4BWE.D | GPC1 – ASTRID

4BWE.D | GPC1

General Structure Information

PDB ID	4bwe
HGNC Gene Label(s)	GPC1
Structure Name	crystal structure of c-terminally truncated glypican-1 after controlled dehydration to 86 percent relative humidity
Resolution	2.46Å
Reference	AUTH W.AWAD,G.SVENSSON BIRKEDAL,M.M.G.M.THUNNISSEN,K.MANI,AUTH 2 D.T.LOGANTITL IMPROVEMENTS OF THE ORDER, ISOTROPY AND ELECTRON DENSITY OFTITL 2 GLYPICAN-1 CRYSTALS BY CONTROLLED DEHYDRATIONREF ACTA CRYSTALLOGR.,SECT.D V. 69 2524 2013REFN ISSN 0907-4449PMID 24311593DOI 10.1107/S0907444913025250

Variant Set Distributions

ExAC Variants

Number Of Residues	421
Number Of SNVs	149
Number Of Permutations	42445
Optimal Distance Threshold	32.0
K Statistic	0.482
p-value	0.026

COSMIC

Number Of Residues	421
Number Of SNVs	3
Number Of Permutations	7
Optimal Distance Threshold	30.0
K Statistic	0.333
p-value	1.0

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	149
Number Of COSMIC SNVs	3
Optimal Distance Threshold	28.0
K Statistic	-0.403
p-value	0.562

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:241375424		R>Q	D:30	(-26.95, 46.20, -24.43)
2:241375451		Y>C	D:39	(-15.21, 32.46, -29.95)
2:241375475	rs371651045	S>N	D:47	(-18.49, 34.78, -37.95)
2:241375488		Q>H	D:51	(-22.98, 43.73, -33.74)
2:241398458		R>W	D:60	(-30.65, 23.96, -25.40)
2:241398459	rs141069921	R>Q	D:60	(-30.65, 23.96, -25.40)
2:241398461		I>V	D:61	(-25.76, 25.00, -21.18)
2:241398486		C>Y	D:69	(-23.23, 33.52, -27.00)
2:241398494	rs200321707	E>K	D:72	(-22.42, 26.61, -32.84)
2:241398518	rs565369538	R>C	D:80	(-11.55, 24.93, -25.92)
2:241398522		S>N	D:81	(-14.14, 23.45, -21.26)
2:241398530		E>K	D:84	(-9.39, 23.56, -21.07)
2:241398543	rs148564112	A>V	D:88	(-5.27, 19.01, -16.42)
2:241398548	rs541416018	R>W	D:90	(-4.42, 13.62, -20.08)
2:241398549	rs150959912	R>Q	D:90	(-4.42, 13.62, -20.08)
2:241398560	COSM1669899	R>C	D:94	(1.68, 13.34, -17.84)
2:241398561	rs140790256	R>H	D:94	(1.68, 13.34, -17.84)
2:241398563	rs146749086	V>I	D:95	(3.28, 14.12, -12.80)
2:241398576	rs6717362	M>T	D:99	(6.75, 9.56, -8.92)
2:241398578	rs138434031	L>F	D:100	(5.15, 6.03, -9.45)
2:241398581		A>T	D:101	(8.51, 5.27, -12.65)
2:241398593		R>C	D:105	(13.71, 2.17, -11.64)
2:241398594	rs373974894	R>H	D:105	(13.71, 2.17, -11.64)
2:241398598		S>R	D:106	(15.37, 3.32, -8.73)
2:241398600	rs377640716	F>Y	D:107	(13.78, 1.10, -5.06)
2:241401631	rs376569826	D>N	D:117	(28.09, -6.54, -5.92)
2:241401640	COSM1018701	R>W	D:120	(30.00, -8.44, -10.03)
2:241401641	rs368981259	R>Q	D:120	(30.00, -8.44, -10.03)
2:241401644	rs139334776	T>M	D:121	(32.27, -10.28, -4.79)
2:241401655		T>A	D:125	(36.77, -13.90, -3.53)
2:241401659	rs200792251	F>C	D:126	(34.42, -17.82, -3.90)
2:241401660		F>L	D:126	(34.42, -17.82, -3.90)
2:241401661	rs150046174	P>S	D:127	(38.80, -18.07, -7.17)
2:241401662		P>H	D:127	(38.80, -18.07, -7.17)
2:241401664	rs373679176	G>S	D:128	(41.50, -18.22, -4.21)
2:241401667		A>T	D:129	(39.93, -19.49, -1.61)
2:241401673	rs34976040	G>R	D:131	(39.74, -22.93, -6.18)
2:241401680		L>P	D:133	(36.54, -26.26, -4.46)
2:241401686		T>M	D:135	(37.09, -23.26, -10.86)
2:241401694		A>T	D:138	(30.79, -21.69, -11.53)
2:241401707	rs140826218	R>Q	D:142	(27.47, -19.16, -13.63)
2:241401709	rs531757424	D>Y	D:143	(22.83, -21.76, -12.77)
2:241401712		L>V	D:144	(21.91, -19.97, -7.57)
2:241401727	COSM1018702	R>C	D:149	(19.05, -13.02, -11.78)
2:241401728	rs138375141	R>H	D:149	(19.05, -13.02, -11.78)
2:241401737		Y>S	D:152	(13.39, -9.21, -8.10)
2:241401739		R>C	D:153	(11.53, -11.32, -13.62)
2:241401740		R>H	D:153	(11.53, -11.32, -13.62)
2:241401742		G>S	D:154	(7.91, -13.14, -10.67)
2:241401746		A>D	D:155	(8.83, -15.67, -11.98)
2:241401749		N>I	D:156	(7.22, -18.18, -8.51)
2:241401760	rs373543083	E>K	D:160	(12.42, -23.60, 0.37)
2:241401767		T>M	D:162	(16.10, -23.64, -5.87)
2:241401775		E>K	D:165	(18.22, -28.58, -6.94)
2:241401780		F>L	D:166	(23.07, -25.05, -5.07)
2:241401785	rs199566765	A>V	D:168	(22.61, -31.49, -3.19)
2:241401787		R>C	D:169	(22.89, -31.27, -8.43)
2:241401788	rs557977354 COSM4092828	R>H	D:169	(22.89, -31.27, -8.43)
2:241401796	rs376762179	E>K	D:172	(26.47, -34.71, -6.05)
2:241401799	rs149353022	R>C	D:173	(30.61, -31.42, -8.52)
2:241401800		R>H	D:173	(30.61, -31.42, -8.52)
2:241401819		H>Q	D:179	(37.33, -37.85, -0.57)
2:241401820		P>S	D:180	(39.81, -37.82, -5.03)
2:241401821		P>L	D:180	(39.81, -37.82, -5.03)
2:241401838	rs533921420	D>N	D:186	(24.57, -42.43, -9.58)
2:241401843		D>E	D:187	(22.66, -45.40, -5.67)
2:241401853		C>R	D:191	(23.09, -42.45, 0.25)
2:241401868		A>T	D:196	(22.69, -34.86, 4.29)
2:241401875	rs200136097 COSM4092829	A>V	D:198	(20.90, -34.23, 9.81)
2:241401881		R>Q	D:200	(22.77, -30.81, 10.64)
2:241401884		P>R	D:201	(27.04, -30.95, 5.83)
2:241401889	rs373944004	G>R	D:203	(25.49, -26.22, 8.31)
2:241401890		G>A	D:203	(25.49, -26.22, 8.31)
2:241401892		E>Q	D:204	(24.88, -22.32, 9.85)
2:241401893		E>V	D:204	(24.88, -22.32, 9.85)
2:241401895		A>P	D:205	(24.20, -21.74, 6.02)
2:241401899	rs371738379	P>L	D:206	(21.93, -23.53, 4.40)
2:241401908		L>P	D:209	(20.58, -18.36, 2.72)
2:241401910	rs200794161 COSM720927	R>C	D:210	(15.99, -21.72, 3.95)
2:241401911		R>H	D:210	(15.99, -21.72, 3.95)
2:241401914		L>P	D:211	(14.95, -18.26, 6.93)
2:241401916		R>W	D:212	(18.21, -14.47, 7.21)
2:241401917	rs545177373	R>Q	D:212	(18.21, -14.47, 7.21)
2:241401925		R>G	D:215	(12.55, -13.28, 6.14)
2:241401926	rs143813409	R>H	D:215	(12.55, -13.28, 6.14)
2:241401928		A>T	D:216	(14.31, -10.09, 1.33)
2:241401934	rs368146643	V>M	D:218	(9.43, -11.28, -0.52)
2:241401943	rs368508405	R>C	D:221	(8.65, -10.25, -5.25)
2:241401959	rs200763451 COSM4133651	G>V	D:226	(3.54, -1.87, -6.21)
2:241401967		V>M	D:229	(0.07, -1.85, -9.31)
2:241401973		S>G	D:231	(1.53, 2.98, -12.47)
2:241401976	rs543077300 COSM1208529	D>N	D:232	(-0.73, 0.00, -14.22)
2:241401979		V>M	D:233	(-4.08, 2.25, -11.26)
2:241401985		R>W	D:235	(-1.79, 3.15, -17.64)
2:241401986	rs146133433	R>Q	D:235	(-1.79, 3.15, -17.64)
2:241402777		P>L	D:244	(-22.12, 14.44, -20.47)
2:241402779		E>Q	D:245	(-24.23, 16.56, -16.54)
2:241402786		S>L	D:247	(-19.33, 19.13, -19.91)
2:241402792	rs368952537	A>V	D:249	(-21.08, 21.97, -15.46)
2:241402795		V>G	D:250	(-17.44, 22.72, -16.73)
2:241402833		P>A	D:263	(-15.90, 38.36, -18.87)
2:241402836	rs150681136	G>S	D:264	(-14.05, 38.87, -15.47)
2:241402839	COSM210603	A>T	D:265	(-15.64, 36.73, -13.89)
2:241402851		P>S	D:269	(-14.05, 28.65, -4.72)
2:241402852		P>L	D:269	(-14.05, 28.65, -4.72)
2:241402855		D>V	D:270	(-16.94, 26.51, -2.72)
2:241402864	COSM1018704	R>Q	D:273	(-14.51, 22.64, -3.49)
2:241402884		L>F	D:280	(-13.43, 13.87, -10.33)
2:241402893	rs149889796	Q>E	D:283	(-11.97, 9.38, -10.15)
2:241402896		A>T	D:284	(-12.61, 9.53, -5.09)
2:241402899		D>N	D:285	(-14.35, 6.06, -4.66)
2:241402905		D>N	D:287	(-8.72, 7.52, -1.00)
2:241402908	rs144394036	A>T	D:288	(-8.90, 3.88, 0.53)
2:241404038		M>V	D:297	(4.52, 0.35, -0.26)
2:241404044		L>F	D:299	(4.99, -1.05, 6.56)
2:241404053	rs550678562 COSM4092830	D>N	D:302	(10.35, -1.27, 7.85)
2:241404057		K>R	D:303	(11.13, -5.78, 6.84)
2:241404062		W>G	D:305	(16.39, -0.82, 6.42)
2:241404066		G>D	D:306	(18.89, -5.48, 9.11)
2:241404072	rs138318645	S>L	D:308	(16.98, -9.98, 7.37)
2:241404077		V>M	D:310	(17.69, -6.18, 1.27)
2:241404081		E>V	D:311	(21.87, -3.81, 1.82)
2:241404084		S>N	D:312	(22.17, -7.98, 4.52)
2:241404092		G>S	D:315	(24.60, -8.91, -1.39)
2:241404105	rs536435940	T>M	D:319	(28.68, -14.80, 2.53)
2:241404126	rs201247940	N>S	D:326	(34.78, -23.15, 4.36)
2:241404128		A>T	D:327	(31.98, -26.19, 6.57)
2:241404150		T>M	D:334	(33.31, -36.44, 11.25)
2:241404158		A>S	D:337	(32.60, -41.78, 8.62)
2:241404297		K>E	D:347	(37.88, -49.09, -1.09)
2:241404379	rs200248156	T>K	D:374	(21.80, 4.01, -2.04)
2:241404391		L>Q	D:378	(16.39, 5.44, -2.59)
2:241404500		E>K	D:381	(12.91, 10.82, -2.20)
2:241404510		A>V	D:384	(8.19, 11.66, 0.50)
2:241404518		R>C	D:387	(3.42, 9.04, 3.44)
2:241404519		R>H	D:387	(3.42, 9.04, 3.44)
2:241404521	COSM1406797	D>N	D:388	(2.98, 14.26, -1.58)
2:241404524	rs78856284	V>I	D:389	(0.88, 11.05, -3.54)
2:241404563		S>G	D:402	(-6.44, 26.51, -6.83)
2:241404571		K>N	D:404	(-4.96, 25.74, -13.01)
2:241404573		M>T	D:405	(-10.13, 27.23, -12.53)
2:241404574		M>I	D:405	(-10.13, 27.23, -12.53)
2:241404575		A>S	D:406	(-10.01, 30.39, -8.76)
2:241404614		M>L	D:419	(-26.88, 33.21, -11.84)
2:241404626		R>W	D:423	(-23.15, 35.21, -1.32)
2:241404897	rs201152753	P>A	D:426	(-24.18, 26.44, -2.08)
2:241404900	rs200876630	E>K	D:427	(-22.45, 23.89, 1.94)
2:241404902		E>D	D:427	(-22.45, 23.89, 1.94)
2:241404904		V>A	D:428	(-18.93, 21.68, -0.27)
2:241404906	rs201849980	M>V	D:429	(-20.88, 18.23, -1.60)
2:241404907		M>T	D:429	(-20.88, 18.23, -1.60)
2:241404910		G>D	D:430	(-18.35, 15.28, -0.48)
2:241404915		G>S	D:432	(-17.64, 10.64, -3.65)
2:241404922	rs370899880	A>V	D:434	(-22.62, 8.90, -2.83)
2:241404940		P>R	D:440	(-25.85, 21.23, -6.64)
2:241404951	rs374378112	V>M	D:444	(-24.44, 12.12, -10.31)
2:241404954		D>Y	D:445	(-26.40, 7.68, -11.20)
2:241404963		K>E	D:448	(-22.44, 4.21, -13.08)
2:241404981		R>W	D:454	(-15.50, -0.03, -8.40)
2:241404987		Q>E	D:456	(-7.98, -0.55, -11.10)
2:241404993		M>V	D:458	(-10.04, -5.78, -6.35)
2:241404994		M>T	D:458	(-10.04, -5.78, -6.35)
2:241404999		L>V	D:460	(-5.31, -1.34, -5.21)
2:241405005		I>V	D:462	(-4.96, -8.14, -4.89)
2:241405007		I>M	D:462	(-4.96, -8.14, -4.89)
2:241405009		M>T	D:463	(-0.55, -5.67, -4.42)
2:241405017	rs370391685	R>W	D:466	(0.20, -9.63, -3.82)
2:241405018	rs544444707	R>Q	D:466	(0.20, -9.63, -3.82)
2:241405023	rs562620992	R>C	D:468	(-1.14, -6.73, 5.30)
2:241405024	rs541996291	R>H	D:468	(-1.14, -6.73, 5.30)
2:241405026		S>G	D:469	(1.93, -11.39, 3.23)
2:241405029		A>T	D:470	(5.39, -9.74, 2.85)
2:241405035		N>D	D:472	(4.36, -11.51, 7.87)
2:241405038	rs151028466	G>S	D:473	(7.60, -13.53, 5.26)
2:241405044		D>N	D:475	(5.62, -16.21, -1.25)
2:241405047		V>M	D:476	(1.64, -15.30, -2.30)

4BWE.D | GPC1.

4BWE.D | GPC1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants