3IJE.B | ITGB3

General Structure Information

PDB ID	3ije
HGNC Gene Label(s)	ITGB3
Structure Name	crystal structure of the complete integrin alhavbeta3 ectodomain plus an alpha/beta transmembrane fragment
Resolution	2.9Å
Reference	AUTH J.P.XIONG,B.MAHALINGHAM,J.L.ALONSO,L.A.BORRELLI,X.RUI,AUTH 2 S.ANAND,B.T.HYMAN,T.RYSIOK,D.MULLER-POMPALLA,S.L.GOODMAN,AUTH 3 M.A.ARNAOUTTITL CRYSTAL STRUCTURE OF THE COMPLETE INTEGRIN ALPHAVBETA3TITL 2 ECTODOMAIN PLUS AN ALPHA/BETA TRANSMEMBRANE FRAGMENT.REF J.CELL BIOL. V. 186 589 2009REFN ISSN 0021-9525PMID 19704023DOI 10.1083/JCB.200905085

Variant Set Distributions

ExAC Variants

Number Of Residues	695
Number Of SNVs	158
Number Of Permutations	59824
Optimal Distance Threshold	8.0
K Statistic	0.012
p-value	0.8

ClinVar

Number Of Residues	695
Number Of SNVs	10
Number Of Permutations	4326
Optimal Distance Threshold	13.0
K Statistic	0.133
p-value	0.458

COSMIC

Number Of Residues	695
Number Of SNVs	9
Number Of Permutations	13159
Optimal Distance Threshold	49.0
K Statistic	0.389
p-value	0.222

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	158
Number Of ClinVar SNVs	10
Optimal Distance Threshold	13.0
K Statistic	0.087
p-value	0.36

Cosmic vs. ExAC

Number Of ExAC SNVs	158
Number Of COSMIC SNVs	11
Optimal Distance Threshold	36.0
K Statistic	-0.185
p-value	0.029

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:45351803		T>M	B:7	(-46.32, 15.29, 10.51)
17:45351806		R>L	B:8	(-42.20, 16.82, 11.72)
17:45351816		S>R	B:11	(-40.89, 14.33, 2.20)
17:45351825		Q>H	B:14	(-32.35, 12.18, 3.99)
17:45351827	rs368427993	Q>R	B:15	(-36.72, 14.45, 4.94)
17:45351847		M>V	B:22	(-39.23, 7.30, 16.70)
17:45351860		C>F	B:26	(-40.96, 2.00, 2.74)
17:45360721		A>D	B:30	(-45.23, -2.16, -0.50)
17:45360730	rs5918	L>P	B:33	(-50.28, 4.67, -4.14)
17:45360735		S>P	B:35	(-51.17, 6.09, 3.35)
17:45360741	rs199866795	R>C	B:37	(-44.87, 6.34, 3.34)
17:45360742	rs370054364	R>H	B:37	(-44.87, 6.34, 3.34)
17:45360751	rs36080296	L>R	B:40	(-43.48, 5.01, 14.15)
17:45360771		D>N	B:47	(-48.93, -1.57, 7.58)
17:45360784	rs148562034	P>R	B:51	(-39.13, -7.11, 4.09)
17:45360817	rs200358667	R>Q	B:62	(-19.47, -2.25, 17.59)
17:45360825		E>Q	B:65	(-8.86, -1.96, 22.31)
17:45360849		G>S	B:73	(3.78, -0.69, 36.55)
17:45360869		Q>H	B:79	(0.69, -2.92, 26.80)
17:45360884		S>R	B:84	(-10.56, -0.12, 30.20)
17:45360889	rs78408552	Q>R	B:86	(-8.55, 1.21, 25.07)
17:45360895		I>T	B:88	(-15.50, 3.37, 21.41)
17:45360904		R>Q	B:91	(-22.09, 3.13, 13.63)
17:45360909	COSM1710392 COSM1710393 CM021113	R>W	B:93	(-30.85, 7.75, 13.68)
17:45360910	rs147782061	R>Q	B:93	(-30.85, 7.75, 13.68)
17:45361833		Q>L	B:103	(-13.31, 2.26, 33.61)
17:45361835		V>M	B:104	(-9.50, 5.94, 35.12)
17:45361838	rs199866698	R>W	B:105	(-6.39, 1.60, 37.79)
17:45361875	rs121918452	L>W	B:117	(14.37, 23.53, 35.54)
17:45361895		M>V	B:124	(20.25, 29.69, 43.68)
17:45361902		D>A	B:126	(23.00, 28.46, 48.88)
17:45361910		W>R	B:129	(27.49, 22.68, 48.92)
17:45361913		S>G	B:130	(22.51, 21.28, 49.03)
17:45361920		Q>R	B:132	(26.17, 17.92, 46.53)
17:45361946	rs376401679	Q>E	B:141	(12.89, 8.58, 49.76)
17:45361953	rs5917	R>Q	B:143	(13.93, 2.49, 45.60)
17:45361973	COSM980415 COSM1521337 COSM1255047 COSM1521338	R>W	B:150	(14.82, 7.38, 33.59)
17:45361976	rs375645378	I>V	B:151	(16.80, 11.76, 37.46)
17:45361985	rs569479486	G>R	B:154	(18.47, 22.06, 34.34)
17:45361988		A>S	B:155	(19.54, 25.54, 33.92)
17:45362004	rs61736876	P>L	B:160	(21.74, 36.43, 26.58)
17:45362010	rs143146734	S>L	B:162	(21.35, 44.26, 25.97)
17:45362018		M>V	B:165	(23.32, 40.66, 29.52)
17:45362019		M>T	B:165	(23.32, 40.66, 29.52)
17:45362022		Y>C	B:166	(25.58, 43.15, 33.68)
17:45362055		C>Y	B:177	(31.27, 38.73, 39.18)
17:45362058		Y>C	B:178	(33.56, 43.26, 37.13)
17:45363666		V>M	B:193	(23.01, 19.33, 31.92)
17:45363673		T>M	B:195	(19.58, 13.25, 29.69)
17:45363681		D>N	B:198	(18.73, 4.86, 35.30)
17:45363685		Q>R	B:199	(23.50, 6.22, 36.11)
17:45363715		K>R	B:209	(30.38, 19.39, 36.60)
17:45363722		S>R	B:211	(28.17, 27.35, 38.12)
17:45363729	rs121918446	R>W	B:214	(25.45, 39.34, 38.40)
17:45363765	rs56173532	I>V	B:226	(9.08, 25.80, 31.66)
17:45363777		T>A	B:230	(7.94, 20.76, 27.74)
17:45363780		V>I	B:231	(8.91, 20.91, 23.66)
17:45364440	rs200636313	K>R	B:235	(18.07, 16.63, 24.08)
17:45364445	rs368829511	G>S	B:237	(13.69, 12.04, 27.71)
17:45364460		A>T	B:242	(5.73, 7.88, 32.58)
17:45364466		H>Y	B:244	(6.13, 12.99, 32.62)
17:45364472		L>M	B:246	(9.14, 20.16, 35.12)
17:45364527		G>V	B:264	(13.92, 43.49, 20.52)
17:45364575	rs13306476 CM981080	H>R	B:280	(23.03, 26.16, 25.34)
17:45364581		S>F	B:282	(19.01, 28.95, 20.07)
17:45364593	COSM3712515 COSM3712517 COSM3712516	T>S	B:286	(15.57, 35.53, 18.60)
17:45367057		S>F	B:291	(2.21, 32.44, 26.72)
17:45367077	rs147263592	K>E	B:298	(2.81, 22.50, 24.20)
17:45367092	rs201550717	N>D	B:303	(1.40, 14.42, 29.43)
17:45367098		N>H	B:305	(3.17, 17.44, 35.90)
17:45367120		E>A	B:312	(7.40, 32.65, 51.29)
17:45367123		N>S	B:313	(9.89, 35.85, 48.35)
17:45367132	rs146336675	N>S	B:316	(1.79, 34.85, 46.90)
17:45367561	rs377062987	E>A	B:323	(-5.09, 30.02, 40.01)
17:45367599	rs150029332	D>N	B:336	(19.10, 26.14, 51.24)
17:45367624	rs371006520	I>T	B:344	(9.58, 16.39, 44.78)
17:45368324		I>T	B:351	(0.19, 15.10, 40.68)
17:45368326	COSM35501 COSM1563794 COSM1153080 COSM1563795	R>C	B:352	(-0.57, 9.40, 40.90)
17:45368327		R>H	B:352	(-0.57, 9.40, 40.90)
17:45368353		D>N	B:361	(-10.11, 16.48, 17.97)
17:45368360		P>L	B:363	(-16.98, 16.57, 16.78)
17:45368374	rs148794549	L>V	B:368	(-19.96, 15.06, 25.35)
17:45368384		N>S	B:371	(-22.14, 11.28, 35.18)
17:45368395		L>V	B:375	(-17.09, 7.46, 46.86)
17:45368402		N>S	B:377	(-21.23, 2.73, 44.07)
17:45368410	rs559147730	I>V	B:380	(-21.07, 13.00, 41.23)
17:45368419		L>F	B:383	(-18.18, 15.83, 37.53)
17:45368423		K>R	B:384	(-14.87, 16.03, 33.34)
17:45368426	rs78121013	S>F	B:385	(-13.46, 15.59, 37.68)
17:45368446		G>R	B:392	(-4.86, 2.26, 43.21)
17:45368453	rs147758772	T>M	B:394	(-10.29, 2.78, 40.01)
17:45369515	rs550153970	S>N	B:398	(-20.82, 8.21, 32.31)
17:45369517		I>F	B:399	(-19.66, 9.34, 28.48)
17:45369529	rs376656815	V>M	B:403	(-25.89, 14.23, 17.07)
17:45369533	rs369970972	R>Q	B:404	(-27.29, 20.13, 16.62)
17:45369539		C>Y	B:406	(-26.55, 15.20, 9.32)
17:45369566		T>S	B:415	(-9.49, 11.92, 22.27)
17:45369577	rs377628203 COSM3387976 COSM3387978 COSM3387977	V>M	B:419	(-4.85, 15.26, 32.66)
17:45369592		S>G	B:424	(-6.71, 6.90, 25.50)
17:45369601	rs5921	V>I	B:427	(-14.35, 7.99, 19.84)
17:45369620	rs553184182	C>F	B:433	(-27.64, 10.24, 8.02)
17:45369629		A>V	B:436	(-29.39, 2.30, 1.26)
17:45369634		Q>E	B:438	(-30.29, 7.89, -0.85)
17:45369649		P>A	B:443	(-33.97, 11.00, -11.34)
17:45369656	rs566673492 CM087464	S>I	B:445	(-37.82, 12.25, -16.22)
17:45369657		S>R	B:445	(-37.82, 12.25, -16.22)
17:45369661	rs200388813	R>C	B:447	(-38.50, 4.11, -14.46)
17:45369662		R>H	B:447	(-38.50, 4.11, -14.46)
17:45369671	rs145103142	N>I	B:450	(-46.60, 9.35, -18.46)
17:45369678		N>K	B:452	(-41.30, 14.71, -16.71)
17:45369680		G>E	B:453	(-39.22, 13.60, -12.58)
17:45369712		P>S	B:464	(-39.95, 21.94, -10.52)
17:45369728		S>Y	B:469	(-48.82, 10.57, -5.37)
17:45369745		E>K	B:475	(-49.15, 25.48, -12.61)
17:45369755		Y>C	B:478	(-56.19, 19.24, -12.27)
17:45369758	COSM706032	R>H	B:479	(-57.40, 22.76, -5.64)
17:45369775	rs150951945	E>K	B:485	(-56.52, 13.65, 4.22)
17:45369784		P>A	B:488	(-56.02, 17.54, 11.71)
17:45369787	rs150138754	R>W	B:489	(-59.89, 17.89, 14.20)
17:45369793		G>S	B:491	(-62.53, 21.95, 10.45)
17:45369794		G>V	B:491	(-62.53, 21.95, 10.45)
17:45369814	rs145572861	R>W	B:498	(-50.06, 32.10, 7.09)
17:45369815	rs560812344	R>Q	B:498	(-50.06, 32.10, 7.09)
17:45369820	rs138793107	E>Q	B:500	(-52.39, 27.55, 0.15)
17:45369832		G>S	B:504	(-52.51, 16.23, -1.20)
17:45369871		T>A	B:517	(-41.05, 22.96, 6.89)
17:45369872		T>M	B:517	(-41.05, 22.96, 6.89)
17:45369877		K>E	B:519	(-46.40, 17.78, 4.26)
17:45369895	COSM1211039 COSM1211040	D>N	B:525	(-36.91, 28.06, 11.30)
17:45369910	rs370244559	R>C	B:530	(-36.94, 35.36, 21.68)
17:45369927	rs146310248	M>I	B:535	(-32.57, 32.33, 19.30)
17:45376737		N>S	B:559	(-30.55, 29.54, 29.76)
17:45376746		T>M	B:562	(-22.63, 22.53, 31.15)
17:45376748		R>C	B:563	(-19.12, 26.80, 32.63)
17:45376749		R>H	B:563	(-19.12, 26.80, 32.63)
17:45376751		T>S	B:564	(-18.27, 23.12, 36.94)
17:45376754	rs554164072	D>H	B:565	(-15.68, 26.76, 36.43)
17:45376758		T>S	B:566	(-18.52, 29.08, 38.22)
17:45376767		S>F	B:569	(-13.50, 26.62, 45.20)
17:45376784		C>R	B:575	(-20.18, 24.10, 46.03)
17:45376790		G>S	B:577	(-19.23, 20.89, 50.00)
17:45376794		R>H	B:578	(-21.28, 23.94, 52.50)
17:45376821		V>A	B:587	(-28.09, 25.70, 44.82)
17:45376826		I>F	B:589	(-27.69, 22.56, 50.69)
17:45376827	rs368080215	I>T	B:589	(-27.69, 22.56, 50.69)
17:45376833	COSM1581084 COSM1581085 COSM3983517	P>L	B:591	(-26.12, 24.28, 55.94)
17:45376851		T>I	B:597	(-18.96, 28.72, 46.38)
17:45376887		T>S	B:609	(-18.85, 18.76, 64.72)
17:45377845		E>K	B:613	(-17.71, 12.53, 61.94)
17:45377861		K>T	B:618	(-9.27, 6.86, 60.92)
17:45377872	rs139166528	R>W	B:622	(-16.87, 4.14, 67.03)
17:45377878		A>T	B:624	(-20.91, 7.84, 59.86)
17:45377885		H>R	B:626	(-17.32, 2.68, 59.74)
17:45377890	rs70940817	E>K	B:628	(-21.37, 6.01, 55.05)
17:45377915	rs369443204	R>H	B:636	(-6.52, 12.83, 52.83)
17:45377919		D>E	B:637	(-6.48, 15.05, 58.49)
17:45377920	rs373150039 COSM980431 COSM1588945	E>K	B:638	(-1.27, 13.61, 59.84)
17:45377921		E>A	B:638	(-1.27, 13.61, 59.84)
17:45377932		V>L	B:642	(-1.16, 12.82, 72.43)
17:45377941	COSM3958472 COSM3958474 COSM3958473	L>F	B:645	(-3.29, 18.60, 74.83)
17:45377942		L>R	B:645	(-3.29, 18.60, 74.83)
17:45380093		T>I	B:648	(1.65, 25.87, 72.15)
17:45380104	COSM1161917 COSM1161918	A>T	B:652	(-5.29, 25.67, 69.09)
17:45380117		T>I	B:656	(-14.62, 18.03, 73.83)
17:45380134		D>N	B:662	(-20.44, 6.91, 77.92)
17:45380143	rs534325095 COSM269396 COSM1195611 COSM4067242	V>I	B:665	(-12.76, 12.29, 73.57)
17:45380159		Y>C	B:670	(-1.10, 22.64, 64.19)
17:45380186		L>P	B:679	(-5.84, 15.54, 64.74)
17:45380203	rs138729147	P>S	B:685	(-10.02, 8.78, 77.24)
17:45380206		E>K	B:686	(-12.03, 11.95, 80.83)
17:45384846	rs538875423	K>T	B:689	(-13.77, 6.52, 87.87)

3IJE.B | ITGB3.

3IJE.B | ITGB3

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:45361973	COSM4498754	R>W	B:150	(14.82, 7.38, 33.59)
17:45362045	COSM3518480	E>K	B:174	(30.82, 39.47, 28.51)
17:45364593	COSM3712516	T>N	B:286	(15.57, 35.53, 18.60)
17:45368326	COSM1563794	R>G	B:352	(-0.57, 9.40, 40.90)
17:45369695	COSM1383905	G>V	B:458	(-40.58, 4.06, -3.28)
17:45369725	COSM1722100	G>E	B:468	(-47.96, 13.95, -6.47)
17:45369764	COSM3518512	S>F	B:481	(-60.38, 18.53, -6.28)
17:45369802	COSM5030255	V>I	B:494	(-56.07, 24.94, 4.97)
17:45376749	COSM4411245	R>H	B:563	(-19.12, 26.80, 32.63)
17:45376833	COSM1581084	P>L	B:591	(-26.12, 24.28, 55.94)
17:45376847	COSM3712344	D>N	B:596	(-20.81, 32.78, 44.66)
17:45380104	COSM4410589	A>S	B:652	(-5.29, 25.67, 69.09)
17:45380143	COSM1195611	V>I	B:665	(-12.76, 12.29, 73.57)