3EH2.C | SEC24C

General Structure Information

PDB ID	3eh2
HGNC Gene Label(s)	SEC24C
Structure Name	crystal structure of the human copii-coat protein sec24c
Resolution	2.35Å
Reference	AUTH J.D.MANCIAS,J.GOLDBERGTITL STRUCTURAL BASIS OF CARGO MEMBRANE PROTEINTITL 2 DISCRIMINATION BY THE HUMAN COPII COAT MACHINERY.REF EMBO J. V. 27 2918 2008REFN ISSN 0261-4189PMID 18843296DOI 10.1038/EMBOJ.2008.208

Variant Set Distributions

ExAC Variants

Number Of Residues	739
Number Of SNVs	163
Number Of Permutations	70694
Optimal Distance Threshold	21.0
K Statistic	0.162
p-value	0.173

COSMIC

Number Of Residues	739
Number Of SNVs	8
Number Of Permutations	3217
Optimal Distance Threshold	37.0
K Statistic	0.25
p-value	0.151

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	163
Number Of COSMIC SNVs	7
Optimal Distance Threshold	41.0
K Statistic	-0.311
p-value	0.235

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
10:75523252		Q>R	C:4	(-18.81, -29.89, 46.59)
10:75523258	rs368640437	I>T	C:6	(-16.85, -35.10, 43.77)
10:75523275		N>Y	C:12	(-14.71, -40.88, 52.06)
10:75523279	rs372903334 COSM126064	R>Q	C:13	(-15.44, -43.45, 47.23)
10:75523281	rs376499962	G>S	C:14	(-9.30, -42.00, 49.37)
10:75523282	rs201403781	G>D	C:14	(-9.30, -42.00, 49.37)
10:75523285	rs139950165	T>I	C:15	(-7.61, -42.12, 52.87)
10:75523288		E>G	C:16	(-6.18, -45.93, 50.93)
10:75523317		V>L	C:26	(-6.29, -41.81, 37.38)
10:75523623		S>N	C:43	(4.21, -38.57, 41.77)
10:75523628		R>G	C:45	(2.53, -35.02, 45.22)
10:75523629		R>Q	C:45	(2.53, -35.02, 45.22)
10:75523634	rs35528438	I>V	C:47	(3.76, -35.54, 36.52)
10:75523658		P>S	C:55	(-5.48, -41.41, 21.84)
10:75523662		C>F	C:56	(-3.67, -44.65, 19.21)
10:75523665		T>I	C:57	(-5.05, -42.38, 16.11)
10:75523672	rs375942607	D>E	C:59	(-7.65, -39.30, 12.95)
10:75523674	rs151207669	M>T	C:60	(-9.33, -41.10, 18.21)
10:75523681	COSM920377	K>N	C:62	(-8.07, -34.25, 15.12)
10:75523691	rs528745330	V>M	C:66	(-9.26, -34.56, 24.56)
10:75523715		P>S	C:74	(9.93, -30.41, 38.41)
10:75523716		P>L	C:74	(9.93, -30.41, 38.41)
10:75523736		E>Q	C:81	(5.43, -38.95, 55.16)
10:75523737	rs374994100	E>V	C:81	(5.43, -38.95, 55.16)
10:75525216	rs181032721	P>L	C:85	(14.45, -37.73, 44.94)
10:75525249	rs548423646	L>W	C:96	(23.40, -45.19, 30.91)
10:75525261		R>H	C:100	(18.93, -43.68, 18.18)
10:75525277	rs369857370	M>I	C:105	(18.45, -45.99, 32.33)
10:75525282		P>L	C:107	(12.20, -48.04, 34.95)
10:75525300		E>A	C:113	(21.08, -60.45, 25.10)
10:75525302		G>R	C:114	(21.32, -61.43, 30.31)
10:75525306		G>E	C:115	(22.16, -58.12, 30.48)
10:75525308	rs372521067	R>G	C:116	(24.87, -58.69, 26.03)
10:75525311	rs571535869 COSM1675353	R>C	C:117	(22.80, -56.00, 24.07)
10:75525339		I>T	C:126	(19.62, -52.63, 20.94)
10:75525342		N>S	C:127	(21.88, -49.90, 23.88)
10:75525563		P>S	C:131	(31.37, -53.31, 31.97)
10:75525567		Q>P	C:132	(31.97, -50.35, 35.40)
10:75525569		Y>D	C:133	(24.98, -50.48, 35.21)
10:75525593		G>S	C:141	(14.17, -59.55, 32.94)
10:75525597		K>R	C:142	(13.49, -57.33, 37.16)
10:75525630		S>F	C:153	(12.86, -48.90, 40.54)
10:75525639		S>C	C:156	(11.58, -40.39, 40.39)
10:75525653		A>S	C:161	(26.51, -34.06, 36.21)
10:75525654		A>V	C:161	(26.51, -34.06, 36.21)
10:75525660	rs377689283	V>A	C:163	(31.92, -31.51, 32.48)
10:75525847		N>D	C:169	(33.24, -28.32, 29.82)
10:75525855	rs200672501	F>L	C:171	(32.01, -29.06, 37.10)
10:75525861	rs200016285	S>R	C:173	(30.01, -21.77, 40.76)
10:75525863		P>L	C:174	(28.50, -21.16, 44.01)
10:75525869	rs141567992	A>V	C:176	(23.94, -15.40, 44.07)
10:75525911		T>I	C:190	(5.78, 3.58, 53.04)
10:75525919	rs368096920	V>L	C:193	(13.37, 1.21, 52.46)
10:75525924	rs200985881	R>S	C:194	(13.98, 1.42, 58.40)
10:75525932	rs375272522	C>S	C:197	(16.58, -3.01, 55.78)
10:75525950		L>Q	C:203	(15.96, -13.30, 55.86)
10:75525959		F>S	C:206	(17.53, -18.32, 58.02)
10:75526116		G>E	C:212	(24.77, -29.89, 55.75)
10:75526122		E>G	C:214	(27.01, -26.58, 58.84)
10:75526133	rs372652234	I>L	C:218	(23.93, -18.41, 48.39)
10:75526136	rs554903997	R>C	C:219	(28.52, -14.87, 47.08)
10:75526137	rs144210286	R>H	C:219	(28.52, -14.87, 47.08)
10:75526139	COSM4015789	V>I	C:220	(24.72, -11.41, 49.25)
10:75526157	rs369206859	N>D	C:226	(16.12, 6.68, 41.96)
10:75526174	COSM164239	F>L	C:231	(26.41, -0.70, 42.54)
10:75526234		D>E	C:251	(26.73, 2.19, 29.01)
10:75526271	rs377675100	V>I	C:264	(26.30, -13.43, 55.24)
10:75526275		N>S	C:265	(28.71, -15.64, 57.83)
10:75526283	rs148361947	R>W	C:268	(26.65, -10.90, 60.10)
10:75526295		T>P	C:272	(24.31, -4.66, 59.86)
10:75526529	rs141508840	Q>R	C:277	(23.64, 3.97, 55.87)
10:75526538		E>A	C:280	(18.33, 7.42, 57.78)
10:75526562		T>K	C:288	(9.49, 10.79, 41.73)
10:75526585		I>V	C:296	(17.60, -6.15, 35.74)
10:75526591	rs376045280	A>S	C:298	(23.24, -4.56, 37.03)
10:75526603		A>T	C:302	(27.26, -8.85, 38.28)
10:75526821		C>R	C:308	(27.85, -16.81, 38.96)
10:75526861		I>T	C:321	(8.79, 8.01, 34.37)
10:75526876		G>E	C:326	(12.54, 1.51, 29.44)
10:75526881		L>V	C:328	(6.90, 2.84, 30.28)
10:75526893		D>N	C:332	(-4.70, 2.45, 30.65)
10:75526900	COSM1225080	R>M	C:334	(-10.71, 1.60, 30.55)
10:75526903		K>R	C:335	(-11.92, 3.47, 25.22)
10:75526911		N>D	C:338	(-14.70, -5.33, 23.54)
10:75526912		N>S	C:338	(-14.70, -5.33, 23.54)
10:75526919	rs145369251	D>E	C:340	(-9.04, -5.78, 17.78)
10:75526920		K>Q	C:341	(-6.17, -1.95, 20.06)
10:75527601		F>L	C:346	(-2.63, -8.10, 28.65)
10:75527614	rs564682376	T>I	C:350	(9.92, -1.38, 25.34)
10:75527623	rs142679640	Y>C	C:353	(11.29, -4.54, 29.29)
10:75527676	COSM3440494	L>F	C:371	(5.29, -4.59, 42.51)
10:75527703		A>T	C:380	(2.78, -6.50, 31.86)
10:75527710		L>H	C:382	(7.40, -4.02, 35.00)
10:75527713		S>C	C:383	(6.36, -8.93, 34.61)
10:75527746		Y>C	C:394	(5.86, -11.81, 45.21)
10:75528568	rs376707409	V>L	C:401	(3.46, -0.89, 57.26)
10:75528586	rs555997918	R>W	C:407	(0.50, -9.72, 51.45)
10:75528587		R>Q	C:407	(0.50, -9.72, 51.45)
10:75528591		F>L	C:408	(6.95, -8.05, 52.24)
10:75528601		L>V	C:412	(10.76, -11.84, 51.59)
10:75528605	rs35875855	R>H	C:413	(10.59, -14.36, 56.43)
10:75528607		R>C	C:414	(7.81, -19.57, 50.73)
10:75528613		V>I	C:416	(15.09, -16.04, 50.53)
10:75528626		V>A	C:420	(16.09, -22.94, 44.54)
10:75528770		R>C	C:435	(7.33, -35.16, 18.64)
10:75528797		Y>H	C:444	(13.85, -17.71, 26.23)
10:75528800	rs201538148	M>V	C:445	(11.15, -21.77, 24.59)
10:75528810	rs375292598	T>M	C:448	(10.28, -27.13, 20.04)
10:75528818	rs139460623	V>M	C:451	(12.47, -25.50, 28.96)
10:75528819	rs149334764	V>A	C:451	(12.47, -25.50, 28.96)
10:75528824		L>V	C:453	(14.31, -22.74, 33.67)
10:75528855		T>I	C:463	(2.20, -27.19, 31.00)
10:75528857	rs144592679	V>L	C:464	(3.62, -30.19, 28.10)
10:75528878	rs371855467	R>W	C:471	(-0.75, -45.82, 13.87)
10:75528879		R>Q	C:471	(-0.75, -45.82, 13.87)
10:75529127		C>S	C:489	(22.48, -24.21, 46.34)
10:75529137		Q>H	C:492	(26.02, -30.46, 42.59)
10:75529139	rs561152217	R>H	C:493	(24.73, -28.88, 36.52)
10:75529142		R>Q	C:494	(21.73, -32.08, 41.12)
10:75529163	rs142601631	A>V	C:501	(3.20, -44.39, 32.01)
10:75529174	rs201770092	C>G	C:505	(-7.07, -46.03, 23.28)
10:75529192		L>V	C:511	(-10.22, -41.14, 26.13)
10:75529217		T>M	C:519	(-5.41, -31.36, 34.80)
10:75529229		Y>C	C:523	(-4.23, -26.92, 28.49)
10:75529232		M>T	C:524	(-8.56, -25.14, 29.49)
10:75529240		F>L	C:527	(-4.57, -22.17, 25.09)
10:75529379		R>Q	C:530	(-0.57, -18.53, 25.26)
10:75529385		V>A	C:532	(-5.64, -12.71, 26.02)
10:75529396	rs551845130 COSM139841	P>S	C:536	(-9.28, -11.23, 20.44)
10:75529412	rs147907875	R>H	C:541	(-15.35, -15.91, 25.81)
10:75529418	rs113203770	T>M	C:543	(-11.90, -21.31, 21.25)
10:75529450	rs372331589	C>G	C:554	(-17.67, -37.19, 21.04)
10:75529621	rs374240603	L>V	C:577	(-15.90, -29.48, 32.55)
10:75529649	rs201191700	K>R	C:586	(-17.35, -16.26, 35.54)
10:75529666		P>S	C:592	(-13.56, -7.54, 32.29)
10:75529684		T>A	C:598	(-5.09, -3.23, 33.80)
10:75529685	rs368958996	T>I	C:598	(-5.09, -3.23, 33.80)
10:75529693		R>C	C:601	(-6.93, -7.79, 33.18)
10:75529700	rs553026455	Y>C	C:603	(-0.47, -10.27, 40.15)
10:75529706	rs571977799	R>Q	C:605	(-1.59, -13.70, 32.05)
10:75529715		V>A	C:608	(-2.87, -18.77, 36.48)
10:75529721	rs76327331	S>F	C:610	(2.74, -20.84, 37.17)
10:75529732		T>A	C:614	(-4.06, -27.44, 43.86)
10:75529738	rs544559326	T>S	C:616	(-6.33, -24.11, 39.36)
10:75529747	rs201728396	F>V	C:619	(-8.33, -18.75, 41.05)
10:75529749		F>L	C:619	(-8.33, -18.75, 41.05)
10:75529759		R>W	C:623	(-11.53, -23.97, 50.87)
10:75529760	rs575161818	R>Q	C:623	(-11.53, -23.97, 50.87)
10:75529768		P>S	C:626	(-19.04, -22.70, 57.75)
10:75529769		P>L	C:626	(-19.04, -22.70, 57.75)
10:75530038	rs35005181	T>A	C:628	(-21.08, -21.14, 62.86)
10:75530065	COSM1470398	E>K	C:637	(-11.07, -27.68, 57.75)
10:75530081		R>Q	C:642	(-22.77, -25.73, 46.17)
10:75530095		R>C	C:647	(-25.40, -23.22, 50.80)
10:75530096		R>H	C:647	(-25.40, -23.22, 50.80)
10:75530138		N>S	C:661	(-7.65, -13.43, 48.43)
10:75530140	rs149858657	L>F	C:662	(-8.52, -15.16, 53.30)
10:75530152		V>M	C:666	(-20.95, -11.03, 58.72)
10:75530164	rs201121390 COSM1225083	V>I	C:670	(-27.15, -12.00, 65.63)
10:75530169		Q>H	C:671	(-28.43, -12.97, 69.10)
10:75530180		V>A	C:675	(-20.50, -10.81, 66.55)
10:75530474		L>P	C:694	(-8.68, -11.02, 63.48)
10:75530480		V>G	C:696	(-5.84, -11.59, 69.78)
10:75530488		N>D	C:699	(-12.55, -16.57, 72.77)
10:75530500		K>Q	C:703	(-8.56, -19.83, 70.46)
10:75530502	COSM3440498	K>N	C:703	(-8.56, -19.83, 70.46)
10:75530503		K>Q	C:704	(-12.40, -22.28, 66.68)
10:75530510		R>Q	C:706	(-7.16, -16.46, 66.04)
10:75530531	rs200834483	R>Q	C:713	(-2.84, -17.28, 55.89)
10:75530543		S>F	C:717	(2.35, -20.60, 48.11)
10:75530545		R>W	C:718	(1.96, -16.05, 46.79)
10:75530546		R>Q	C:718	(1.96, -16.05, 46.79)
10:75530551		M>L	C:720	(-4.12, -15.78, 51.95)
10:75530722	rs146383433	V>L	C:725	(-17.06, -8.47, 54.59)
10:75530732		E>G	C:728	(-26.23, -5.90, 54.68)
10:75530735		D>G	C:729	(-24.66, -1.54, 52.23)
10:75530741		M>R	C:731	(-16.68, -5.06, 49.94)
10:75530794		A>T	C:749	(-23.59, -17.41, 34.03)
10:75530806		D>N	C:753	(-28.31, -21.12, 33.41)
10:75530821		M>V	C:758	(-23.07, -26.71, 27.14)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
10:75525312	COSM1349037	R>H	C:117	(22.80, -56.00, 24.07)
10:75526174	COSM164239	F>L	C:231	(26.41, -0.70, 42.54)
10:75526292	COSM1675354	I>L	C:271	(25.89, -6.50, 55.88)
10:75526586	COSM1745889	I>T	C:296	(17.60, -6.15, 35.74)
10:75528652	COSM1675355	R>W	C:429	(12.38, -37.96, 24.26)
10:75529596	COSM1702641	L>F	C:568	(-28.62, -33.89, 30.78)
10:75530738	COSM1506190	K>R	C:730	(-20.00, -1.81, 52.83)
10:75530798	COSM1745891	S>C	C:750	(-25.71, -19.73, 36.27)

3EH2.C | SEC24C.

3EH2.C | SEC24C

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