25	0	7084	0	ATM	11	108196879	Frame_Shift_Ins	INS	-	TCGA-G5-6641-01A-11D-1826-10	18167	108196879	26809637	82	32121										
PRMT8	56341	hgsc.bcm.edu	37	chr12	3686063	3686063	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agaatgtctatggctttgacAtgacctgcatccgggacgtg	12	9	1	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:3686063A>G	ENST00000382622.3	+	7	1129	c.739A>G	c.(739-741)Atg>Gtg	p.M247V	PRMT8_ENST00000452611.2_Missense_Mutation_p.M238V|PRMT8_ENST00000261252.4_3'UTR	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	247	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)			TGGCTTTGACATGACCTGCAT	0.557																																																0			12											284	255	265					12																	3686063		2203	4300	6503	3556324	SO:0001583	missense	56341			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.739A>G	12.37:g.3686063A>G	ENSP00000372067:p.Met247Val		3556324	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	37	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	A	13.82	2.352590	0.41700	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	T;T	0.78707	-1.2;-1.2	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.82226	0.4991	H	0.94542	3.55	0.80722	D	1	B;B	0.33807	0.426;0.087	B;B	0.27262	0.078;0.016	D	0.85180	0.1003	10	0.87932	D	0	.	13.0795	0.59104	1.0:0.0:0.0:0.0	.	238;247	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	V	238;247	ENSP00000414507:M238V;ENSP00000372067:M247V	ENSP00000372067:M247V	M	+	1	0	PRMT8	3556324	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	9.297000	0.96120	1.978000	0.57642	0.533000	0.62120	ATG		0.557	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854		G	3686063	A	G	3686063	3	3	122	1	0	0	0	0	1	0	0	0	12576	217	8	4	765	4	PRMT8	12	3686063	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10		3686063	130165832	83	32122										
DYRK4	8798	hgsc.bcm.edu	37	chr12	4705885	4705885	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atcacttctgcatcacctttGagctcctggggtcagctgcc	9	14	4	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:4705885G>T	ENST00000540757.2	+	6	710	c.550G>T	c.(550-552)Gag>Tag	p.E184*	DYRK4_ENST00000010132.5_Nonsense_Mutation_p.E184*|DYRK4_ENST00000543431.1_Nonsense_Mutation_p.E184*	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	184	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.E586Q(2)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			CATCACCTTTGAGCTCCTGGG	0.418																																																2	Substitution - Missense(2)	lung(2)	12											159	142	148					12																	4705885		2203	4300	6503	4576146	SO:0001587	stop_gained	8798			Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.550G>T	12.37:g.4705885G>T	ENSP00000441755:p.Glu184*		4576146	A8K8F7|Q8NEF2|Q92631	Nonsense_Mutation	SNP	ENST00000540757.2	37	CCDS8530.1	.	.	.	.	.	.	.	.	.	.	G	38	6.642747	0.97730	.	.	ENSG00000010219	ENST00000542744;ENST00000540757;ENST00000010132;ENST00000543431	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.1192	0.86697	0.0:0.0:1.0:0.0	.	.	.	.	X	299;184;184;184	.	ENSP00000010132:E184X	E	+	1	0	DYRK4	4576146	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.272000	0.95707	2.570000	0.86706	0.655000	0.94253	GAG		0.418	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2			T	4705885	G	T	4705885	4	4	122	1	0	0	0	0	0	1	0	0	4869	1291	45	2	564	2	DYRK4	12	4705885	Nonsense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	1019822	4705885	129146010	84	32123										
PRB2	653247	hgsc.bcm.edu	37	chr12	11546440	11546440	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gaggaggtgggggaccttggGgctggttgcctccttgtggg	21	7	0	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:11546440G>A	ENST00000389362.4	-	3	607	c.572C>T	c.(571-573)cCc>cTc	p.P191L	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	191	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)				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)			GGGACCTTGGGGCTGGTTGCC	0.597																																																0			12											133	134	134					12																	11546440		2161	4262	6423	11437707	SO:0001583	missense	653247			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.572C>T	12.37:g.11546440G>A	ENSP00000374013:p.Pro191Leu		11437707	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	11.70	1.717191	0.30413	.	.	ENSG00000121335	ENST00000389362	T	0.04083	3.71	1.56	-3.11	0.05299	.	1.158660	0.07210	U	0.859059	T	0.04770	0.0129	L	0.49778	1.585	0.09310	N	1	B	0.16603	0.018	B	0.11329	0.006	T	0.44174	-0.9345	10	0.54805	T	0.06	.	2.3046	0.04171	0.4478:0.0:0.2522:0.3	.	191	P02812	PRB2_HUMAN	L	191	ENSP00000374013:P191L	ENSP00000374013:P191L	P	-	2	0	PRB2	11437707	0.034000	0.19679	0.000000	0.03702	0.727000	0.41649	1.017000	0.29989	-0.973000	0.03555	0.282000	0.19409	CCC		0.597	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		A	11546440	G	A	11546440	3	1	122	1	0	0	0	0	1	0	0	0	12477	1232	43	3	682	3	PRB2	12	11546440	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	6840555	11546440	122305455	85	32124										
ETNK1	55500	hgsc.bcm.edu	37	chr12	22811990	22811990	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aaaatccatgctattcatgcAcacaatggctggatccccaa	6	12	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:22811990A>G	ENST00000266517.4	+	3	815	c.726A>G	c.(724-726)gcA>gcG	p.A242A		NM_018638.4	NP_061108.2	Q9HBU6	EKI1_HUMAN	ethanolamine kinase 1	242					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CTATTCATGCACACAATGGCT	0.368																																					Esophageal Squamous(42;87 913 3224 6226 43339)											0			12											101	97	98					12																	22811990		2203	4300	6503	22703257	SO:0001819	synonymous_variant	55500			BC006111	CCDS8698.1, CCDS41760.1	12p12.2	2004-07-09			ENSG00000139163	ENSG00000139163			24649	protein-coding gene	gene with protein product		609858				11912161, 11044454	Standard	XM_005253420		Approved	EKI1, EKI	uc001rft.3	Q9HBU6	OTTHUMG00000169008	ENST00000266517.4:c.726A>G	12.37:g.22811990A>G			22703257	G5E969	Silent	SNP	ENST00000266517.4	37	CCDS8698.1	.	.	.	.	.	.	.	.	.	.	A	10.53	1.375172	0.24857	.	.	ENSG00000139163	ENST00000538218;ENST00000541247	.	.	.	5.23	2.82	0.32997	.	.	.	.	.	T	0.52451	0.1735	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44112	-0.9349	4	.	.	.	-10.0838	5.1403	0.14955	0.6853:0.1529:0.1618:0.0	.	.	.	.	R	233;122	.	.	H	+	2	0	ETNK1	22703257	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.723000	0.25939	0.793000	0.33875	0.397000	0.26171	CAC		0.368	ETNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401926.2	NM_018638		G	22811990	A	G	22811990	2	3	122	1	0	0	0	0	0	0	0	1	5286	146	6	4		4	ETNK1	12	22811990	Silent	SNP	A	TCGA-G5-6641-01A-11D-1826-10	11265550	22811990	111039905	86	32125										
TSPAN11	441631	hgsc.bcm.edu	37	chr12	31106967	31106967	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	caggacgactggctgatcatCtacttgaagtatttactctt	8	9	3	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:31106967C>G	ENST00000261177.9	+	2	101	c.42C>G	c.(40-42)atC>atG	p.I14M	TSPAN11_ENST00000535215.1_Intron|TSPAN11_ENST00000544427.1_Intron|TSPAN11_ENST00000546076.1_Missense_Mutation_p.I14M|TSPAN11_ENST00000545802.1_Missense_Mutation_p.I14M	NM_001080509.2	NP_001073978.1	A1L157	TSN11_HUMAN	tetraspanin 11	14						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)					GGCTGATCATCTACTTGAAGT	0.507																																																0			12											255	193	214					12																	31106967		2203	4300	6503	30998234	SO:0001583	missense	441631				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.42C>G	12.37:g.31106967C>G	ENSP00000261177:p.Ile14Met		30998234	A1L158|B2RUX6	Missense_Mutation	SNP	ENST00000261177.9	37	CCDS31765.1	.	.	.	.	.	.	.	.	.	.	C	9.783	1.175891	0.21704	.	.	ENSG00000110900	ENST00000545802;ENST00000546076;ENST00000261177	T;T	0.36340	1.26;1.26	3.35	3.35	0.38373	.	0.290858	0.26616	U	0.023392	T	0.26122	0.0637	N	0.20574	0.59	0.80722	D	1	B	0.22800	0.075	B	0.36289	0.221	T	0.11792	-1.0573	10	0.49607	T	0.09	.	6.6291	0.22847	0.0:0.8661:0.0:0.1339	.	14	A1L157	TSN11_HUMAN	M	14	ENSP00000437403:I14M;ENSP00000261177:I14M	ENSP00000261177:I14M	I	+	3	3	TSPAN11	30998234	1.000000	0.71417	0.938000	0.37757	0.426000	0.31534	0.997000	0.29731	1.843000	0.53566	0.455000	0.32223	ATC		0.507	TSPAN11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399888.1	XM_497334		G	31106967	C	G	31106967	3	3	122	1	0	0	0	0	1	0	0	0	16675	903	32	5	44	5	TSPAN11	12	31106967	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	8294977	31106967	102744928	87	32126										
E2F7	144455	hgsc.bcm.edu	37	chr12	77444416	77444416	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ctcagttgacaagggataacTtggatagcgagctagaaact	11	7	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:77444416T>C	ENST00000322886.7	-	4	713	c.478A>G	c.(478-480)Agt>Ggt	p.S160G	E2F7_ENST00000416496.2_Missense_Mutation_p.S160G	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	160					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)	p.S160R(1)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						AAGGGATAACTTGGATAGCGA	0.443																																																1	Substitution - Missense(1)	ovary(1)	12											201	184	190					12																	77444416		2203	4300	6503	75968547	SO:0001583	missense	144455			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.478A>G	12.37:g.77444416T>C	ENSP00000323246:p.Ser160Gly		75968547	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.014967	0.54468	.	.	ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669	T;T;T	0.18810	2.45;2.19;2.2	5.95	5.95	0.96441	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.075950	0.85682	D	0.000000	T	0.30541	0.0768	L	0.35542	1.07	0.47341	D	0.999398	D;D	0.56968	0.972;0.978	P;P	0.55615	0.673;0.78	T	0.01684	-1.1296	10	0.59425	D	0.04	-18.0679	15.6048	0.76658	0.0:0.0:0.0:1.0	.	160;160	F8VSE7;Q96AV8	.;E2F7_HUMAN	G	160	ENSP00000323246:S160G;ENSP00000393639:S160G;ENSP00000448245:S160G	ENSP00000323246:S160G	S	-	1	0	E2F7	75968547	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.715000	0.68430	2.279000	0.76181	0.533000	0.62120	AGT		0.443	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		C	77444416	T	C	77444416	3	2	122	1	0	0	0	0	1	0	0	0	4883	1609	56	4	2297	4	E2F7	12	77444416	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	46337449	77444416	56407479	88	32127										
CEP290	80184	hgsc.bcm.edu	37	chr12	88474161	88474161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttttcacttcatcttcatggTtttcttgaagcctgatgtaa	6	8	5	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:88474161T>C	ENST00000552810.1	-	38	5367	c.5024A>G	c.(5023-5025)aAc>aGc	p.N1675S	CEP290_ENST00000397838.3_Missense_Mutation_p.N735S|CEP290_ENST00000309041.7_Missense_Mutation_p.N1677S|CEP290_ENST00000547691.2_Missense_Mutation_p.N735S	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1675					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						ATCTTCATGGTTTTCTTGAAG	0.363																																																0			12											109	97	101					12																	88474161		1818	4077	5895	86998292	SO:0001583	missense	80184			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.5024A>G	12.37:g.88474161T>C	ENSP00000448012:p.Asn1675Ser		86998292	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	6.030	0.373827	0.11409	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77	4.35	3.17	0.36434	.	0.424145	0.27420	N	0.019448	T	0.81250	0.4783	N	0.24115	0.695	0.26987	N	0.965227	B	0.17852	0.024	B	0.17433	0.018	T	0.62338	-0.6875	10	0.10111	T	0.7	.	10.8553	0.46796	0.0:0.0:0.1651:0.8349	.	1675	O15078	CE290_HUMAN	S	735;1675;1677;735	ENSP00000446905:N735S;ENSP00000448012:N1675S;ENSP00000308021:N1677S;ENSP00000380938:N735S	ENSP00000308021:N1677S	N	-	2	0	CEP290	86998292	1.000000	0.71417	1.000000	0.80357	0.300000	0.27592	3.309000	0.51903	0.614000	0.30107	0.377000	0.23210	AAC		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88474161	T	C	88474161	3	2	122	1	0	0	0	0	1	0	0	0	3259	1725	60	4	2483	4	CEP290	12	88474161	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	11029745	88474161	45377734	89	32128										
CHST11	50515	hgsc.bcm.edu	37	chr12	105150990	105150990	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atcccggccaacgaggcacaCgtctccgccaacctgaagac	9	17	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:105150990C>T	ENST00000303694.5	+	3	907	c.468C>T	c.(466-468)caC>caT	p.H156H	CHST11_ENST00000549260.1_Silent_p.H151H	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	156					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						ACGAGGCACACGTCTCCGCCA	0.592																																																0			12											72	71	71					12																	105150990		2203	4300	6503	103675120	SO:0001819	synonymous_variant	50515			AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"Sulfotransferases, membrane-bound"	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.468C>T	12.37:g.105150990C>T			103675120	A8K4F8|Q9NXY6|Q9NY36	Silent	SNP	ENST00000303694.5	37	CCDS9099.1																																																																																				0.592	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413		T	105150990	C	T	105150990	2	4	122	1	0	0	0	0	0	0	0	1	3405	535	19	1		1	CHST11	12	105150990	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	16676829	105150990	28700905	90	32129										
GPR109A	338442	hgsc.bcm.edu	37	chr12	123187815	123187815	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttccagaaagtgatcctgcaGatggtgccgattcatgagtg	12	8	1	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr12:123187815G>T	ENST00000328880.5	-	1	75	c.16C>A	c.(16-18)Ctg>Atg	p.L6M	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	6					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	TGATCCTGCAGATGGTGCCGA	0.527																																																0			12											97	89	92					12																	123187815		2203	4300	6503	121753768	SO:0001583	missense	338442			AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	24827	protein-coding gene	gene with protein product	"niacin receptor 1"	609163	"G protein-coupled receptor 109A"	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.16C>A	12.37:g.123187815G>T	ENSP00000375066:p.Leu6Met		121753768	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	37	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.467024	0.01053	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.62639	0.01	3.47	0.518	0.17030	.	3.538480	0.01061	U	0.004651	T	0.43211	0.1237	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.18808	-1.0325	10	0.33141	T	0.24	0.1248	2.9622	0.05896	0.2397:0.0:0.5456:0.2147	.	6	Q8TDS4	HCAR2_HUMAN	M	6	ENSP00000375066:L6M	ENSP00000375066:L6M	L	-	1	2	HCAR2	121753768	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.215000	0.17562	0.106000	0.17784	-0.216000	0.12614	CTG		0.527	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		T	123187815	G	T	123187815	3	4	122	1	0	0	0	0	1	0	0	0	6645	933	33	2	1079	2	GPR109A	12	123187815	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	18036825	123187815	10664080	91	32130										
TPTE2	93492	hgsc.bcm.edu	37	chr13	20039692	20039692	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ataagtcgtagaagtcgaacTaaatgtgtccatctaacaat	7	7	1	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr13:20039692T>A	ENST00000400230.2	-	8	569	c.525A>T	c.(523-525)ttA>ttT	p.L175F	TPTE2_ENST00000382977.4_Missense_Mutation_p.L175F|TPTE2_ENST00000400103.2_Missense_Mutation_p.L64F|TPTE2_ENST00000382975.4_Missense_Mutation_p.L135F|TPTE2_ENST00000390680.2_Missense_Mutation_p.L98F|TPTE2_ENST00000457266.2_Missense_Mutation_p.L64F|TPTE2_ENST00000382978.1_Missense_Mutation_p.L135F|TPTE2_ENST00000255310.6_Missense_Mutation_p.L98F			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	175					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)		GAAGTCGAACTAAATGTGTCC	0.323																																																0			13											34	33	33					13																	20039692		2200	4299	6499	18937692	SO:0001583	missense	93492			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.525A>T	13.37:g.20039692T>A	ENSP00000383089:p.Leu175Phe		18937692	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	t	4.587	0.109009	0.08780	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.98822	-4.34;-3.88;-5.16;-4.34;-4.34;-5.16;-4.34;-3.88	2.79	-3.67	0.04476	Ion transport (1);	0.260709	0.33772	U	0.004569	D	0.92609	0.7652	N	0.22421	0.69	0.09310	N	1	B;B;B	0.30584	0.286;0.047;0.039	B;B;B	0.27796	0.039;0.032;0.083	D	0.88373	0.2996	9	.	.	.	-6.3457	1.1417	0.01766	0.1887:0.1283:0.3851:0.2978	.	64;98;175	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	F	135;64;175;98;98;175;135;64;175;44	ENSP00000372438:L135F;ENSP00000382974:L64F;ENSP00000383089:L175F;ENSP00000255310:L98F;ENSP00000375098:L98F;ENSP00000372437:L175F;ENSP00000372435:L135F;ENSP00000442218:L64F	.	L	-	3	2	TPTE2	18937692	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.764000	0.04735	-0.737000	0.04824	0.383000	0.25322	TTA		0.323	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		A	20039692	T	A	20039692	3	1	122	1	0	0	0	0	1	0	0	0	16471	1519	53	5	1095	5	TPTE2	13	20039692	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10		20039692	95130186	92	32131										
NAA16	79612	hgsc.bcm.edu	37	chr13	41943234	41943234	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggatatttatagaaaacttgTcagccaaagaattgaagaaa	8	4	1	4			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr13:41943234T>A	ENST00000379406.3	+	15	2086	c.1762T>A	c.(1762-1764)Tca>Aca	p.S588T	NAA16_ENST00000497143.1_3'UTR	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	588					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						AGAAAACTTGTCAGCCAAAGA	0.343																																																0			13											79	86	83					13																	41943234		2203	4300	6503	40841234	SO:0001583	missense	0			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.1762T>A	13.37:g.41943234T>A	ENSP00000368716:p.Ser588Thr		40841234	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.953072	0.34471	.	.	ENSG00000172766	ENST00000379406	T	0.47528	0.84	5.67	5.67	0.87782	.	0.220930	0.32416	N	0.006138	T	0.37376	0.1001	L	0.33624	1.015	0.80722	D	1	B	0.19331	0.035	B	0.26864	0.074	T	0.18429	-1.0337	10	0.10636	T	0.68	-9.8749	14.4926	0.67663	0.0:0.0:0.0:1.0	.	588	Q6N069	NAA16_HUMAN	T	588	ENSP00000368716:S588T	ENSP00000368716:S588T	S	+	1	0	NAA16	40841234	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.444000	0.44890	2.161000	0.67846	0.533000	0.62120	TCA		0.343	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		A	41943234	T	A	41943234	3	1	122	1	0	0	0	0	1	0	0	0	10149	1667	58	5	1853	5	NAA16	13	41943234	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	21903542	41943234	73226644	93	32132										
RBM26	64062	hgsc.bcm.edu	37	chr13	79933778	79933778	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atggttcttttccttgattcTgagtccactactatcctcat	5	11	3	2	rs372998044		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr13:79933778T>C	ENST00000438737.2	-	10	1901	c.1461A>G	c.(1459-1461)tcA>tcG	p.S487S	RBM26_ENST00000438724.1_Silent_p.S487S|RBM26_ENST00000267229.7_Silent_p.S487S			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	487					mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S487S(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		TCCTTGATTCTGAGTCCACTA	0.343																																																1	Substitution - coding silent(1)	ovary(1)	13						T		1,4405	2.1+/-5.4	0,1,2202	151	143	146		1461	5.7	1	13		146	0,8600		0,0,4300	no	coding-synonymous	RBM26	NM_022118.3		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		487/981	79933778	1,13005	2203	4300	6503	78831779	SO:0001819	synonymous_variant	64062			AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	20327	protein-coding gene	gene with protein product	"acidic rich RS domain containing 2", "protein phosphatase 1, regulatory 132"		"chromosome 13 open reading frame 10"	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.1461A>G	13.37:g.79933778T>C			78831779	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Silent	SNP	ENST00000438737.2	37																																																																																					0.343	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118		C	79933778	T	C	79933778	2	2	122	1	0	0	0	0	0	0	0	1	13163	1567	55	4		4	RBM26	13	79933778	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10	37990544	79933778	35236100	94	32133										
LIG4	3981	hgsc.bcm.edu	37	chr13	108861616	108861616	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggctggctatctgttccactCataacacaaaactctacatc	5	13	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr13:108861616C>G	ENST00000356922.4	-	2	2273	c.2001G>C	c.(1999-2001)atG>atC	p.M667I	LIG4_ENST00000405925.1_Missense_Mutation_p.M667I|LIG4_ENST00000442234.1_Missense_Mutation_p.M667I	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	667	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				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)					CTGTTCCACTCATAACACAAA	0.363								Non-homologous end-joining																																								0			13											70	72	71					13																	108861616		2203	4300	6503	107659617	SO:0001583	missense	3981			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.2001G>C	13.37:g.108861616C>G	ENSP00000349393:p.Met667Ile		107659617	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	C	3.334	-0.136117	0.06711	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.60040	0.22;0.22;0.22	5.69	5.69	0.88448	BRCT (4);	0.085609	0.85682	D	0.000000	T	0.47801	0.1465	L	0.28344	0.845	0.47905	D	0.999544	B	0.17465	0.022	B	0.12837	0.008	T	0.30357	-0.9981	10	0.30078	T	0.28	.	18.8676	0.92300	0.0:1.0:0.0:0.0	.	667	P49917	DNLI4_HUMAN	I	667	ENSP00000385955:M667I;ENSP00000402030:M667I;ENSP00000349393:M667I	ENSP00000349393:M667I	M	-	3	0	LIG4	107659617	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	2.531000	0.45650	2.688000	0.91661	0.539000	0.68188	ATG		0.363	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		G	108861616	C	G	108861616	3	3	122	1	0	0	0	0	1	0	0	0	8806	826	29	5	738	5	LIG4	13	108861616	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	28927838	108861616	6308262	95	32134										
NDNL2	56160	hgsc.bcm.edu	37	chr15	29561261	29561261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aatgagtttctttggatctcCgaaaattaaatgcttcttgg	8	6	3	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr15:29561261C>T	ENST00000332303.4	-	1	772	c.649G>A	c.(649-651)Gga>Aga	p.G217R	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	217	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		TTTGGATCTCCGAAAATTAAA	0.512																																																0			15											55	61	59					15																	29561261		2203	4300	6503	27348553	SO:0001583	missense	56160			AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.649G>A	15.37:g.29561261C>T	ENSP00000330694:p.Gly217Arg		27348553	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920150	0.52653	.	.	ENSG00000185115	ENST00000332303	T	0.05717	3.4	4.1	4.1	0.47936	.	0.059842	0.64402	N	0.000003	T	0.25005	0.0607	M	0.82923	2.615	0.47584	D	0.999466	D	0.76494	0.999	D	0.72625	0.978	T	0.00747	-1.1583	10	0.72032	D	0.01	.	12.1457	0.54022	0.0:1.0:0.0:0.0	.	217	Q96MG7	MAGG1_HUMAN	R	217	ENSP00000330694:G217R	ENSP00000330694:G217R	G	-	1	0	NDNL2	27348553	0.949000	0.32298	0.905000	0.35620	0.231000	0.25187	3.280000	0.51677	2.564000	0.86499	0.563000	0.77884	GGA		0.512	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704		T	29561261	C	T	29561261	3	4	122	1	0	0	0	0	1	0	0	0	10279	661	23	1	269	1	NDNL2	15	29561261	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10		29561261	72970131	96	32135										
MGA	23269	hgsc.bcm.edu	37	chr15	42003205	42003205	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agtggccgaactaaatcatcTtataaatccattttaccata	4	9	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr15:42003205T>G	ENST00000570161.1	+	7	2742	c.2742T>G	c.(2740-2742)tcT>tcG	p.S914S	MGA_ENST00000389936.4_Silent_p.S914S|MGA_ENST00000545763.1_Silent_p.S914S|MGA_ENST00000219905.7_Silent_p.S914S|MGA_ENST00000566586.1_Silent_p.S914S			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)	CTAAATCATCTTATAAATCCA	0.403																																																0			15											138	137	137					15																	42003205		1857	4099	5956	39790497	SO:0001819	synonymous_variant	23269			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.2742T>G	15.37:g.42003205T>G			39790497	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																				0.403	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42003205	T	G	42003205	2	3	122	1	0	0	0	0	0	0	0	1	9570	1596	56	4		4	MGA	15	42003205	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10	12441944	42003205	60528187	97	32136										
DENND4A	10260	hgsc.bcm.edu	37	chr15	66044813	66044813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	catatgtcagtgacagccaaCgtattctgagtcatgttttc	8	9	3	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr15:66044813C>T	ENST00000431932.2	-	4	673	c.465G>A	c.(463-465)acG>acA	p.T155T	DENND4A_ENST00000443035.3_Silent_p.T155T	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	155	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				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						TGACAGCCAACGTATTCTGAG	0.423																																																0			15											103	95	98					15																	66044813		1886	4105	5991	63831867	SO:0001819	synonymous_variant	10260			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.465G>A	15.37:g.66044813C>T			63831867	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																				0.423	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	66044813	C	T	66044813	2	4	122	1	0	0	0	0	0	0	0	1	4444	523	19	1		1	DENND4A	15	66044813	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	24041608	66044813	36486579	98	32137										
TNP2	7142	hgsc.bcm.edu	37	chr16	11362995	11362995	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agctctggctccggctgccaCgatggctctgtctgcaactc	11	15	3	0	rs200495915	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr16:11362995C>T	ENST00000312693.3	-	1	194	c.125G>A	c.(124-126)cGt>cAt	p.R42H	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	42					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						CCGGCTGCCACGATGGCTCTG	0.632													C|||	3	0.000599042	0.0023	0	5008	,	,		15900	0		0	False		,,,				2504	0															1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	16						C	HIS/ARG	10,4128		0,10,2059	129	147	141		125	-0.9	0	16		141	0,8418		0,0,4209	yes	missense	TNP2	NM_005425.4	29	0,10,6268	TT,TC,CC		0.0,0.2417,0.0796	benign	42/139	11362995	10,12546	2069	4209	6278	11270496	SO:0001583	missense	7142				CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.125G>A	16.37:g.11362995C>T	ENSP00000325738:p.Arg42His		11270496	Q9NZB0	Missense_Mutation	SNP	ENST00000312693.3	37	CCDS45410.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	7.355	0.623570	0.14193	0.002417	0.0	ENSG00000178279	ENST00000312693	T	0.50548	0.74	2.37	-0.951	0.10369	.	.	.	.	.	T	0.27454	0.0674	N	0.22421	0.69	0.09310	N	1	B	0.15141	0.012	B	0.06405	0.002	T	0.17440	-1.0369	9	0.27082	T	0.32	.	5.1818	0.15163	0.0:0.4552:0.0:0.5448	.	42	Q05952	STP2_HUMAN	H	42	ENSP00000325738:R42H	ENSP00000325738:R42H	R	-	2	0	TNP2	11270496	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.240000	0.18042	-0.213000	0.10094	-0.254000	0.11334	CGT		0.632	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425		T	11362995	C	T	11362995	3	4	122	1	0	0	0	0	1	0	0	0	16373	536	19	1	299	1	TNP2	16	11362995	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10		11362995	78991758	99	32138										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77353780	77353780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tctcatttgtgggccctggcGcgtacagacgttccgggcgg	15	12	1	1	rs147816593		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr16:77353780G>A	ENST00000282849.5	-	16	2916	c.2498C>T	c.(2497-2499)gCg>gTg	p.A833V		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	833	Spacer.				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						GGGCCCTGGCGCGTACAGACG	0.542																																																0			16						G	VAL/ALA	1,4395	2.1+/-5.4	0,1,2197	61	60	60		2498	5.5	0.2	16	dbSNP_134	60	0,8600		0,0,4300	no	missense	ADAMTS18	NM_199355.2	64	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	833/1222	77353780	1,12995	2198	4300	6498	75911281	SO:0001583	missense	170692			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.2498C>T	16.37:g.77353780G>A	ENSP00000282849:p.Ala833Val		75911281	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141924	0.77775	2.27E-4	0.0	ENSG00000140873	ENST00000282849	T	0.56941	0.43	5.54	5.54	0.83059	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.81914	0.897;0.995	T	0.81191	-0.1045	10	0.87932	D	0	.	18.4764	0.90793	0.0:0.0:1.0:0.0	.	833;833	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	V	833	ENSP00000282849:A833V	ENSP00000282849:A833V	A	-	2	0	ADAMTS18	75911281	1.000000	0.71417	0.242000	0.24170	0.254000	0.26022	9.378000	0.97191	2.618000	0.88619	0.563000	0.77884	GCG		0.542	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			A	77353780	G	A	77353780	3	1	122	1	0	0	0	0	1	0	0	0	263	1087	38	1	1199	1	ADAMTS18	16	77353780	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	65990785	77353780	13000973	100	32139										
KPNA2	3838	hgsc.bcm.edu	37	chr17	66033285	66033285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	atgctaatacaccagctgccCgtcttcacagattcaagaac	6	13	3	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr17:66033285C>A	ENST00000537025.2	+	2	657	c.37C>A	c.(37-39)Cgt>Agt	p.R13S	KPNA2_ENST00000330459.3_Missense_Mutation_p.R13S			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	13	IBB. {ECO:0000255|PROSITE- ProRule:PRU00561}.				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)			ACCAGCTGCCCGTCTTCACAG	0.413																																																0			17											157	162	160					17																	66033285		2203	4296	6499	63463747	SO:0001583	missense	3838			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.37C>A	17.37:g.66033285C>A	ENSP00000438483:p.Arg13Ser		63463747	B9EJD6|Q53YE3|Q9BRU5	Missense_Mutation	SNP	ENST00000537025.2	37	CCDS32713.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.184771	0.38609	.	.	ENSG00000182481	ENST00000330459;ENST00000537025	T;T	0.76316	-1.01;-1.01	4.5	4.5	0.54988	Importin-alpha, importin-beta-binding domain (2);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	D	0.89026	0.6598	M	0.89478	3.035	0.80722	D	1	D	0.57899	0.981	P	0.62813	0.907	D	0.91732	0.5397	10	0.87932	D	0	.	17.1906	0.86878	0.0:1.0:0.0:0.0	.	13	P52292	IMA2_HUMAN	S	13	ENSP00000332455:R13S;ENSP00000438483:R13S	ENSP00000332455:R13S	R	+	1	0	KPNA2	63463747	1.000000	0.71417	0.998000	0.56505	0.515000	0.34225	5.363000	0.66104	2.053000	0.61076	0.305000	0.20034	CGT		0.413	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266		A	66033285	C	A	66033285	3	1	122	1	0	0	0	0	1	0	0	0	8451	652	23	2	39	2	KPNA2	17	66033285	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10		66033285	15161925	101	32140										
RNF213	57674	hgsc.bcm.edu	37	chr17	78317684	78317684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ctggaatttgggtgtttcttTtcaagctcctcattttacaa	7	8	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr17:78317684T>C	ENST00000582970.1	+	28	6354	c.6211T>C	c.(6211-6213)Ttc>Ctc	p.F2071L	RNF213_ENST00000508628.2_Missense_Mutation_p.F2120L|RNF213_ENST00000336301.6_Missense_Mutation_p.F144L	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2071					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)			GGTGTTTCTTTTCAAGCTCCT	0.443																																																0			17											178	160	166					17																	78317684		2203	4300	6503	75932279	SO:0001583	missense	57674			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.6211T>C	17.37:g.78317684T>C	ENSP00000464087:p.Phe2071Leu		75932279	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.424080	0.62733	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.59906	0.23	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.68824	0.3043	L	0.36672	1.1	0.41316	D	0.987141	D	0.89917	1.0	D	0.91635	0.999	T	0.72187	-0.4366	10	0.87932	D	0	.	16.3544	0.83230	0.0:0.0:0.0:1.0	.	144	Q63HN8	RN213_HUMAN	L	2071;2120;144	ENSP00000338218:F144L	ENSP00000338218:F144L	F	+	1	0	RNF213	75932279	1.000000	0.71417	0.985000	0.45067	0.952000	0.60782	7.232000	0.78116	2.265000	0.75225	0.459000	0.35465	TTC		0.443	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78317684	T	C	78317684	3	2	122	1	0	0	0	0	1	0	0	0	13514	1841	64	4	6636	4	RNF213	17	78317684	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	12284399	78317684	2877526	102	32141										
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3582068	3582068	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttcatactgtccaggctctcGgtggagttgctgagtccaga	12	10	2	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr18:3582068G>T	ENST00000315677.3	-	8	2365	c.1770C>A	c.(1768-1770)acC>acA	p.T590T	DLGAP1_ENST00000581527.1_Silent_p.T590T|DLGAP1_ENST00000539435.1_Silent_p.T298T|DLGAP1_ENST00000400147.2_Silent_p.T288T|DLGAP1_ENST00000400149.3_Silent_p.T280T|DLGAP1_ENST00000581699.1_Silent_p.T296T|DLGAP1_ENST00000584874.1_Silent_p.T590T|DLGAP1_ENST00000400155.1_Silent_p.T296T|DLGAP1_ENST00000534970.1_Silent_p.T274T|DLGAP1_ENST00000515196.2_Silent_p.T590T|DLGAP1_ENST00000400145.2_Silent_p.T288T|DLGAP1_ENST00000400150.3_Silent_p.T306T	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	590					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)				CCAGGCTCTCGGTGGAGTTGC	0.572																																																0			18											123	107	112					18																	3582068		2203	4300	6503	3572068	SO:0001819	synonymous_variant	9229			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.1770C>A	18.37:g.3582068G>T			3572068	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Silent	SNP	ENST00000315677.3	37	CCDS11836.1																																																																																				0.572	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			T	3582068	G	T	3582068	2	4	122	1	0	0	0	0	0	0	0	1	4570	1103	39	2		2	DLGAP1	18	3582068	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10		3582068	74495180	103	32142										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8384563	8384563	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tatgttttgaattcagttgtGtccacagtactggccagaaa	9	7	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr18:8384563G>T	ENST00000332175.8	+	28	4921	c.3884G>T	c.(3883-3885)tGt>tTt	p.C1295F	PTPRM_ENST00000580170.1_Missense_Mutation_p.C1308F|PTPRM_ENST00000444013.1_Missense_Mutation_p.C1082F|PTPRM_ENST00000400053.4_Missense_Mutation_p.C1233F|PTPRM_ENST00000400060.4_Missense_Mutation_p.C1309F	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1295	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)				ATTCAGTTGTGTCCACAGTAC	0.413																																																0			18											117	104	109					18																	8384563		2203	4300	6503	8374563	SO:0001583	missense	5797			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.3884G>T	18.37:g.8384563G>T	ENSP00000331418:p.Cys1295Phe		8374563	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149452	0.78001	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.20069	2.1;2.1;2.1;2.1	5.33	4.45	0.53987	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.56396	0.1982	M	0.92604	3.325	0.80722	D	1	D;P;D	0.76494	0.999;0.64;0.996	D;B;D	0.83275	0.996;0.348;0.996	T	0.69694	-0.5076	10	0.87932	D	0	.	15.4794	0.75514	0.0:0.0:0.8604:0.1396	.	1082;1308;1295	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	F	1295;1309;1233;1082	ENSP00000331418:C1295F;ENSP00000382933:C1309F;ENSP00000382927:C1233F;ENSP00000387608:C1082F	ENSP00000331418:C1295F	C	+	2	0	PTPRM	8374563	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.734000	0.98822	1.242000	0.43836	0.579000	0.79373	TGT		0.413	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8384563	G	T	8384563	3	4	122	1	0	0	0	0	1	0	0	0	12843	1377	48	2	4041	2	PTPRM	18	8384563	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	4802495	8384563	69692685	104	32143										
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32927392	32927392	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gataataaaactgaatctatGaagacaattaacctccttca	4	8	2	3			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:32927392G>T	ENST00000342179.5	+	5	584	c.369G>T	c.(367-369)atG>atT	p.M123I	DPY19L3_ENST00000586987.1_Missense_Mutation_p.M123I|DPY19L3_ENST00000392250.2_Missense_Mutation_p.M123I	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	123						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)					CTGAATCTATGAAGACAATTA	0.289																																																0			19											56	62	60					19																	32927392		2201	4288	6489	37619232	SO:0001583	missense	147991				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.369G>T	19.37:g.32927392G>T	ENSP00000344937:p.Met123Ile		37619232	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	37	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759383	0.49468	.	.	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.54071	0.59;0.59	5.87	5.87	0.94306	.	0.140544	0.64402	D	0.000004	T	0.49218	0.1544	L	0.51422	1.61	0.33347	D	0.570627	B	0.30146	0.27	B	0.24541	0.054	T	0.55231	-0.8173	10	0.26408	T	0.33	-23.9901	20.2191	0.98319	0.0:0.0:1.0:0.0	.	123	Q6ZPD9	D19L3_HUMAN	I	123	ENSP00000376081:M123I;ENSP00000344937:M123I	ENSP00000315672:M123I	M	+	3	0	DPY19L3	37619232	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.418000	0.59828	2.780000	0.95670	0.655000	0.94253	ATG		0.289	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		T	32927392	G	T	32927392	3	4	122	1	0	0	0	0	1	0	0	0	4753	1290	45	2	383	2	DPY19L3	19	32927392	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10		32927392	26201591	105	32144										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42312886	42312886	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gccttcctgtgggggccgtcGccggcatcgtgaccggggtc	17	14	0	1	rs377521292		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:42312886G>A	ENST00000357396.3	+	3	701	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	CEACAM3_ENST00000221999.4_Missense_Mutation_p.A154T|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000344550.4_Missense_Mutation_p.A154T	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	154						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						GGGGGCCGTCGCCGGCATCGT	0.607																																																0			19						G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	113	117	116		460	0.3	0	19		116	0,8600		0,0,4300	no	missense	CEACAM3	NM_001815.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	154/253	42312886	1,13005	2203	4300	6503	47004726	SO:0001583	missense	90273			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.460G>A	19.37:g.42312886G>A	ENSP00000349971:p.Ala154Thr		47004726	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	37	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527784	0.27299	2.27E-4	0.0	ENSG00000170956	ENST00000357396;ENST00000221999;ENST00000344550	T;T;T	0.01685	4.69;4.73;4.73	2.79	0.354	0.16063	.	.	.	.	.	T	0.04048	0.0113	M	0.85777	2.775	0.09310	N	1	D;D	0.57899	0.981;0.968	P;B	0.50570	0.644;0.441	T	0.32134	-0.9918	9	0.09590	T	0.72	.	3.6759	0.08291	0.1499:0.0:0.6094:0.2406	.	154;154	G5E978;P40198	.;CEAM3_HUMAN	T	154	ENSP00000349971:A154T;ENSP00000221999:A154T;ENSP00000341725:A154T	ENSP00000221999:A154T	A	+	1	0	CEACAM3	47004726	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.769000	0.04710	0.011000	0.14865	0.514000	0.50259	GCC		0.607	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		A	42312886	G	A	42312886	3	1	122	1	0	0	0	0	1	0	0	0	3199	1087	38	1	470	1	CEACAM3	19	42312886	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	9385494	42312886	16816097	106	32145										
MARK4	57787	hgsc.bcm.edu	37	chr19	45783945	45783945	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cagccacagcaaagggcagcGgagttcctcttccacctacc	9	16	1	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:45783945G>A	ENST00000262891.4	+	12	1560	c.1229G>A	c.(1228-1230)cGg>cAg	p.R410Q	MARK4_ENST00000300843.4_Missense_Mutation_p.R410Q	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	410					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)	p.R410Q(1)		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)		AAAGGGCAGCGGAGTTCCTCT	0.662																																																1	Substitution - Missense(1)	ovary(1)	19											97	78	85					19																	45783945		2203	4300	6503	50475785	SO:0001583	missense	57787			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.1229G>A	19.37:g.45783945G>A	ENSP00000262891:p.Arg410Gln		50475785	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	ENST00000262891.4	37	CCDS56097.1	.	.	.	.	.	.	.	.	.	.	G	34	5.376741	0.95945	.	.	ENSG00000007047	ENST00000262891;ENST00000300843	T;T	0.35421	1.31;1.31	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000001	T	0.62877	0.2464	M	0.78049	2.395	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.998	P;D;D	0.75484	0.769;0.978;0.986	T	0.62656	-0.6808	10	0.52906	T	0.07	.	17.7884	0.88545	0.0:0.0:1.0:0.0	.	276;410;410	Q8N2N5;Q96L34;Q96L34-2	.;MARK4_HUMAN;.	Q	410	ENSP00000262891:R410Q;ENSP00000300843:R410Q	ENSP00000262891:R410Q	R	+	2	0	MARK4	50475785	1.000000	0.71417	0.993000	0.49108	0.939000	0.58152	6.619000	0.74219	2.804000	0.96469	0.462000	0.41574	CGG		0.662	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		A	45783945	G	A	45783945	3	1	122	1	0	0	0	0	1	0	0	0	9345	1116	39	1	1275	1	MARK4	19	45783945	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	3471059	45783945	13345038	107	32146										
SLC6A16	28968	hgsc.bcm.edu	37	chr19	49814193	49814193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ctggtccccagacttacagcCtccactgttaagccacaggt	8	15	0	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:49814193C>T	ENST00000335875.4	-	2	653	c.412G>A	c.(412-414)Ggc>Agc	p.G138S	MIR4324_ENST00000584846.1_RNA|SLC6A16_ENST00000454748.3_Missense_Mutation_p.G138S	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	138					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		GACTTACAGCCTCCACTGTTA	0.502																																																0			19											71	65	67					19																	49814193		1863	4100	5963	54506005	SO:0001583	missense	28968			AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"Solute carriers"	13622	protein-coding gene	gene with protein product	"NTT5 protein"	607972	"solute carrier family 6 (neurotransmitter transporter), member 16"			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.412G>A	19.37:g.49814193C>T	ENSP00000338627:p.Gly138Ser		54506005	Q8IYV4|Q9Y5I9	Missense_Mutation	SNP	ENST00000335875.4	37	CCDS42590.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.821270	0.71028	.	.	ENSG00000063127	ENST00000335875;ENST00000454748	D;D	0.97138	-4.26;-4.26	5.11	-0.069	0.13753	.	0.058272	0.64402	N	0.000002	D	0.97739	0.9258	M	0.89715	3.055	0.46609	D	0.999124	D;D	0.69078	0.997;0.997	P;P	0.62649	0.905;0.905	D	0.95685	0.8735	10	0.87932	D	0	.	5.2105	0.15314	0.0:0.5451:0.1464:0.3085	.	138;138	Q8IYV4;Q9GZN6	.;S6A16_HUMAN	S	138	ENSP00000338627:G138S;ENSP00000404022:G138S	ENSP00000338627:G138S	G	-	1	0	SLC6A16	54506005	0.994000	0.37717	0.075000	0.20258	0.028000	0.11728	2.641000	0.46587	-0.014000	0.14175	0.655000	0.94253	GGC		0.502	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		T	49814193	C	T	49814193	3	4	122	1	0	0	0	0	1	0	0	0	14716	681	24	3	1842	3	SLC6A16	19	49814193	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	4030248	49814193	9314790	108	32147										
ZNF610	162963	hgsc.bcm.edu	37	chr19	52869756	52869756	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gagaagccctacaaatgtaaCgaatgtggaagagcatttca	10	7	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:52869756C>T	ENST00000403906.3	+	6	1581	c.1125C>T	c.(1123-1125)aaC>aaT	p.N375N	ZNF610_ENST00000601151.1_Silent_p.N332N|ZNF610_ENST00000321287.8_Silent_p.N375N|ZNF610_ENST00000327920.8_Silent_p.N375N	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	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)			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)		ACAAATGTAACGAATGTGGAA	0.403																																																0			19											82	84	84					19																	52869756		2203	4300	6503	57561568	SO:0001819	synonymous_variant	162963			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.1125C>T	19.37:g.52869756C>T			57561568	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																				0.403	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530		T	52869756	C	T	52869756	2	4	122	1	0	0	0	0	0	0	0	1	18075	535	19	1		1	ZNF610	19	52869756	Silent	SNP	C	TCGA-G5-6641-01A-11D-1826-10	3055563	52869756	6259227	109	32148										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53652530	53652530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cctataattctccaacatcaCgtccctgtacaaagtcctct	3	15	3	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:53652530C>T	ENST00000334197.7	-	3	174	c.106G>A	c.(106-108)Gtg>Atg	p.V36M	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.V36M|ZNF347_ENST00000452676.2_Missense_Mutation_p.V36M	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	36	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.V36M(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TCCAACATCACGTCCCTGTAC	0.493																																					Melanoma(64;205 1597 17324 45721)											1	Substitution - Missense(1)	endometrium(1)	19											121	124	123					19																	53652530		2203	4300	6503	58344342	SO:0001583	missense	84671			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.106G>A	19.37:g.53652530C>T	ENSP00000334146:p.Val36Met		58344342	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.248955	0.22880	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.04015	3.73;3.73	2.38	2.38	0.29361	Krueppel-associated box (4);	.	.	.	.	T	0.25975	0.0633	H	0.95260	3.645	0.23464	N	0.997621	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.984	T	0.08269	-1.0730	9	0.87932	D	0	.	5.0786	0.14644	0.0:0.826:0.0:0.174	.	36;36	G5E9N4;Q96SE7	.;ZN347_HUMAN	M	36	ENSP00000334146:V36M;ENSP00000405218:V36M	ENSP00000334146:V36M	V	-	1	0	ZNF347	58344342	0.779000	0.28652	0.707000	0.30419	0.020000	0.10135	1.234000	0.32660	1.337000	0.45525	0.591000	0.81541	GTG		0.493	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53652530	C	T	53652530	3	4	122	1	0	0	0	0	1	0	0	0	17900	536	19	1	2428	1	ZNF347	19	53652530	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10	782774	53652530	5476453	110	32149										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54314025	54314025	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aaagaaggcttgagctcatcGaagccgtcgatgatgaaaag	12	7	1	4	rs538564043		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:54314025G>A	ENST00000324134.6	-	3	1056	c.888C>T	c.(886-888)ttC>ttT	p.F296F	NLRP12_ENST00000391772.1_Silent_p.F296F|NLRP12_ENST00000345770.5_Silent_p.F296F|NLRP12_ENST00000391775.3_Silent_p.F296F|NLRP12_ENST00000535162.1_Silent_p.F296F|NLRP12_ENST00000354278.3_Silent_p.F296F|NLRP12_ENST00000351894.4_Silent_p.F296F|NLRP12_ENST00000391773.1_Silent_p.F296F	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	296	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		TGAGCTCATCGAAGCCGTCGA	0.587													G|||	1	0.000199681	0	0.0014	5008	,	,		17741	0		0	False		,,,				2504	0															0			19											47	48	48					19																	54314025		2203	4300	6503	59005837	SO:0001819	synonymous_variant	91662			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.888C>T	19.37:g.54314025G>A			59005837	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																				0.587	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54314025	G	A	54314025	2	1	122	1	0	0	0	0	0	0	0	1	10505	1049	37	1		1	NLRP12	19	54314025	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10	661495	54314025	4814958	111	32150										
LILRA4	23547	hgsc.bcm.edu	37	chr19	54848271	54848271	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tccgtacattgatctcagacGcaacgggggatgggctgccc	13	12	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:54848271G>A	ENST00000291759.4	-	6	1152	c.1096C>T	c.(1096-1098)Cgt>Tgt	p.R366C	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	366	Ig-like C2-type 4.				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)		GATCTCAGACGCAACGGGGGA	0.587																																																0			19											158	146	150					19																	54848271		2203	4300	6503	59540083	SO:0001583	missense	23547			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.1096C>T	19.37:g.54848271G>A	ENSP00000291759:p.Arg366Cys		59540083	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	7.586	0.669823	0.14776	.	.	ENSG00000239961	ENST00000291759	T	0.03181	4.02	2.51	-4.04	0.04010	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.685783	0.12505	N	0.463016	T	0.03434	0.0099	L	0.50847	1.595	0.09310	N	1	B	0.24258	0.1	B	0.27170	0.077	T	0.38329	-0.9666	10	0.49607	T	0.09	.	3.2998	0.06979	0.5097:0.0:0.2945:0.1958	.	366	P59901	LIRA4_HUMAN	C	366	ENSP00000291759:R366C	ENSP00000291759:R366C	R	-	1	0	LILRA4	59540083	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.042000	0.13949	-0.817000	0.04335	0.455000	0.32223	CGT		0.587	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		A	54848271	G	A	54848271	3	1	122	1	0	0	0	0	1	0	0	0	8810	1087	38	1	415	1	LILRA4	19	54848271	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	534246	54848271	4280712	112	32151										
NCR1	9437	hgsc.bcm.edu	37	chr19	55418070	55418070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	agtcaaattctacatcccggAcatgaactcccgcatggcag	8	13	2	1			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr19:55418070A>G	ENST00000291890.4	+	3	298	c.260A>G	c.(259-261)gAc>gGc	p.D87G	NCR1_ENST00000594765.1_Missense_Mutation_p.D87G|NCR1_ENST00000447255.1_Missense_Mutation_p.D87G|NCR1_ENST00000338835.5_Missense_Mutation_p.D87G|NCR1_ENST00000350790.5_Intron|NCR1_ENST00000598576.1_Missense_Mutation_p.D75G|NCR1_ENST00000357397.5_Intron	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	87	Ig-like 1.		D -> Y (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		TACATCCCGGACATGAACTCC	0.527																																																0			19											76	79	78					19																	55418070		2203	4300	6503	60109882	SO:0001583	missense	9437			AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6731	protein-coding gene	gene with protein product		604530	"lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.260A>G	19.37:g.55418070A>G	ENSP00000291890:p.Asp87Gly		60109882	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Missense_Mutation	SNP	ENST00000291890.4	37	CCDS12911.1	.	.	.	.	.	.	.	.	.	.	A	7.906	0.735491	0.15574	.	.	ENSG00000189430	ENST00000291890;ENST00000447255;ENST00000338835	T;T;T	0.09445	2.98;2.98;2.98	3.74	-3.02	0.05446	Immunoglobulin-like fold (1);	2.570310	0.01184	N	0.007141	T	0.09335	0.0230	L	0.34521	1.04	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.15484	0.013;0.004;0.007	T	0.36986	-0.9725	10	0.42905	T	0.14	.	6.5141	0.22239	0.644:0.2547:0.0:0.1012	.	87;87;87	B0V3L5;O76036-6;O76036	.;.;NCTR1_HUMAN	G	87	ENSP00000291890:D87G;ENSP00000404434:D87G;ENSP00000339515:D87G	ENSP00000291890:D87G	D	+	2	0	NCR1	60109882	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.284000	0.08422	-0.408000	0.07565	-0.310000	0.09108	GAC		0.527	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1			G	55418070	A	G	55418070	3	3	122	1	0	0	0	0	1	0	0	0	10268	275	10	4	270	4	NCR1	19	55418070	Missense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	569799	55418070	3710913	113	32152										
PREX1	57580	hgsc.bcm.edu	37	chr20	47266636	47266636	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggggtaggacacttccatgaGgttgatgtggcaattggtgg	17	5	0	2	rs368033397		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr20:47266636G>C	ENST00000371941.3	-	24	2948	c.2926C>G	c.(2926-2928)Ctc>Gtc	p.L976V	PREX1_ENST00000396220.1_Missense_Mutation_p.L976V	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	976					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)			ACTTCCATGAGGTTGATGTGG	0.617																																																0			20											112	115	114					20																	47266636		2203	4300	6503	46700043	SO:0001583	missense	57580			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.2926C>G	20.37:g.47266636G>C	ENSP00000361009:p.Leu976Val		46700043	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	9.686	1.150571	0.21371	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.41758	0.99;0.99	5.71	2.54	0.30619	.	0.129470	0.33875	U	0.004469	T	0.26521	0.0648	L	0.29908	0.895	0.45502	D	0.998466	B;P	0.35780	0.002;0.52	B;B	0.34824	0.011;0.19	T	0.03086	-1.1074	10	0.15066	T	0.55	.	9.7637	0.40548	0.0656:0.0:0.6839:0.2505	.	976;273	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	V	976	ENSP00000361009:L976V;ENSP00000379522:L976V	ENSP00000361009:L976V	L	-	1	0	PREX1	46700043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.657000	0.37366	0.280000	0.22209	0.655000	0.94253	CTC		0.617	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		C	47266636	G	C	47266636	3	2	122	1	0	0	0	0	1	0	0	0	12510	1000	35	5	2121	5	PREX1	20	47266636	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10		47266636	15758884	114	32153										
SIK1	150094	hgsc.bcm.edu	37	chr21	44841904	44841904	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tgacgatgtaaagcatgtccTttgtttccataacctaaaga	7	8	0	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr21:44841904T>C	ENST00000270162.6	-	4	419	c.287A>G	c.(286-288)aAg>aGg	p.K96R		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	AAGCATGTCCTTTGTTTCCAT	0.418																																																0			21											110	100	103					21																	44841904		2203	4300	6503	43666332	SO:0001583	missense	150094			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.287A>G	21.37:g.44841904T>C	ENSP00000270162:p.Lys96Arg		43666332	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.170280	0.78452	.	.	ENSG00000142178	ENST00000270162	T	0.25085	1.82	4.77	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055010	0.64402	D	0.000001	T	0.29256	0.0728	N	0.20807	0.61	0.53688	D	0.999973	P	0.42649	0.786	P	0.52031	0.688	T	0.12578	-1.0542	10	0.87932	D	0	.	14.3245	0.66509	0.0:0.0:0.0:1.0	.	96	P57059	SIK1_HUMAN	R	96	ENSP00000270162:K96R	ENSP00000270162:K96R	K	-	2	0	SIK1	43666332	1.000000	0.71417	0.984000	0.44739	0.942000	0.58702	5.516000	0.67055	1.789000	0.52484	0.533000	0.62120	AAG		0.418	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		C	44841904	T	C	44841904	3	2	122	1	0	0	0	0	1	0	0	0	14354	1609	56	4	2108	4	SIK1	21	44841904	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10		44841904	3287991	115	32154										
EP300	2033	hgsc.bcm.edu	37	chr22	41564512	41564512	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	gtgtgaatgactttctgaggCgacagaatcaccctgagtca	11	9	3	5			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr22:41564512C>T	ENST00000263253.7	+	24	5153	c.3934C>T	c.(3934-3936)Cga>Tga	p.R1312*	RNU6-375P_ENST00000517050.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1312	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)	p.R1312*(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						CTTTCTGAGGCGACAGAATCA	0.428			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																														Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	1	Substitution - Nonsense(1)	ovary(1)	22											121	113	116					22																	41564512		2203	4300	6503	39894458	SO:0001587	stop_gained	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	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.3934C>T	22.37:g.41564512C>T	ENSP00000263253:p.Arg1312*		39894458	B1AKC2	Nonsense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	51	18.252331	0.99902	.	.	ENSG00000100393	ENST00000263253	.	.	.	5.75	3.52	0.40303	.	0.000000	0.40818	N	0.001006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.3062	13.8573	0.63537	0.4746:0.5254:0.0:0.0	.	.	.	.	X	1312	.	ENSP00000263253:R1312X	R	+	1	2	EP300	39894458	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.771000	0.26633	1.397000	0.46682	0.557000	0.71058	CGA		0.428	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41564512	C	T	41564512	4	4	122	1	0	0	0	0	0	1	0	0	5161	760	27	1	4028	1	EP300	22	41564512	Nonsense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10		41564512	9740054	116	32155										
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42524322	42524322	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cttgccagccagcgctgggaTatgcaggaggacggggacag	17	10	0	0	rs574057781		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr22:42524322T>A	ENST00000360608.5	-	5	811	c.697A>T	c.(697-699)Atc>Ttc	p.I233F	NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.I233F|NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.I182F	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	233					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)	AGCGCTGGGATATGCAGGAGG	0.592																																																0			22											70	61	64					22																	42524322		2197	4300	6497	40854266	SO:0001583	missense	1565			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.697A>T	22.37:g.42524322T>A	ENSP00000353820:p.Ile233Phe		40854266	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.343594	0.61073	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.66280	-0.2;-0.2;-0.2	4.55	2.38	0.29361	.	0.141592	0.47852	D	0.000201	T	0.57975	0.2090	L	0.37561	1.115	0.45733	D	0.998635	P;P	0.49253	0.921;0.594	P;P	0.51742	0.678;0.676	T	0.53287	-0.8460	10	0.46703	T	0.11	.	8.2626	0.31795	0.0:0.1729:0.0:0.8271	.	182;233	Q6NXU8;Q6NWU0	.;.	F	233;233;179;182;182	ENSP00000353820:I233F;ENSP00000374620:I233F;ENSP00000351927:I182F	ENSP00000351927:I182F	I	-	1	0	CYP2D6	40854266	0.329000	0.24696	0.694000	0.30210	0.016000	0.09150	0.437000	0.21543	0.207000	0.20607	0.397000	0.26171	ATC		0.592	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			A	42524322	T	A	42524322	3	1	122	1	0	0	0	0	1	0	0	0	4175	1406	49	5	816	5	CYP2D6	22	42524322	Missense_Mutation	SNP	T	TCGA-G5-6641-01A-11D-1826-10	959810	42524322	8780244	117	32156										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50439538	50439538	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ggtgatggaggcgcgtacacGcaggagcatcgcgcagccgt	17	11	0	1	rs147243670		TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chr22:50439538G>A	ENST00000389983.2	-	4	346	c.82C>T	c.(82-84)Cgt>Tgt	p.R28C	IL17REL_ENST00000341280.5_Missense_Mutation_p.R28C	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	28										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)		GCGCGTACACGCAGGAGCATC	0.652																																																0			22											39	31	34					22																	50439538		2194	4294	6488	48781665	SO:0001583	missense	400935			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.82C>T	22.37:g.50439538G>A	ENSP00000374633:p.Arg28Cys		48781665	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	37	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	g	16.61	3.170922	0.57584	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.26660	1.72;1.72	3.16	2.03	0.26663	.	0.606522	0.14777	U	0.298998	T	0.30541	0.0768	L	0.40543	1.245	0.09310	N	0.999999	D	0.71674	0.998	P	0.56916	0.809	T	0.04737	-1.0930	10	0.87932	D	0	.	6.4872	0.22095	0.0:0.0:0.6826:0.3174	.	28	Q6ZVW7	I17EL_HUMAN	C	28	ENSP00000374633:R28C;ENSP00000342520:R28C	ENSP00000342520:R28C	R	-	1	0	IL17REL	48781665	0.396000	0.25262	0.097000	0.21041	0.053000	0.15095	1.299000	0.33424	1.591000	0.50007	0.651000	0.88453	CGT		0.652	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		A	50439538	G	A	50439538	3	1	122	1	0	0	0	0	1	0	0	0	7665	1087	38	1	972	1	IL17REL	22	50439538	Missense_Mutation	SNP	G	TCGA-G5-6641-01A-11D-1826-10	7915216	50439538	865028	118	32157										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86873048	86873048	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	ttctcataaagcagctccatCcttcaaactgcttagggatt	6	11	2	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chrX:86873048C>A	ENST00000373119.4	+	4	986	c.841C>A	c.(841-843)Cct>Act	p.P281T	KLHL4_ENST00000373114.4_Missense_Mutation_p.P281T	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	281						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						GCAGCTCCATCCTTCAAACTG	0.428																																																0			X											107	88	95					X																	86873048		2203	4300	6503	86759704	SO:0001583	missense	56062			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.841C>A	X.37:g.86873048C>A	ENSP00000362211:p.Pro281Thr		86759704	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242197	0.79912	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.76578	-1.03;-1.01	4.74	4.74	0.60224	.	0.061530	0.64402	D	0.000003	D	0.88640	0.6491	M	0.86502	2.82	0.80722	D	1	P;D	0.54964	0.947;0.969	P;D	0.63488	0.768;0.915	D	0.91038	0.4869	10	0.87932	D	0	.	15.9642	0.79952	0.0:1.0:0.0:0.0	.	281;281	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	T	281	ENSP00000362211:P281T;ENSP00000362206:P281T	ENSP00000362206:P281T	P	+	1	0	KLHL4	86759704	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.243000	0.78219	1.960000	0.56953	0.502000	0.49764	CCT		0.428	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			A	86873048	C	A	86873048	3	1	122	1	0	0	0	0	1	0	0	0	8412	855	30	2	855	2	KLHL4	23	86873048	Missense_Mutation	SNP	C	TCGA-G5-6641-01A-11D-1826-10		86873048	68397512	119	32158										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118975081	118975081	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	aatttgtccctttctggaatTctgtctatcttctttagctt	5	9	5	0			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chrX:118975081T>C	ENST00000276201.2	-	7	834	c.765A>G	c.(763-765)agA>agG	p.R255R	UPF3B_ENST00000345865.2_Silent_p.R255R|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	255	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						TTTCTGGAATTCTGTCTATCT	0.323																																																0			X											296	226	250					X																	118975081		2203	4299	6502	118859109	SO:0001819	synonymous_variant	65109			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.765A>G	X.37:g.118975081T>C			118859109	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Silent	SNP	ENST00000276201.2	37	CCDS14588.1																																																																																				0.323	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			C	118975081	T	C	118975081	2	2	122	1	0	0	0	0	0	0	0	1	17046	1780	62	4		4	UPF3B	23	118975081	Silent	SNP	T	TCGA-G5-6641-01A-11D-1826-10	32102033	118975081	36295479	120	32159										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123630962	123630962	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	tgccatcagggccagaagctAaggcgacaggagcaaagagt	14	9	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chrX:123630962A>C	ENST00000371130.3	-	20	3662	c.3599T>G	c.(3598-3600)tTa>tGa	p.L1200*	TENM1_ENST00000422452.2_Nonsense_Mutation_p.L1200*|TENM1_ENST00000461429.1_5'UTR	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1200					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)										GCCAGAAGCTAAGGCGACAGG	0.458																																																0			X											115	103	107					X																	123630962		2203	4300	6503	123458643	SO:0001587	stop_gained	10178			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.3599T>G	X.37:g.123630962A>C	ENSP00000360171:p.Leu1200*		123458643	B2RTR5|Q5JZ17	Nonsense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	46	12.159681	0.99642	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	.	.	.	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3411	0.66627	1.0:0.0:0.0:0.0	.	.	.	.	X	1200	.	ENSP00000360171:L1200X	L	-	2	0	ODZ1	123458643	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.335000	0.96500	1.765000	0.52091	0.486000	0.48141	TTA		0.458	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123630962	A	C	123630962	4	2	122	1	0	0	0	0	0	1	0	0	10865	372	13	4	4651	4	ODZ1	23	123630962	Nonsense_Mutation	SNP	A	TCGA-G5-6641-01A-11D-1826-10	4655881	123630962	31639598	121	32160										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993904	140993906	+	In_Frame_Del	DEL	CCC	CCC	-													0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cctctccagattcctgtgagCccctcctcctcctccacttt					rs146816736|rs176040	byFrequency	TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	CCC	CCC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chrX:140993904_140993906delCCC	ENST00000285879.4	+	4	1000_1002	c.714_716delCCC	c.(712-717)agcccc>agc	p.P239del	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	239				P -> S (in Ref. 1 and 2). {ECO:0000305}.				p.P239S(2)		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)					TTCCTGTGAGCCCCTCCTCCTCC	0.478										HNSCC(15;0.026)																																						2	Substitution - Missense(2)	stomach(2)	X																																								140821572	SO:0001651	inframe_deletion	9947			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.714_716delCCC	X.37:g.140993904_140993906delCCC	ENSP00000285879:p.Pro239del		140821570	A0PK03|O75451|Q8TCV4	In_Frame_Del	DEL	ENST00000285879.4	37	CCDS35417.1																																																																																				0.478	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		-	140993906	CCC	-	140993904	7	5	122	1	0	1	0	1	0	0	0	0	9210	738	26	0	720	0	MAGEC1	23	140993904	In_Frame_Del	DEL	CCC	TCGA-G5-6641-01A-11D-1826-10	17362942	140993904	14276656	122	32161										
TGIF2LY	90655	hgsc.bcm.edu	37	chrY	3447837	3447837	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.228795085216013	2.65402298850575	0	0.444444444444444	1	0	cccctagccagaagctcaccGgaatagcccagccaaagaaa	8	15	1	2			TCGA-G5-6641-01A-11D-1826-10	TCGA-G5-6641-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	1876b42e-efaa-4075-99fe-1ea84d258394	4bbe8e9b-8a4f-42c8-974b-720cc2e9e7a2	g.chrY:3447837G>A	ENST00000559055.2	+	1	682	c.552G>A	c.(550-552)ccG>ccA	p.P184P	TGIF2LY_ENST00000321217.4_Silent_p.P184P			Q8IUE0	TF2LY_HUMAN	TGFB-induced factor homeobox 2-like, Y-linked	184					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|upper_aerodigestive_tract(1)	2						GAAGCTCACCGGAATAGCCCA	0.537																																																0			Y											27	33	31					Y																	3447837		610	1951	2561	3507837	SO:0001819	synonymous_variant	90655			AF332223	CCDS14775.1	Yp11.2	2011-06-20	2007-02-07		ENSG00000176679	ENSG00000176679		"Homeoboxes / TALE class"	18569	protein-coding gene	gene with protein product		400025	"TGFB-induced factor 2-like, Y-linked"				Standard	NM_139214		Approved		uc004fqk.3	Q8IUE0	OTTHUMG00000036153	ENST00000559055.2:c.552G>A	Y.37:g.3447837G>A			3507837	A2VCU1	Silent	SNP	ENST00000559055.2	37	CCDS14775.1																																																																																				0.537	TGIF2LY-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417915.2	NM_139214		A	3447837	G	A	3447837	2	1	122	1	0	0	0	0	0	0	0	1	15867	1103	39	1		1	TGIF2LY	24	3447837	Silent	SNP	G	TCGA-G5-6641-01A-11D-1826-10		3447837	55925729	123	32162										
