1KFX.L | CAPN2

General Structure Information

PDB ID	1kfx
HGNC Gene Label(s)	CAPN2
Structure Name	crystal structure of human m-calpain form i
Resolution	3.15Å
Reference	AUTH S.STROBL,C.FERNANDEZ-CATALAN,M.BRAUN,R.HUBER,H.MASUMOTO,AUTH 2 K.NAKAGAWA,A.IRIE,H.SORIMACHI,G.BOURENKOW,H.BARTUNIK,AUTH 3 K.SUZUKI,W.BODETITL THE CRYSTAL STRUCTURE OF CALCIUM-FREE HUMAN M-CALPAINTITL 2 SUGGESTS AN ELECTROSTATIC SWITCH MECHANISM FOR ACTIVATION BYTITL 3 CALCIUM.REF PROC.NATL.ACAD.SCI.USA V. 97 588 2000REFN ISSN 0027-8424PMID 10639123DOI 10.1073/PNAS.97.2.588

Variant Set Distributions

ExAC Variants

Number Of Residues	640
Number Of SNVs	188
Number Of Permutations	58317
Optimal Distance Threshold	15.0
K Statistic	0.071
p-value	0.689

COSMIC

Number Of Residues	640
Number Of SNVs	12
Number Of Permutations	5960
Optimal Distance Threshold	5.0
K Statistic	0.015
p-value	0.579

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	188
Number Of COSMIC SNVs	13
Optimal Distance Threshold	5.0
K Statistic	0.01
p-value	0.92

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
1:223900347		A>V	L:2	(5.79, -20.63, 8.81)
1:223900358	rs375899944	A>T	L:6	(2.25, -19.48, 13.00)
1:223900383		A>V	L:14	(-0.13, -14.95, 23.65)
1:223900388		E>K	L:16	(-3.32, -18.76, 27.16)
1:223900404		H>R	L:21	(8.31, -12.69, 34.00)
1:223900406		D>N	L:22	(4.86, -15.26, 34.43)
1:223900408	rs25655	D>E	L:22	(4.86, -15.26, 34.43)
1:223900410	rs549923241	R>M	L:23	(3.27, -18.66, 29.34)
1:223900412	rs571626275	A>S	L:24	(8.44, -16.72, 28.78)
1:223900421		Y>H	L:27	(16.33, -17.19, 21.36)
1:223900425		L>P	L:28	(16.44, -20.62, 19.52)
1:223900436	rs369686010	Y>H	L:32	(18.05, -24.24, 32.71)
1:223900437		Y>C	L:32	(18.05, -24.24, 32.71)
1:223900439		E>K	L:33	(13.99, -27.11, 32.85)
1:223900443	rs139934619	A>E	L:34	(16.13, -29.78, 29.83)
1:223900449		R>Q	L:36	(19.44, -28.02, 34.46)
1:223900458		C>Y	L:39	(23.94, -32.27, 30.84)
1:223900461		L>P	L:40	(23.58, -33.26, 34.98)
1:223900469		G>R	L:43	(28.26, -35.74, 32.11)
1:223900488		P>R	L:49	(24.15, -25.29, 19.55)
1:223900509	rs576417116	S>L	L:56	(30.82, -15.96, 15.13)
1:223900533	rs202121109	G>A	L:64	(36.11, -10.27, 13.57)
1:223900542		S>F	L:67	(40.63, -9.70, 13.46)
1:223900544	rs2230083	S>G	L:68	(43.48, -9.08, 15.68)
1:223900551		T>I	L:70	(39.17, -11.75, 17.72)
1:223900553		R>W	L:71	(44.04, -13.08, 15.05)
1:223900556		G>S	L:72	(43.30, -15.47, 19.98)
1:223900557	rs150166660	G>D	L:72	(43.30, -15.47, 19.98)
1:223900562	rs142691066	E>K	L:74	(42.87, -18.33, 25.94)
1:223905471		C>Y	L:82	(38.80, -18.90, 39.78)
1:223905473	rs146935874	A>T	L:83	(37.84, -20.75, 42.41)
1:223905492	rs200558564	I>T	L:89	(27.11, -13.03, 46.21)
1:223905495		G>V	L:90	(24.00, -10.68, 47.25)
1:223905501		A>D	L:92	(26.13, -4.79, 47.67)
1:223905506	rs144316024	R>C	L:94	(31.23, -0.99, 46.41)
1:223905507	COSM904426	R>H	L:94	(31.23, -0.99, 46.41)
1:223905509		T>A	L:95	(29.33, -2.64, 41.75)
1:223905512		D>Y	L:96	(33.43, -4.80, 41.33)
1:223905515		I>V	L:97	(31.06, -3.71, 37.05)
1:223905519	rs573090048	C>Y	L:98	(34.37, -4.26, 34.72)
1:223905523		Q>H	L:99	(34.09, -4.07, 30.20)
1:223905527	rs371602613	A>P	L:101	(39.03, -4.66, 26.07)
1:223905533		G>S	L:103	(34.12, -4.14, 25.47)
1:223931805		D>G	L:104	(30.95, -1.22, 25.22)
1:223931817		L>P	L:108	(29.34, -0.95, 32.85)
1:223931825		I>V	L:111	(24.68, -4.33, 34.74)
1:223931853		I>T	L:120	(14.95, -4.89, 39.16)
1:223931858		A>T	L:122	(14.76, -10.87, 39.60)
1:223931862	rs369599821	R>Q	L:123	(11.30, -9.29, 36.31)
1:223931867	rs375820403	V>I	L:125	(18.93, -12.86, 36.89)
1:223931882	rs563242004	S>C	L:130	(25.13, -22.58, 41.08)
1:223931894		N>D	L:134	(22.24, -28.94, 39.47)
1:223933020	rs12122278	G>S	L:147	(6.50, -6.72, 24.68)
1:223933023	rs546379947 COSM1185749	E>K	L:148	(6.99, -10.43, 23.94)
1:223933035		V>M	L:152	(18.23, -16.80, 26.86)
1:223933059		T>P	L:160	(39.69, -15.30, 27.72)
1:223933068	rs552650859	G>R	L:163	(42.93, -14.75, 31.83)
1:223933078		L>H	L:166	(38.07, -9.65, 26.52)
1:223933093		A>D	L:171	(37.26, -6.84, 39.81)
1:223933095		E>K	L:172	(36.62, -9.27, 44.02)
1:223933116	COSM1199520	A>T	L:179	(29.41, -12.17, 31.99)
1:223933131	rs147235023	A>T	L:184	(23.11, -13.56, 26.61)
1:223933135		Y>C	L:185	(21.39, -8.31, 25.26)
1:223933138		A>V	L:186	(24.72, -11.23, 22.65)
1:223934706	rs541384226	G>R	L:190	(23.72, -12.37, 17.70)
1:223934707		G>E	L:190	(23.72, -12.37, 17.70)
1:223934716		E>V	L:193	(30.31, -6.48, 16.79)
1:223934722		L>R	L:195	(26.36, -5.25, 22.29)
1:223934731	COSM532758	G>V	L:198	(24.01, 1.03, 22.61)
1:223934733		A>T	L:199	(21.46, 2.47, 24.58)
1:223934739		T>P	L:201	(18.17, 3.94, 26.84)
1:223934740		T>S	L:201	(18.17, 3.94, 26.84)
1:223934751	COSM210115	E>K	L:205	(13.54, -0.50, 27.82)
1:223934763		G>R	L:209	(10.17, -2.99, 30.62)
1:223934767		G>V	L:210	(10.26, -0.18, 30.73)
1:223934772		A>S	L:212	(13.07, 5.36, 28.50)
1:223934794	rs147824152	K>R	L:219	(19.27, 23.00, 26.56)
1:223934802		P>T	L:222	(9.90, 23.81, 32.85)
1:223934813		F>L	L:225	(12.69, 19.63, 40.80)
1:223934818		I>T	L:227	(9.05, 14.95, 37.14)
1:223934829		A>P	L:231	(10.09, 9.61, 39.59)
1:223934842		G>D	L:235	(10.30, 3.82, 41.04)
1:223934865		D>N	L:243	(31.62, 15.29, 28.78)
1:223938604		G>R	L:276	(14.73, 31.82, 52.87)
1:223938625	rs149096348	R>C	L:283	(19.58, 11.24, 47.61)
1:223938626		R>H	L:283	(19.58, 11.24, 47.61)
1:223938644		G>V	L:289	(30.84, 4.06, 46.29)
1:223938665	rs146546882	R>Q	L:296	(25.31, 20.93, 49.80)
1:223940509		S>N	L:329	(24.75, 23.62, 40.45)
1:223940521		R>K	L:333	(28.72, 21.42, 37.51)
1:223940524	rs146147085	H>L	L:334	(25.76, 16.10, 36.01)
1:223940527		Y>S	L:335	(25.78, 15.75, 28.55)
1:223940530		S>F	L:336	(22.79, 13.14, 30.79)
1:223940532	rs142874360	R>C	L:337	(17.36, 12.85, 33.74)
1:223940533	rs139659399	R>H	L:337	(17.36, 12.85, 33.74)
1:223940565		L>V	L:348	(5.02, -8.62, 42.86)
1:223940587		K>R	L:355	(0.89, 2.62, 41.19)
1:223940606		M>I	L:361	(-1.81, -2.64, 21.57)
1:223940622	COSM309846	R>W	L:367	(5.50, -2.15, -0.15)
1:223940623	rs374476504	R>Q	L:367	(5.50, -2.15, -0.15)
1:223940637	rs199728877	G>R	L:372	(1.87, 5.66, 5.32)
1:223943185		T>I	L:380	(-1.41, 7.10, 3.02)
1:223943200	rs201781579	P>L	L:385	(-2.44, 1.75, 12.23)
1:223943209		L>R	L:388	(-9.35, 4.29, 21.38)
1:223943220		E>K	L:392	(-11.51, 7.21, 33.08)
1:223943260		C>Y	L:405	(-4.77, 12.54, 32.50)
1:223943263		T>I	L:406	(-0.92, 12.21, 32.90)
1:223943274		G>R	L:410	(5.46, 4.62, 22.92)
1:223943277		L>F	L:411	(6.43, 4.01, 18.67)
1:223943281		I>T	L:412	(9.33, 0.26, 20.22)
1:223943293		R>Q	L:416	(13.97, -4.45, 10.55)
1:223943295	COSM904432	R>W	L:417	(15.78, -10.78, 8.14)
1:223943296	rs148370103	R>Q	L:417	(15.78, -10.78, 8.14)
1:223943301		Q>E	L:419	(18.27, -4.35, 12.04)
1:223943320		D>V	L:425	(19.53, -0.55, 9.96)
1:223943321	rs371353695	D>E	L:425	(19.53, -0.55, 9.96)
1:223943325		H>Y	L:427	(12.42, 2.25, 9.96)
1:223943326		H>R	L:427	(12.42, 2.25, 9.96)
1:223943328		T>A	L:428	(11.90, 7.47, 10.65)
1:223943332		I>T	L:429	(9.36, 6.05, 14.11)
1:223943334		G>S	L:430	(6.11, 8.36, 14.65)
1:223943335		G>D	L:430	(6.11, 8.36, 14.65)
1:223946985	rs376104085	T>N	L:444	(-14.67, 1.71, 17.08)
1:223947006	rs538158979	N>I	L:451	(-12.69, 13.24, 5.53)
1:223947018		T>M	L:455	(-10.58, 17.52, 8.83)
1:223947021		N>S	L:456	(-9.56, 16.94, 12.37)
1:223947023		R>C	L:457	(-3.12, 19.96, 12.15)
1:223947026	rs370722848	A>T	L:458	(-4.48, 17.66, 15.54)
1:223947036	rs148169772	R>H	L:461	(1.14, 15.32, 15.59)
1:223947054		N>S	L:467	(16.85, 7.32, 13.07)
1:223947056		L>V	L:468	(15.07, 6.07, 17.35)
1:223947059		R>W	L:469	(14.72, 0.68, 20.16)
1:223947060	rs143885626	R>Q	L:469	(14.72, 0.68, 20.16)
1:223947068		L>F	L:472	(9.11, 8.77, 24.49)
1:223947074		R>C	L:474	(5.75, 13.18, 29.94)
1:223947075	COSM904434	R>H	L:474	(5.75, 13.18, 29.94)
1:223947081	rs9804140	K>R	L:476	(0.31, 16.55, 30.13)
1:223947095	rs148678361	E>Q	L:481	(-12.52, 10.02, 22.90)
1:223947096	rs151234089	E>G	L:481	(-12.52, 10.02, 22.90)
1:223947101		I>L	L:483	(-7.24, 8.86, 18.16)
1:223947102		I>T	L:483	(-7.24, 8.86, 18.16)
1:223947107	COSM1199519	V>M	L:485	(-1.57, 7.48, 13.80)
1:223947116	rs144006318	T>P	L:488	(6.70, 5.57, 9.11)
1:223947122	COSM3418806	E>K	L:490	(9.16, 7.88, 3.86)
1:223947152		R>W	L:500	(5.11, 0.48, 25.83)
1:223947153	rs201053061	R>Q	L:500	(5.11, 0.48, 25.83)
1:223949290	rs369320951 COSM279558	D>N	L:513	(-10.06, -1.21, 12.28)
1:223949309	rs192016088	N>S	L:519	(-23.07, -7.35, 3.24)
1:223949317		E>K	L:522	(-28.36, -13.51, -2.15)
1:223949319		E>D	L:522	(-28.36, -13.51, -2.15)
1:223949897		S>C	L:526	(-35.96, -18.95, -10.12)
1:223949900	rs145816861	E>K	L:527	(-35.62, -20.36, -14.18)
1:223949909	rs556721976	I>V	L:530	(-34.19, -13.77, -17.82)
1:223949910	rs369150450	I>T	L:530	(-34.19, -13.77, -17.82)
1:223949929		R>S	L:536	(-32.02, -13.81, -27.66)
1:223949936	rs372646959	A>P	L:539	(-27.29, -21.22, -24.81)
1:223951856		A>V	L:546	(-26.13, -25.53, -22.27)
1:223951862		I>S	L:548	(-20.72, -22.90, -18.88)
1:223951871		F>C	L:551	(-11.65, -24.88, -18.77)
1:223951880		Q>L	L:554	(-11.08, -18.80, -19.94)
1:223951883		T>S	L:555	(-13.22, -18.74, -23.79)
1:223951889		L>P	L:557	(-15.77, -13.98, -20.19)
1:223951903		A>T	L:562	(-14.21, -4.37, -26.75)
1:223954080	rs17599	K>Q	L:568	(-1.72, -4.34, -19.87)
1:223954081		K>R	L:568	(-1.72, -4.34, -19.87)
1:223954087		D>G	L:570	(-6.43, -10.89, -21.50)
1:223954094		F>L	L:572	(-11.02, -12.75, -16.29)
1:223954098		I>V	L:574	(-8.51, -20.79, -15.41)
1:223954101		E>K	L:575	(-6.57, -19.72, -11.99)
1:223954102	rs200417819	E>V	L:575	(-6.57, -19.72, -11.99)
1:223954104		T>A	L:576	(-10.59, -16.67, -11.94)
1:223957549		G>R	L:588	(-21.09, -30.86, -8.06)
1:223957550		G>E	L:588	(-21.09, -30.86, -8.06)
1:223957582		I>V	L:599	(-25.42, -14.37, -10.49)
1:223957583		I>T	L:599	(-25.42, -14.37, -10.49)
1:223957586	rs192780261	L>P	L:600	(-21.06, -14.29, -12.84)
1:223957592		T>M	L:602	(-24.48, -9.31, -12.70)
1:223957598		I>T	L:604	(-18.64, -9.36, -13.56)
1:223957600		Q>K	L:605	(-21.38, -5.96, -15.37)
1:223958159	rs566818883	R>Q	L:612	(-11.93, 1.14, -15.75)
1:223958167	rs144592508	D>N	L:615	(-8.22, 2.75, -13.93)
1:223958170		V>I	L:616	(-9.08, 7.40, -13.90)
1:223958179		S>P	L:619	(-4.12, 1.07, -16.95)
1:223958183		G>D	L:620	(-5.13, -1.75, -15.87)
1:223958205		M>I	L:627	(-8.43, -3.07, -2.91)
1:223958206	COSM904436	R>W	L:628	(-9.28, -0.45, 3.19)
1:223958207	rs148485450	R>Q	L:628	(-9.28, -0.45, 3.19)
1:223958213	rs372461819	A>V	L:630	(-13.00, -1.29, -3.23)
1:223958222	rs199643396	E>A	L:633	(-17.54, 0.06, -3.93)
1:223959516		K>E	L:637	(-15.83, -3.38, 5.71)
1:223959523		P>L	L:639	(-9.45, -5.79, 9.55)
1:223959534		H>Y	L:643	(-7.01, -5.08, 3.98)
1:223959538		Q>P	L:644	(-1.85, -6.72, 5.45)
1:223959543	rs146423555	I>V	L:646	(-5.80, -8.65, 0.09)
1:223959546		V>L	L:647	(-1.66, -6.48, -0.92)
1:223959547	rs531849554	V>A	L:647	(-1.66, -6.48, -0.92)
1:223959552	rs143262618	R>W	L:649	(-1.95, -14.02, -3.13)
1:223959553		R>Q	L:649	(-1.95, -14.02, -3.13)
1:223959561		D>N	L:652	(3.04, -5.99, -8.64)
1:223959570	rs200435825	L>F	L:655	(2.22, -1.86, -5.05)
1:223959583		F>C	L:659	(-10.38, -6.39, -13.51)
1:223959598	rs150465838	R>Q	L:664	(-8.28, -15.36, -7.87)
1:223959609		R>W	L:668	(-10.40, -17.17, -2.75)
1:223959622	rs139047155	L>P	L:672	(-13.93, -18.56, 1.50)
1:223959889		F>S	L:676	(-17.26, -19.30, 8.32)
1:223959891	rs2230082	K>Q	L:677	(-22.59, -17.55, 7.01)
1:223959895		Q>P	L:678	(-23.47, -21.25, 4.79)
1:223959897		L>M	L:679	(-20.13, -24.51, 8.04)
1:223959906	rs200476814	E>K	L:682	(-26.39, -21.47, 15.03)
1:223959913	rs201100784	T>S	L:684	(-20.76, -19.42, 17.04)
1:223959919		T>K	L:686	(-16.32, -21.00, 15.46)
1:223959922		I>T	L:687	(-15.69, -23.24, 11.16)
1:223962539		L>F	L:695	(-7.15, -31.00, 3.57)
1:223962549	rs148122411	S>L	L:698	(-7.65, -25.92, 1.95)
1:223962552	rs184347397	V>A	L:699	(-7.73, -26.93, -2.16)

1KFX.L | CAPN2.

1KFX.L | CAPN2

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
1:223900400	COSM1247321	S>P	L:20	(4.49, -13.34, 30.39)
1:223900408	COSM4143383	D>E	L:22	(4.86, -15.26, 34.43)
1:223905507	COSM904426	R>H	L:94	(31.23, -0.99, 46.41)
1:223933116	COSM1199520	A>T	L:179	(29.41, -12.17, 31.99)
1:223938632	COSM1199522	R>Q	L:285	(24.09, 5.77, 44.84)
1:223940540	COSM3376991	E>D	L:339	(13.24, 9.51, 33.87)
1:223940622	COSM309846	R>W	L:367	(5.50, -2.15, -0.15)
1:223940635	COSM1162867	A>V	L:371	(2.18, 2.20, 4.73)
1:223949290	COSM279558	D>N	L:513	(-10.06, -1.21, 12.28)
1:223951889	COSM4669148	L>P	L:557	(-15.77, -13.98, -20.19)
1:223954080	COSM146791	K>Q	L:568	(-1.72, -4.34, -19.87)
1:223957548	COSM4565131	DG>DK	L:587	(-24.48, -29.31, -8.37)
1:223958164	COSM1601699	I>L	L:614	(-10.90, 4.07, -9.51)