1TR2.A | VCL – ASTRID

1TR2.A | VCL

General Structure Information

PDB ID	1tr2
HGNC Gene Label(s)	VCL
Structure Name	crystal structure of human full-length vinculin (residues 1- 1066)
Resolution	2.9Å
Reference	AUTH R.A.BORGON,C.VONRHEIN,G.BRICOGNE,P.R.BOIS,T.IZARDTITL CRYSTAL STRUCTURE OF HUMAN VINCULINREF STRUCTURE V. 12 1189 2004REFN ISSN 0969-2126PMID 15242595DOI 10.1016/J.STR.2004.05.00

Variant Set Distributions

ExAC Variants

Number Of Residues	992
Number Of SNVs	176
Number Of Permutations	51405
Optimal Distance Threshold	8.0
K Statistic	0.012
p-value	0.644

COSMIC

Number Of Residues	992
Number Of SNVs	9
Number Of Permutations	3331
Optimal Distance Threshold	15.0
K Statistic	0.167
p-value	0.306

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	176
Number Of COSMIC SNVs	9
Optimal Distance Threshold	15.0
K Statistic	0.114
p-value	0.448

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
10:75757985		R>L	A:7	(-0.07, -5.06, 56.59)
10:75757997		S>N	A:11	(-4.97, -9.69, 52.93)
10:75757999		I>V	A:12	(-6.84, -13.05, 53.98)
10:75758032		L>M	A:23	(-24.07, -12.87, 50.37)
10:75758095	rs554116863	V>M	A:44	(-22.14, -19.38, 48.12)
10:75758123		N>S	A:53	(-7.03, -23.53, 50.42)
10:75802856	rs147809878	V>I	A:62	(-2.39, -28.92, 62.96)
10:75802857		V>A	A:62	(-2.39, -28.92, 62.96)
10:75802869		E>G	A:66	(6.39, -30.02, 68.33)
10:75802891		D>E	A:73	(-5.81, -22.78, 70.06)
10:75802896	rs373830664	P>L	A:75	(-8.44, -27.17, 65.98)
10:75802910		K>Q	A:80	(-16.04, -21.39, 63.87)
10:75830460		A>E	A:91	(-29.06, -21.90, 52.53)
10:75830746	rs373744314	I>T	A:135	(8.16, -14.02, 72.98)
10:75830754		C>G	A:138	(13.14, -12.47, 73.98)
10:75830797		E>G	A:152	(34.00, -12.79, 88.90)
10:75830814	rs371583362	V>F	A:158	(34.91, -14.00, 75.95)
10:75830824	rs376226543	T>I	A:161	(30.80, -11.35, 74.23)
10:75832496		K>E	A:170	(17.97, -14.31, 66.12)
10:75832515	rs573623641	D>G	A:176	(12.99, -5.43, 61.39)
10:75832536		T>I	A:183	(-1.34, -2.38, 60.82)
10:75832551		R>Q	A:188	(5.92, -0.13, 62.59)
10:75832578	rs189242810	T>I	A:197	(17.62, 1.35, 73.56)
10:75834513	COSM3967155	F>S	A:212	(33.65, -6.16, 87.39)
10:75834519		T>I	A:214	(39.80, -4.16, 86.38)
10:75834566	rs139312390	R>C	A:230	(27.14, -5.29, 86.27)
10:75834567	COSM1349102	R>H	A:230	(27.14, -5.29, 86.27)
10:75834579		V>A	A:234	(21.08, -5.09, 82.95)
10:75834582		E>G	A:235	(17.28, -2.91, 86.00)
10:75834597		E>A	A:240	(13.14, -1.59, 76.79)
10:75834624		Q>R	A:249	(1.63, -10.33, 73.55)
10:75842215	rs142233726	T>S	A:263	(4.54, 4.67, 86.83)
10:75842216	rs150443513	T>S	A:263	(4.54, 4.67, 86.83)
10:75842234		A>G	A:269	(8.32, 13.95, 91.02)
10:75842237		L>S	A:270	(8.61, 11.58, 94.11)
10:75842240		A>V	A:271	(12.92, 12.62, 93.01)
10:75842245		I>L	A:273	(9.65, 16.59, 95.58)
10:75842246		I>T	A:273	(9.65, 16.59, 95.58)
10:75842251		S>A	A:275	(16.02, 16.99, 95.18)
10:75842255		K>R	A:276	(14.20, 20.20, 94.83)
10:75842257	rs71579353	L>M	A:277	(12.19, 19.28, 100.48)
10:75842272		G>C	A:282	(16.00, 27.08, 103.87)
10:75842281		R>C	A:285	(14.39, 26.00, 107.64)
10:75842291	rs138270989	S>T	A:288	(17.67, 36.24, 105.17)
10:75843137		E>D	A:296	(11.18, 31.41, 95.72)
10:75843172		K>I	A:308	(3.71, 17.08, 87.15)
10:75843177		G>S	A:310	(-2.41, 15.16, 90.47)
10:75843190		A>E	A:314	(-8.97, 11.38, 90.65)
10:75843196	rs143944164	K>T	A:316	(-10.79, 13.41, 96.33)
10:75843198		E>Q	A:317	(-7.27, 12.34, 94.88)
10:75843201	rs397517247	R>C	A:318	(-7.48, 15.98, 90.15)
10:75843217		G>E	A:323	(-5.04, 23.03, 96.18)
10:75843255	rs565546734	A>T	A:336	(8.59, 37.01, 99.76)
10:75843256		A>V	A:336	(8.59, 37.01, 99.76)
10:75843264	COSM1349103	R>C	A:339	(11.46, 37.77, 102.89)
10:75843268	rs374928228	A>V	A:340	(9.54, 43.46, 100.31)
10:75848961		G>R	A:344	(11.10, 39.20, 107.44)
10:75848962		G>A	A:344	(11.10, 39.20, 107.44)
10:75848970	rs566961713	P>S	A:347	(6.07, 38.15, 113.33)
10:75848971	rs148619523	P>L	A:347	(6.07, 38.15, 113.33)
10:75848976		A>T	A:349	(7.65, 36.17, 108.06)
10:75848977		A>V	A:349	(7.65, 36.17, 108.06)
10:75849045		R>C	A:372	(1.82, 4.14, 98.08)
10:75849046	rs377289804	R>L	A:372	(1.82, 4.14, 98.08)
10:75849052		L>P	A:374	(-0.53, 4.18, 90.09)
10:75849064		T>I	A:378	(1.53, -1.13, 87.74)
10:75849088	rs200342284	K>R	A:386	(4.41, -12.84, 85.17)
10:75849796	rs201528612	P>S	A:398	(-2.26, -32.91, 79.58)
10:75849802	rs201361282	G>C	A:400	(0.77, -31.03, 84.97)
10:75849809		P>L	A:402	(0.27, -28.47, 91.01)
10:75849841	rs146278697	A>T	A:413	(-5.17, -12.95, 93.71)
10:75849850		R>W	A:416	(-9.20, -11.04, 94.90)
10:75849851	COSM1321202	R>Q	A:416	(-9.20, -11.04, 94.90)
10:75849857	rs147566238	I>T	A:418	(-6.86, -4.89, 90.55)
10:75849862		E>K	A:420	(-8.91, -4.77, 96.80)
10:75849872		D>G	A:423	(-13.49, 3.84, 93.11)
10:75849891	rs139371702	D>E	A:429	(-18.46, -6.63, 91.41)
10:75849896		I>S	A:431	(-13.22, -8.50, 88.48)
10:75849898	rs144146254	L>V	A:432	(-14.68, -10.50, 92.39)
10:75849901	rs139559937	R>C	A:433	(-18.62, -11.49, 90.35)
10:75849902		R>H	A:433	(-18.62, -11.49, 90.35)
10:75849905		S>Y	A:434	(-14.71, -14.03, 86.97)
10:75849913		E>K	A:437	(-16.51, -18.30, 86.64)
10:75849916	rs150016624	I>L	A:438	(-11.72, -18.91, 86.42)
10:75849938		L>S	A:445	(-8.87, -29.54, 84.04)
10:75849950		R>L	A:449	(-4.71, -32.58, 83.65)
10:75854031		G>V	A:452	(-7.88, -39.05, 82.62)
10:75854052		A>G	A:459	(-10.20, -31.13, 78.07)
10:75854066	rs200710859	K>E	A:464	(-9.34, -22.91, 74.93)
10:75854070		Q>P	A:465	(-13.76, -23.10, 79.03)
10:75854078		T>A	A:468	(-10.47, -17.92, 76.92)
10:75854079	rs147957747	T>M	A:468	(-10.47, -17.92, 76.92)
10:75854100		T>N	A:475	(-9.62, -7.36, 79.36)
10:75854103		K>R	A:476	(-12.69, -7.99, 82.95)
10:75854109		N>S	A:478	(-6.35, -4.03, 81.46)
10:75854111	rs369055603	R>W	A:479	(-10.98, -2.24, 79.93)
10:75854152		H>Q	A:492	(-0.29, 18.51, 70.25)
10:75854166	rs572757800	I>T	A:497	(-5.74, 25.32, 72.10)
10:75854178		Q>R	A:501	(-12.19, 26.37, 72.37)
10:75854180	COSM1675359	R>W	A:502	(-13.56, 20.43, 71.47)
10:75854181	rs201808867	R>Q	A:502	(-13.56, 20.43, 71.47)
10:75854187		I>T	A:504	(-14.92, 26.92, 75.97)
10:75854210		R>C	A:512	(-13.78, 11.09, 79.49)
10:75855425	rs141033098	I>L	A:519	(-7.09, 24.74, 80.28)
10:75855429		R>L	A:520	(-6.04, 21.35, 84.40)
10:75855445	rs548487697	E>D	A:525	(3.98, 24.31, 80.42)
10:75855453		R>H	A:528	(6.08, 24.00, 83.96)
10:75855477	rs200624351	P>H	A:536	(7.96, 41.89, 85.60)
10:75855483	rs566596830	R>Q	A:538	(8.88, 35.20, 87.52)
10:75855490	rs533622785	D>E	A:540	(2.83, 39.43, 83.14)
10:75855491	rs370229150	L>V	A:541	(3.05, 34.73, 82.45)
10:75855495		L>P	A:542	(2.16, 33.95, 86.94)
10:75855510	COSM920479	R>Q	A:547	(-7.76, 36.32, 84.89)
10:75855560	rs374538684	G>W	A:564	(-25.01, 26.94, 79.49)
10:75855588		A>G	A:573	(-15.91, 32.64, 77.28)
10:75855591	rs574643494	S>F	A:574	(-14.68, 35.84, 75.65)
10:75856974	COSM4144862	R>W	A:586	(2.65, 36.50, 76.99)
10:75856975		R>Q	A:586	(2.65, 36.50, 76.99)
10:75856983	rs187247459	E>K	A:589	(8.17, 35.35, 73.26)
10:75857011		V>A	A:598	(19.67, 26.63, 78.29)
10:75857034		I>V	A:606	(30.88, 17.12, 80.01)
10:75857059		T>M	A:614	(41.92, 13.24, 84.38)
10:75857062	rs148669762	A>V	A:615	(43.37, 14.87, 87.63)
10:75857074		A>V	A:619	(45.66, 17.72, 92.87)
10:75857079	rs374309823	N>D	A:621	(41.14, 21.31, 96.43)
10:75857081		N>K	A:621	(41.14, 21.31, 96.43)
10:75857083	COSM3867828	R>K	A:622	(41.84, 14.61, 93.72)
10:75857089		E>V	A:624	(37.41, 19.11, 97.33)
10:75860721		A>T	A:630	(29.24, 16.73, 89.19)
10:75860734		E>A	A:634	(24.20, 16.09, 87.92)
10:75860740	rs71579374	H>R	A:636	(23.37, 22.16, 82.18)
10:75860748		K>Q	A:639	(19.29, 22.98, 83.66)
10:75860754		G>S	A:641	(15.34, 18.90, 79.69)
10:75860761	rs150643310	T>M	A:643	(14.03, 23.55, 78.24)
10:75860766		E>K	A:645	(10.18, 18.46, 78.67)
10:75860770		K>T	A:646	(9.47, 23.96, 78.50)
10:75860773	rs534449109	A>V	A:647	(9.49, 22.72, 73.35)
10:75860784		G>S	A:651	(5.54, 24.14, 70.13)
10:75860802		T>A	A:657	(9.12, 15.94, 67.24)
10:75860803		T>I	A:657	(9.12, 15.94, 67.24)
10:75860806	rs372691803	V>A	A:658	(6.78, 15.47, 71.11)
10:75860826		V>L	A:665	(14.57, 14.04, 77.99)
10:75863585		S>L	A:677	(30.14, 7.22, 87.60)
10:75863590	rs375392559	A>S	A:679	(34.00, 10.04, 86.19)
10:75863593		R>C	A:680	(32.78, 9.72, 91.30)
10:75863601	rs565398652	L>F	A:682	(38.93, 8.18, 86.19)
10:75863657		Q>P	A:701	(26.42, 7.61, 74.85)
10:75864818		D>G	A:714	(16.40, 24.49, 67.10)
10:75864859	rs144717954	E>K	A:728	(17.96, 41.27, 69.41)
10:75864883		K>E	A:736	(26.49, 42.03, 77.95)
10:75864896		A>V	A:740	(33.05, 45.86, 79.69)
10:75864914		P>H	A:746	(38.59, 41.61, 80.33)
10:75864918		Q>H	A:747	(35.57, 38.47, 83.10)
10:75864945		I>M	A:756	(28.63, 36.53, 70.01)
10:75864962	rs540039788	R>Q	A:762	(22.55, 28.14, 67.77)
10:75864982	rs566257885	R>G	A:769	(18.23, 22.24, 59.83)
10:75865015		R>C	A:780	(20.31, 23.92, 48.46)
10:75865030		A>T	A:785	(25.84, 32.14, 50.66)
10:75865042		E>K	A:789	(29.57, 35.44, 53.51)
10:75865048	rs552164143	S>R	A:791	(31.86, 32.03, 58.39)
10:75865055		T>N	A:793	(32.17, 37.04, 60.39)
10:75865063		P>S	A:796	(37.88, 37.68, 62.78)
10:75865070		V>A	A:798	(37.57, 35.60, 67.95)
10:75865078		A>T	A:801	(38.39, 39.72, 71.39)
10:75865091		A>V	A:805	(41.98, 41.50, 76.64)
10:75865105	COSM1232239	D>N	A:810	(43.43, 50.50, 73.67)
10:75865109	rs568363284	P>R	A:811	(41.66, 52.76, 71.88)
10:75866991		L>P	A:813	(42.15, 47.13, 70.37)
10:75866997	rs373010557	K>R	A:815	(37.65, 50.77, 68.21)
10:75866998		K>N	A:815	(37.65, 50.77, 68.21)
10:75867017		Y>H	A:822	(28.51, 46.30, 64.85)
10:75867020		R>W	A:823	(32.34, 43.20, 59.66)
10:75867021		R>Q	A:823	(32.34, 43.20, 59.66)
10:75867025	rs140381835	I>M	A:824	(28.75, 39.04, 62.88)
10:75867054		A>G	A:834	(17.28, 33.53, 52.77)
10:75867068		E>K	A:839	(7.58, 39.80, 47.39)
10:75867074	rs150385900	D>H	A:841	(4.24, 37.59, 41.62)
10:75867081		P>L	A:843	(-1.40, 37.12, 37.02)
10:75868799	rs570362710	P>L	A:877	(-16.42, 34.33, 41.56)
10:75868888		D>Y	A:907	(-15.85, 21.86, 61.82)
10:75868897	rs375595550	R>G	A:910	(-17.33, 25.09, 57.04)
10:75873961	rs150595117	A>V	A:922	(-13.20, 14.73, 50.30)
10:75873967		K>R	A:924	(-16.38, 19.65, 52.79)
10:75873999		R>W	A:935	(-27.73, 9.17, 61.90)
10:75874018		S>I	A:941	(-34.86, 0.17, 59.42)
10:75874059		A>T	A:955	(-13.33, 4.33, 51.07)
10:75874083		R>W	A:963	(-5.14, 10.66, 44.32)
10:75874106		K>N	A:970	(6.59, 13.57, 45.13)
10:75874625	rs397517241 COSM920489	R>W	A:1008	(-30.60, -10.37, 65.77)
10:75874626		R>Q	A:1008	(-30.60, -10.37, 65.77)
10:75877789	rs149300310	E>D	A:1021	(-16.55, -0.74, 71.45)
10:75877827		V>A	A:1034	(-8.41, 13.64, 57.30)
10:75877841		R>W	A:1039	(-3.75, 21.21, 59.90)
10:75877862		I>V	A:1046	(4.05, 27.37, 51.01)
10:75877895	rs373317423 CM103198	R>C	A:1057	(-5.37, 26.83, 44.05)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
10:75830800	COSM4495670	T>I	A:153	(36.43, -14.29, 84.65)
10:75849787	COSM1675358	L>F	A:395	(-3.54, -24.85, 80.08)
10:75849877	COSM1702650	P>S	A:425	(-18.20, -0.67, 92.94)
10:75849923	COSM3375537	A>D	A:440	(-13.67, -23.93, 88.80)
10:75849943	COSM1193357	D>H	A:447	(-9.68, -34.35, 88.87)
10:75854036	COSM1603734	G>R	A:454	(-7.72, -36.17, 78.20)
10:75855510	COSM920479	R>Q	A:547	(-7.76, 36.32, 84.89)
10:75874605	COSM1964854	V>A	A:1001	(-19.52, -7.38, 61.18)
10:75874610	COSM1169337	A>T	A:1003	(-24.52, -5.87, 59.20)

1TR2.A | VCL.

1TR2.A | VCL

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