1YO8.A | THBS2

General Structure Information

PDB ID	1yo8
HGNC Gene Label(s)	THBS2
Structure Name	structure of the c-terminal domain of human thrombospondin-2
Resolution	2.6Å
Reference	AUTH C.B.CARLSON,D.A.BERNSTEIN,D.S.ANNIS,T.M.MISENHEIMER,AUTH 2 B.L.HANNAH,D.F.MOSHER,J.L.KECKTITL STRUCTURE OF THE CALCIUM-RICH SIGNATURE DOMAIN OF HUMANTITL 2 THROMBOSPONDIN-2REF NAT.STRUCT.MOL.BIOL. V. 12 910 2005REFN ISSN 1545-9993PMID 16186819DOI 10.1038/NSMB997

Variant Set Distributions

ExAC Variants

Number Of Residues	616
Number Of SNVs	145
Number Of Permutations	62198
Optimal Distance Threshold	12.0
K Statistic	0.042
p-value	0.682

COSMIC

Number Of Residues	616
Number Of SNVs	14
Number Of Permutations	17894
Optimal Distance Threshold	31.0
K Statistic	0.549
p-value	0.155

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	145
Number Of COSMIC SNVs	12
Optimal Distance Threshold	13.0
K Statistic	-0.052
p-value	0.569

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:169633080	rs375814540	A>T	A:562	(-37.25, 9.70, 82.41)
6:169633069		S>R	A:565	(-42.21, 8.88, 90.51)
6:169633061		P>L	A:568	(-50.54, 7.77, 96.38)
6:169633062		P>S	A:568	(-50.54, 7.77, 96.38)
6:169633018		L>F	A:582	(-30.46, 19.59, 80.46)
6:169633013		N>S	A:584	(-36.49, 20.20, 84.23)
6:169632996	rs199509417	D>N	A:590	(-28.36, 17.72, 74.10)
6:169632875		K>E	A:606	(-7.42, 23.23, 64.98)
6:169632872		V>M	A:607	(-10.34, 24.91, 68.28)
6:169632847	rs555199606	P>L	A:615	(-28.00, 11.30, 70.74)
6:169632829		P>H	A:621	(-11.59, 10.60, 62.73)
6:169632815		Y>H	A:626	(-1.48, 12.46, 63.45)
6:169632800		P>T	A:631	(-13.71, 8.39, 70.85)
6:169632797	COSM741105	V>I	A:632	(-18.10, 6.67, 70.88)
6:169632794	rs375967631	G>R	A:633	(-20.52, 8.48, 73.64)
6:169632787		G>A	A:635	(-22.87, 10.77, 77.93)
6:169632788		G>S	A:635	(-22.87, 10.77, 77.93)
6:169632767		E>K	A:642	(-13.03, 7.35, 76.46)
6:169632293		V>M	A:645	(-4.45, 8.62, 71.67)
6:169632283		P>L	A:648	(2.81, 10.21, 65.13)
6:169632284		P>S	A:648	(2.81, 10.21, 65.13)
6:169632243		K>N	A:661	(13.85, -7.83, 50.34)
6:169632242		H>Y	A:662	(16.51, -5.77, 47.95)
6:169632238		A>V	A:663	(14.20, -1.12, 49.55)
6:169632217	rs143976396	H>L	A:670	(4.42, 14.78, 60.22)
6:169632214	COSM1267754	F>C	A:671	(4.03, 18.41, 58.56)
6:169632212		S>C	A:672	(5.68, 15.46, 53.44)
6:169632209	rs146067041	D>N	A:673	(2.95, 15.80, 50.60)
6:169632205		P>H	A:674	(4.81, 12.04, 50.16)
6:169632178		G>D	A:683	(22.88, -2.25, 43.81)
6:169632173		A>T	A:685	(17.41, -0.53, 40.44)
6:169632164		G>R	A:688	(10.85, 0.85, 44.96)
6:169632151		G>E	A:692	(17.42, -4.54, 40.79)
6:169632152		G>R	A:692	(17.42, -4.54, 40.79)
6:169632149	COSM315902	E>K	A:693	(21.12, -6.64, 40.53)
6:169632142		S>L	A:695	(26.43, -3.68, 38.46)
6:169632127		W>L	A:700	(19.25, 3.78, 34.32)
6:169632110		V>F	A:706	(8.05, -5.34, 36.22)
6:169632091	rs182641150	T>N	A:712	(10.13, 7.89, 34.31)
6:169632089		Y>H	A:713	(13.50, 8.62, 35.09)
6:169629753		N>D	A:725	(25.72, 5.29, 31.57)
6:169629747	rs557791983	G>R	A:727	(22.06, 9.10, 30.92)
6:169629735		F>L	A:731	(23.20, 10.06, 18.30)
6:169629723	rs140600818	G>R	A:735	(21.44, 0.03, 22.72)
6:169629714	rs61736310	D>N	A:738	(27.13, 7.12, 23.70)
6:169629707	rs369510106	C>Y	A:740	(30.16, 1.60, 25.56)
6:169629696		D>N	A:744	(28.73, 6.95, 19.21)
6:169629687		D>Y	A:747	(29.93, 6.50, 10.65)
6:169629684	rs201813061 COSM2855174	G>S	A:748	(32.55, 3.42, 10.81)
6:169629681		V>L	A:749	(34.40, 6.31, 11.83)
6:169629675		D>N	A:751	(34.63, 7.20, 18.64)
6:169629672		E>K	A:752	(39.34, 7.25, 19.76)
6:169628365	rs142094192	Q>H	A:757	(32.48, 11.40, 18.24)
6:169628366		Q>R	A:757	(32.48, 11.40, 18.24)
6:169628349		R>C	A:763	(32.90, 11.60, 2.13)
6:169628337		Y>D	A:767	(37.80, 24.58, 4.69)
6:169628289		H>Y	A:783	(40.98, 26.70, 14.94)
6:169628286		N>D	A:784	(36.58, 25.94, 16.74)
6:169628280		A>S	A:786	(35.93, 23.64, 21.73)
6:169628272		I>M	A:788	(32.94, 27.31, 22.83)
6:169628259		N>D	A:793	(23.00, 29.47, 18.38)
6:169628255		G>A	A:794	(25.04, 26.75, 16.56)
6:169628247		D>N	A:797	(31.97, 31.64, 20.49)
6:169628235		V>M	A:801	(30.04, 39.29, 16.42)
6:169628228		I>T	A:803	(29.41, 35.15, 22.16)
6:169626387		F>Y	A:809	(28.24, 43.45, 18.37)
6:169626363		Y>C	A:817	(31.82, 35.09, 27.78)
6:169626361		V>I	A:818	(26.71, 37.56, 30.53)
6:169626351		T>I	A:821	(20.71, 44.39, 27.01)
6:169626345	rs376275090	Q>R	A:823	(25.82, 46.98, 28.96)
6:169626336	rs578215810	T>M	A:826	(27.56, 50.89, 39.07)
6:169626324		G>D	A:830	(34.06, 47.48, 32.43)
6:169626325	rs145039765	G>S	A:830	(34.06, 47.48, 32.43)
6:169626309		C>Y	A:835	(30.27, 40.07, 35.17)
6:169626297		P>L	A:839	(29.68, 44.93, 42.06)
6:169625471		D>N	A:848	(38.87, 35.27, 43.06)
6:169625468		V>M	A:849	(42.92, 34.49, 45.28)
6:169625447		D>Y	A:856	(40.71, 40.26, 45.57)
6:169625435		N>D	A:860	(36.87, 41.08, 54.20)
6:169625422		I>T	A:864	(31.25, 36.10, 62.74)
6:169625411		G>S	A:868	(30.74, 32.09, 53.48)
6:169625402		N>H	A:871	(30.02, 40.10, 57.76)
6:169625399		N>H	A:872	(29.39, 42.92, 53.58)
6:169625368		A>V	A:882	(24.82, 29.03, 53.28)
6:169625369		A>T	A:882	(24.82, 29.03, 53.28)
6:169625361		Q>H	A:884	(21.84, 33.44, 52.22)
6:169625347		R>K	A:889	(13.40, 38.84, 47.11)
6:169625333	rs149756243	D>N	A:894	(14.55, 32.13, 55.90)
6:169625330	rs577405635	A>T	A:895	(17.38, 32.11, 59.68)
6:169625306		D>N	A:903	(1.71, 35.31, 56.39)
6:169625300	rs184952882	V>I	A:905	(1.49, 33.42, 60.56)
6:169625297		P>A	A:906	(4.41, 33.10, 62.91)
6:169625291		D>N	A:908	(6.10, 29.05, 65.25)
6:169625275	rs568444513	R>Q	A:913	(8.03, 27.55, 56.66)
6:169625261		P>S	A:918	(-3.20, 34.64, 56.27)
6:169625244	rs188300247	L>F	A:923	(-10.41, 22.36, 54.44)
6:169625245		L>S	A:923	(-10.41, 22.36, 54.44)
6:169623561	rs566007634 COSM3860499	R>Q	A:928	(1.06, 20.85, 54.06)
6:169623562	rs182173220	R>W	A:928	(1.06, 20.85, 54.06)
6:169623556		D>N	A:930	(-4.84, 23.43, 51.58)
6:169623552	rs114156352	I>N	A:931	(-1.83, 27.15, 49.23)
6:169623531	rs570626256	N>S	A:938	(5.52, 27.67, 45.28)
6:169623520		P>S	A:942	(6.86, 18.15, 43.16)
6:169623513	rs146079026	I>T	A:944	(8.32, 13.49, 45.28)
6:169623511		D>N	A:945	(10.39, 15.03, 42.15)
6:169623505		V>M	A:947	(16.43, 17.84, 46.03)
6:169623411		N>S	A:978	(38.76, 17.72, 30.79)
6:169623403		I>V	A:981	(28.89, 17.55, 31.38)
6:169623400	COSM264024	R>G	A:982	(28.04, 12.03, 30.47)
6:169623390		G>D	A:985	(24.55, 17.23, 35.69)
6:169623387		K>R	A:986	(22.54, 14.23, 37.13)
6:169623372		T>R	A:991	(39.85, 13.07, 30.94)
6:169623373		T>P	A:991	(39.85, 13.07, 30.94)
6:169623355		G>S	A:997	(40.79, 20.10, 41.38)
6:169623349		A>T	A:999	(34.16, 21.00, 40.32)
6:169622555	rs138262723	E>K	A:1004	(24.61, 27.67, 48.35)
6:169622548		G>V	A:1006	(23.59, 23.12, 54.76)
6:169622519		V>I	A:1016	(38.50, 4.58, 37.65)
6:169622508	rs143050504	D>E	A:1019	(44.72, 0.71, 33.58)
6:169622507	rs144671564	R>W	A:1020	(45.84, 4.90, 31.89)
6:169622491	rs138932100	A>V	A:1025	(39.47, 11.08, 43.83)
6:169622489		G>S	A:1026	(36.37, 12.92, 44.78)
6:169622483		V>I	A:1028	(34.06, 18.93, 47.80)
6:169622477		G>S	A:1030	(31.63, 23.16, 52.21)
6:169622464		S>N	A:1034	(40.39, 27.81, 47.93)
6:169622458	COSM265364	R>H	A:1036	(36.84, 28.58, 54.34)
6:169622428		T>M	A:1046	(50.71, 4.46, 49.19)
6:169622398		R>Q	A:1056	(59.43, 15.61, 52.96)
6:169622399	rs141219768	R>W	A:1056	(59.43, 15.61, 52.96)
6:169622381		G>S	A:1062	(42.18, 5.76, 51.18)
6:169622378		V>M	A:1063	(38.69, 7.09, 52.27)
6:169622362		V>A	A:1068	(40.85, 23.02, 53.92)
6:169622350		T>K	A:1072	(48.60, 30.10, 51.91)
6:169622344	COSM360274	T>M	A:1074	(46.00, 28.54, 46.02)
6:169622339		E>K	A:1076	(53.95, 25.10, 47.04)
6:169622323	rs575823532	A>V	A:1081	(48.52, 19.17, 52.26)
6:169622299	rs139254686	P>L	A:1089	(50.34, 22.90, 60.14)
6:169622296		G>E	A:1090	(47.87, 25.97, 58.00)
6:169621618	COSM1076104	R>Q	A:1093	(41.95, 19.68, 60.66)
6:169621604	rs368075705 COSM1076103	D>N	A:1098	(40.56, 3.48, 56.02)
6:169621591		I>T	A:1102	(41.04, -0.07, 51.44)
6:169621592		I>V	A:1102	(41.04, -0.07, 51.44)
6:169621582		K>R	A:1105	(39.25, -2.07, 43.03)
6:169621573	rs139601458	T>M	A:1108	(35.45, -0.70, 40.48)
6:169621541		K>E	A:1119	(22.60, 23.32, 62.80)
6:169621537		T>I	A:1120	(25.78, 19.49, 65.01)
6:169621531		Y>C	A:1122	(26.77, 13.81, 61.71)
6:169620431	rs148801026	V>F	A:1125	(31.67, 9.12, 54.93)
6:169620425	rs545179688	V>L	A:1127	(32.06, 4.00, 50.65)
6:169620421	rs375397482	H>L	A:1128	(28.43, 1.28, 49.65)
6:169620422	rs144366283	H>N	A:1128	(28.43, 1.28, 49.65)
6:169620407	rs112533700	V>F	A:1133	(29.64, -1.17, 53.55)
6:169620395		S>T	A:1137	(33.46, 7.49, 59.32)
6:169620389		P>T	A:1139	(30.20, 9.29, 63.77)
6:169620382		Y>C	A:1141	(30.40, 15.41, 65.57)
6:169620368	rs371131576	A>T	A:1146	(28.22, 25.98, 58.37)
6:169620358		R>P	A:1149	(29.84, 25.91, 46.54)
6:169620295		R>K	A:1170	(17.57, 15.36, 54.18)

1YO8.A | THBS2.

1YO8.A | THBS2

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

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:169632779	COSM368209	A>S	A:638	(-18.04, 8.73, 79.30)
6:169632238	COSM4445045	A>V	A:663	(14.20, -1.12, 49.55)
6:169632173	COSM2855181	A>T	A:685	(17.41, -0.53, 40.44)
6:169629774	COSM131372	D>N	A:718	(22.25, -0.32, 31.59)
6:169629759	COSM368208	L>V	A:723	(30.51, 2.09, 31.94)
6:169626325	COSM3697675	G>S	A:830	(34.06, 47.48, 32.43)
6:169623541	COSM3777316	D>N	A:935	(5.11, 22.83, 46.10)
6:169623438	COSM1672978	P>R	A:969	(48.09, 27.86, 40.09)
6:169623439	COSM741108	P>S	A:969	(48.09, 27.86, 40.09)
6:169623400	COSM264024	R>C	A:982	(28.04, 12.03, 30.47)
6:169623354	COSM4769979	G>V	A:997	(40.79, 20.10, 41.38)
6:169623349	COSM5009073	A>T	A:999	(34.16, 21.00, 40.32)
6:169622506	COSM3662292	R>Q	A:1020	(45.84, 4.90, 31.89)
6:169622458	COSM265364	R>H	A:1036	(36.84, 28.58, 54.34)
6:169621604	COSM1076103	D>N	A:1098	(40.56, 3.48, 56.02)
6:169620302	COSM230107	E>K	A:1168	(18.56, 15.23, 49.04)