3VI4.A | ITGA5

General Structure Information

PDB ID	3vi4
HGNC Gene Label(s)	ITGA5
Structure Name	crystal structure of alpha5beta1 integrin headpiece in complex with rgd peptide
Resolution	2.9Å
Reference	AUTH M.NAGAE,S.RE,E.MIHARA,T.NOGI,Y.SUGITA,J.TAKAGITITL CRYSTAL STRUCTURE OF ALPHA5BETA1 INTEGRIN ECTODOMAIN: ATOMICTITL 2 DETAILS OF THE FIBRONECTIN RECEPTORREF J.CELL BIOL. V. 197 131 2012REFN ISSN 0021-9525PMID 22451694DOI 10.1083/JCB.201111077

Variant Set Distributions

ExAC Variants

Number Of Residues	601
Number Of SNVs	150
Number Of Permutations	88503
Optimal Distance Threshold	16.0
K Statistic	0.117
p-value	0.416

COSMIC

Number Of Residues	601
Number Of SNVs	6
Number Of Permutations	2536
Optimal Distance Threshold	25.0
K Statistic	0.067
p-value	0.084

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	150
Number Of COSMIC SNVs	6
Optimal Distance Threshold	21.0
K Statistic	-0.21
p-value	0.822

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
12:54812855		N>S	A:2	(5.95, 17.00, 15.84)
12:54812848		D>E	A:4	(9.88, 10.71, 19.75)
12:54812816	COSM4043204	P>L	A:15	(7.45, -15.29, 16.48)
12:54812790		E>Q	A:24	(-7.01, 1.17, 15.94)
12:54812777		P>Q	A:28	(-13.02, 2.64, 26.54)
12:54812778		P>S	A:28	(-13.02, 2.64, 26.54)
12:54812768		D>A	A:31	(-8.89, 8.09, 28.39)
12:54805747		V>I	A:33	(-5.78, 4.64, 26.13)
12:54805743	rs201444911 COSM1193947	S>N	A:34	(-5.31, 1.15, 24.09)
12:54805668		P>R	A:59	(-2.42, -1.49, 27.50)
12:54805669		P>S	A:59	(-2.42, -1.49, 27.50)
12:54805666	rs200580175	W>R	A:60	(0.71, 4.07, 26.02)
12:54805663		G>C	A:61	(0.40, 2.46, 30.46)
12:54805644		C>F	A:67	(0.29, -7.29, 24.87)
12:54805624		S>G	A:74	(-12.68, -19.48, 22.35)
12:54803379		S>A	A:77	(-15.05, -24.96, 13.89)
12:54803361		S>P	A:83	(-24.12, -34.98, 9.75)
12:54803349		S>P	A:87	(-22.50, -42.26, 9.02)
12:54803331		V>M	A:93	(-19.63, -25.82, 8.63)
12:54803305	COSM941145	F>L	A:101	(-9.18, -12.53, 13.60)
12:54803306		F>S	A:101	(-9.18, -12.53, 13.60)
12:54803298		T>A	A:104	(-8.90, -5.66, 9.49)
12:54803285		H>R	A:108	(-16.68, 4.28, 17.05)
12:54803282		G>D	A:109	(-15.50, 3.56, 20.88)
12:54803279		S>F	A:110	(-16.86, 0.72, 22.97)
12:54803273		I>S	A:112	(-13.54, -3.56, 18.80)
12:54803135	rs200931801	A>V	A:114	(-12.30, -7.85, 13.72)
12:54803111		R>H	A:122	(-19.73, -27.61, 3.75)
12:54803112		R>C	A:122	(-19.73, -27.61, 3.75)
12:54803075		T>I	A:134	(-15.76, -13.24, 9.43)
12:54803058	rs368421506	D>H	A:140	(-20.70, -2.06, 25.14)
12:54803048		T>I	A:143	(-20.71, -6.70, 27.10)
12:54803045	rs540145150	R>Q	A:144	(-23.45, -9.15, 22.70)
12:54803040	COSM1210996	L>V	A:146	(-21.63, -9.39, 17.72)
12:54803022		R>S	A:152	(-21.83, -16.65, 6.73)
12:54802688	rs200109874	E>K	A:171	(-13.37, 2.57, 8.36)
12:54802585		T>A	A:175	(-22.49, 6.78, 13.76)
12:54802579		R>C	A:177	(-23.53, 2.20, 9.42)
12:54802575		V>A	A:178	(-20.06, -1.38, 9.91)
12:54802554		S>N	A:185	(-18.29, -10.46, -4.83)
12:54802548		F>Y	A:187	(-17.23, -14.53, -11.12)
12:54801977		Y>S	A:204	(-25.30, -13.20, 16.52)
12:54801967		E>D	A:207	(-28.03, -21.66, 17.13)
12:54801969	COSM1512428	E>K	A:207	(-28.03, -21.66, 17.13)
12:54801951		V>I	A:213	(-28.87, -8.08, 8.12)
12:54801938		L>R	A:217	(-26.69, -0.97, 2.82)
12:54801934	rs374695746	Q>H	A:218	(-26.20, -5.04, -0.31)
12:54801933		T>A	A:219	(-23.20, -3.04, -3.89)
12:54801923		A>D	A:222	(-23.08, -6.40, -12.44)
12:54801920		S>I	A:223	(-22.57, -7.08, -16.01)
12:54801912		Y>H	A:226	(-18.80, -3.96, -14.92)
12:54801646		V>I	A:237	(-15.30, 7.27, 5.70)
12:54801627	rs150405444	D>V	A:243	(-25.71, 14.76, 3.71)
12:54801468		A>T	A:250	(-14.05, 2.51, -2.84)
12:54801443	rs529704616	T>I	A:258	(-6.24, -2.79, -15.19)
12:54801438		G>S	A:260	(-8.33, 2.55, -11.94)
12:54799710	COSM694651	V>L	A:262	(-12.06, 5.60, -6.53)
12:54799682	rs200642938	R>Q	A:271	(-28.42, 4.88, -4.84)
12:54799677	rs564976660	L>F	A:273	(-22.17, 10.04, -5.75)
12:54799670		N>S	A:275	(-16.26, 7.55, -10.50)
12:54799659	COSM3462807 COSM3462806	E>Q	A:279	(-2.11, 7.86, -14.61)
12:54799470	rs375602887 COSM1362790	A>T	A:291	(-10.58, 10.77, 4.06)
12:54799466		T>I	A:292	(-8.81, 14.19, 5.24)
12:54799461	COSM287536	V>I	A:294	(-5.83, 18.87, 3.72)
12:54799457		N>S	A:295	(-7.78, 22.72, 2.88)
12:54799449	rs141341610	G>R	A:298	(-14.88, 21.63, 6.13)
12:54799153	rs202050846	D>G	A:300	(-13.88, 15.83, 3.79)
12:54799135		A>V	A:306	(-0.66, 4.04, -6.67)
12:54799112		P>S	A:314	(15.47, 12.10, -16.23)
12:54799105	rs146614663	G>E	A:316	(14.57, 6.97, -19.28)
12:54799106		G>R	A:316	(14.57, 6.97, -19.28)
12:54799102		R>Q	A:317	(16.21, 3.83, -15.64)
12:54799103	COSM1299611	R>W	A:317	(16.21, 3.83, -15.64)
12:54799091		V>L	A:321	(7.83, 4.83, -7.59)
12:54799075		V>A	A:326	(-4.88, 14.95, -3.65)
12:54799063		H>P	A:330	(-13.80, 22.69, -3.97)
12:54799055	rs377645220	G>S	A:333	(-17.46, 19.66, -5.53)
12:54799052		I>V	A:334	(-15.14, 16.46, -6.01)
12:54799049		E>Q	A:335	(-10.90, 18.74, -8.99)
12:54799042		T>M	A:337	(-8.74, 16.40, -12.24)
12:54799030		T>I	A:341	(0.62, 14.36, -7.75)
12:54799031	rs554050434	T>S	A:341	(0.62, 14.36, -7.75)
12:54799028		L>V	A:342	(2.72, 12.90, -4.02)
12:54799016	COSM3462800	D>H	A:346	(12.81, 4.72, -3.09)
12:54799003		R>Q	A:350	(5.05, -1.50, -3.35)
12:54798994		S>T	A:353	(0.80, 1.21, 0.26)
12:54798991		S>F	A:354	(-0.30, 3.37, 3.28)
12:54798983		P>S	A:357	(-5.59, 10.46, 8.61)
12:54798979		L>Q	A:358	(-1.77, 12.34, 11.22)
12:54798980	COSM1362789	L>V	A:358	(-1.77, 12.34, 11.22)
12:54798976	COSM1705724	G>E	A:359	(-4.69, 15.31, 11.73)
12:54798971		L>V	A:361	(1.15, 16.52, 13.99)
12:54798967		D>G	A:362	(1.63, 21.03, 13.36)
12:54798962	rs578020993	D>N	A:364	(-0.98, 24.42, 12.03)
12:54798959		G>S	A:365	(-4.88, 24.29, 11.54)
12:54798952		N>S	A:367	(-5.68, 18.40, 8.90)
12:54798953	rs200918284	N>D	A:367	(-5.68, 18.40, 8.90)
12:54798670		I>V	A:371	(2.27, 8.43, 2.94)
12:54798664	rs202005757	A>S	A:373	(7.25, 2.89, 1.70)
12:54798643	rs538916711	Q>E	A:380	(15.05, -2.10, 0.97)
12:54798625	rs200940770	V>I	A:386	(4.86, 13.40, 7.39)
12:54798603		G>E	A:393	(-3.04, 22.21, 0.34)
12:54798597		G>D	A:395	(2.26, 19.19, 0.92)
12:54798586		S>A	A:399	(7.55, 17.20, 7.83)
12:54798581		Q>H	A:400	(9.11, 13.70, 10.07)
12:54798580		V>L	A:401	(11.40, 10.78, 7.32)
12:54798573	rs531610716	Q>P	A:403	(13.76, 5.51, 8.58)
12:54798561		A>V	A:407	(18.64, -3.97, 11.77)
12:54798546		P>Q	A:412	(11.20, -8.28, 4.60)
12:54798547	rs149010571	P>S	A:412	(11.20, -8.28, 4.60)
12:54798541		F>I	A:414	(6.59, -5.68, 4.98)
12:54798538		F>L	A:415	(8.40, 0.73, 8.99)
12:54798535		G>S	A:416	(4.46, 1.05, 6.83)
12:54798526		L>F	A:419	(-0.43, 3.72, 8.84)
12:54798522	rs376218631	R>Q	A:420	(-5.51, 4.35, 12.06)
12:54798513	rs181020771	R>Q	A:423	(-7.76, 8.63, 17.55)
12:54798492		Y>C	A:430	(0.61, 18.31, 20.37)
12:54798253	rs577974426	I>T	A:434	(0.08, 3.40, 15.32)
12:54798245		S>P	A:437	(6.70, -3.78, 11.21)
12:54798227		A>S	A:443	(4.53, -1.86, 16.61)
12:54798025		R>H	A:449	(8.24, 16.46, 20.54)
12:54798026		R>C	A:449	(8.24, 16.46, 20.54)
12:54798022		P>L	A:450	(5.63, 19.72, 22.65)
12:54798011	rs112896207	A>T	A:454	(11.30, 31.16, 18.21)
12:54797999	rs147794441	L>F	A:458	(21.97, 40.20, 16.99)
12:54797993		I>V	A:460	(25.90, 45.66, 16.56)
12:54797984	rs181997225	A>T	A:463	(29.11, 48.98, 13.86)
12:54797980		M>T	A:464	(31.79, 52.13, 13.17)
12:54797962		R>Q	A:470	(40.83, 53.85, 23.63)
12:54797963	rs527756302	R>W	A:470	(40.83, 53.85, 23.63)
12:54797950	rs370538855	L>S	A:474	(38.98, 46.65, 31.83)
12:54797945		G>R	A:476	(43.89, 50.77, 32.99)
12:54797739		S>N	A:485	(21.71, 43.55, 21.63)
12:54797710	rs140478060	V>I	A:495	(4.01, 24.58, 26.25)
12:54797697		I>T	A:499	(10.24, 28.57, 27.65)
12:54797555		V>M	A:503	(22.10, 31.89, 24.45)
12:54797551		E>G	A:504	(26.63, 30.00, 22.16)
12:54797549		L>F	A:505	(27.05, 35.17, 21.93)
12:54797535		W>C	A:509	(31.50, 32.82, 12.53)
12:54797512		R>Q	A:517	(38.66, 34.93, 18.90)
12:54797513	rs143754928	R>W	A:517	(38.66, 34.93, 18.90)
12:54797510		R>W	A:518	(39.86, 40.62, 15.84)
12:54797499		F>L	A:521	(32.14, 39.35, 25.75)
12:54797500		F>S	A:521	(32.14, 39.35, 25.75)
12:54797494		A>V	A:523	(32.93, 40.80, 31.71)
12:54797485		Q>R	A:526	(36.75, 34.93, 27.51)
12:54797473		T>I	A:530	(27.15, 30.39, 27.49)
12:54797443		R>Q	A:540	(7.80, 43.28, 25.91)
12:54797441		E>K	A:541	(11.65, 41.69, 21.94)
12:54797418		I>M	A:548	(31.92, 44.19, 22.80)
12:54797105		E>K	A:553	(46.57, 44.02, 20.71)
12:54797086		K>R	A:559	(43.82, 46.33, 11.16)
12:54797077		P>L	A:562	(35.39, 41.28, 9.13)
12:54797066	rs138215416	A>T	A:566	(27.25, 34.29, 16.52)
12:54797063		L>F	A:567	(22.85, 34.28, 18.33)
12:54797042	rs144650038	Q>K	A:574	(18.77, 20.22, 31.58)
12:54797023		H>R	A:580	(3.10, 11.61, 30.10)
12:54797024		H>D	A:580	(3.10, 11.61, 30.10)
12:54797021		G>S	A:581	(8.09, 12.11, 28.86)
12:54797002		H>R	A:587	(8.65, 25.46, 13.90)
12:54796999		Y>C	A:588	(10.30, 23.11, 10.23)
12:54796984	rs142874592	R>Q	A:593	(23.62, 30.26, 13.80)
12:54796981		I>R	A:594	(21.49, 35.32, 14.02)
12:54796976		D>Y	A:596	(26.12, 40.67, 12.54)
12:54796973	rs138386543	K>E	A:597	(29.54, 41.52, 9.60)
12:54796833	rs202210895	A>G	A:598	(32.06, 44.15, 13.02)

3VI4.A | ITGA5.

3VI4.A | ITGA5

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
12:54801909	COSM1747114	D>N	A:227	(-16.36, -9.69, -13.91)
12:54799461	COSM287536	V>I	A:294	(-5.83, 18.87, 3.72)
12:54799103	COSM1299611	R>W	A:317	(16.21, 3.83, -15.64)
12:54798228	COSM1677034	K>N	A:442	(8.30, -5.10, 15.74)
12:54797727	COSM4411238	N>S	A:489	(9.96, 36.48, 20.84)
12:54797021	COSM4382441	G>S	A:581	(8.09, 12.11, 28.86)