3IFQ.B | JUP – ASTRID

3IFQ.B | JUP

General Structure Information

PDB ID	3ifq
HGNC Gene Label(s)	JUP
Structure Name	interction of plakoglobin and beta-catenin with desmosomal cadherins
Resolution	2.8Å
Reference	AUTH H.J.CHOI,J.C.GROSS,S.POKUTTA,W.I.WEISTITL INTERACTIONS OF PLAKOGLOBIN AND BETA-CATENIN WITHTITL 2 DESMOSOMAL CADHERINS: BASIS OF SELECTIVE EXCLUSIONTITL 3 OF ALPHA- AND BETA-CATENIN FROM DESMOSOMES.REF J.BIOL.CHEM. V. 284 31776 2009REFN ISSN 0021-9258PMID 19759396DOI 10.1074/JBC.M109.047928

Variant Set Distributions

ExAC Variants

Number Of Residues	534
Number Of SNVs	154
Number Of Permutations	50657
Optimal Distance Threshold	12.0
K Statistic	0.054
p-value	0.705

ClinVar

Number Of Residues	534
Number Of SNVs	5
Number Of Permutations	1583
Optimal Distance Threshold	13.0
K Statistic	0.2
p-value	0.723

COSMIC

Number Of Residues	534
Number Of SNVs	6
Number Of Permutations	3733
Optimal Distance Threshold	43.0
K Statistic	0.333
p-value	0.266

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	154
Number Of ClinVar SNVs	5
Optimal Distance Threshold	13.0
K Statistic	0.133
p-value	0.696

Cosmic vs. ExAC

Number Of ExAC SNVs	154
Number Of COSMIC SNVs	5
Optimal Distance Threshold	43.0
K Statistic	-0.263
p-value	0.188

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:39925726	rs150245906	E>K	B:138	(7.55, -31.28, 58.63)
17:39925713	rs41283425	R>H	B:142	(5.14, -35.88, 60.99)
17:39925711	rs375788626 CM105195	A>T	B:143	(-1.07, -36.44, 60.26)
17:39925705		P>S	B:145	(-2.00, -41.05, 58.14)
17:39925702	rs146581757	E>K	B:146	(-4.79, -40.34, 62.38)
17:39925681	rs368479692	D>N	B:153	(-13.92, -44.36, 60.90)
17:39925678		E>K	B:154	(-17.80, -44.81, 57.62)
17:39925671		P>L	B:156	(-20.58, -39.62, 61.31)
17:39925453		V>L	B:159	(-16.13, -38.06, 59.86)
17:39925443	COSM4066438	A>V	B:162	(-12.24, -34.83, 60.80)
17:39925441		A>T	B:163	(-13.50, -32.48, 58.39)
17:39925438		M>V	B:164	(-14.20, -29.69, 61.71)
17:39925435		I>V	B:165	(-8.94, -30.76, 61.90)
17:39925419		S>L	B:170	(-7.20, -26.00, 54.55)
17:39925414		K>E	B:172	(-2.52, -22.88, 57.85)
17:39925408		A>T	B:174	(1.78, -25.46, 55.04)
17:39925404		S>L	B:175	(-1.16, -27.55, 55.77)
17:39925401	rs144171604	R>Q	B:176	(-3.50, -25.16, 51.66)
17:39925402		R>W	B:176	(-3.50, -25.16, 51.66)
17:39925398	rs371481933	R>Q	B:177	(1.05, -26.77, 48.72)
17:39925399	rs148484473	R>W	B:177	(1.05, -26.77, 48.72)
17:39925383	rs145592971	S>L	B:182	(-2.30, -36.98, 49.80)
17:39925380		P>L	B:183	(-3.66, -39.03, 47.18)
17:39925368		A>V	B:187	(-10.34, -39.39, 48.29)
17:39925366		A>T	B:188	(-11.56, -39.16, 51.58)
17:39925357	COSM3927572	R>C	B:191	(-14.83, -41.39, 49.84)
17:39925350	rs139496777	M>T	B:193	(-18.69, -34.29, 49.54)
17:39925351		M>V	B:193	(-18.69, -34.29, 49.54)
17:39925336		D>N	B:198	(-24.29, -32.94, 58.41)
17:39925333		L>V	B:199	(-24.89, -28.58, 56.39)
17:39925327		T>A	B:201	(-19.98, -32.78, 57.04)
17:39925323		A>G	B:202	(-21.12, -30.89, 53.52)
17:39925320	rs200221163	R>H	B:203	(-20.71, -26.12, 56.18)
17:39925321	rs147354282	R>C	B:203	(-20.71, -26.12, 56.18)
17:39925304		I>M	B:208	(-11.55, -28.97, 52.16)
17:39925294		L>V	B:212	(-7.28, -28.17, 47.87)
17:39925285	rs141124805	H>Y	B:215	(-3.26, -24.87, 45.09)
17:39925281		R>Q	B:216	(-2.85, -26.21, 38.12)
17:39925272		L>P	B:219	(-7.41, -28.57, 40.56)
17:39925273		L>M	B:219	(-7.41, -28.57, 40.56)
17:39925267		A>T	B:221	(-6.53, -34.45, 42.89)
17:39925257		K>M	B:224	(-6.99, -38.21, 39.52)
17:39925254		S>L	B:225	(-10.72, -38.27, 43.26)
17:39925246	rs374566089	I>V	B:228	(-16.52, -33.37, 39.11)
17:39925236		L>P	B:231	(-18.60, -30.93, 43.74)
17:39925234	rs137989964	V>I	B:232	(-22.62, -31.89, 40.81)
17:39925231		R>C	B:233	(-24.82, -34.94, 46.07)
17:39925221	rs370138404	S>N	B:236	(-28.98, -29.42, 45.40)
17:39923818		S>L	B:241	(-21.88, -22.33, 51.99)
17:39923801		I>V	B:247	(-19.61, -23.09, 41.90)
17:39923794	COSM4066436	T>M	B:249	(-14.38, -25.89, 43.13)
17:39923762	rs149623442	A>T	B:260	(-13.40, -31.28, 33.16)
17:39923758		K>R	B:261	(-14.38, -29.46, 29.77)
17:39923746	COSM3187803	R>H	B:265	(-19.96, -31.75, 29.08)
17:39923747		R>C	B:265	(-19.96, -31.75, 29.08)
17:39923731	rs374177985	L>Q	B:270	(-25.41, -28.23, 32.43)
17:39923722		M>T	B:273	(-25.19, -25.25, 36.84)
17:39923713		L>R	B:276	(-28.20, -22.44, 40.39)
17:39923707	rs541560189	N>S	B:278	(-32.90, -18.76, 40.78)
17:39923698	rs574465470	N>S	B:281	(-25.50, -13.59, 44.71)
17:39923671		D>A	B:290	(-18.03, -18.69, 33.12)
17:39923650		Y>C	B:297	(-16.43, -22.65, 22.96)
17:39923648	rs199597864	G>S	B:298	(-17.89, -26.50, 21.42)
17:39923644		N>S	B:299	(-20.62, -29.02, 23.09)
17:39923638		E>G	B:301	(-24.34, -31.92, 22.03)
17:39923639		E>Q	B:301	(-24.34, -31.92, 22.03)
17:39923635	rs570714124	S>N	B:302	(-24.02, -28.43, 25.97)
17:39921315		I>T	B:305	(-28.65, -29.77, 27.83)
17:39921283	COSM4066432	V>M	B:316	(-32.74, -13.04, 29.13)
17:39921278		Q>H	B:317	(-34.37, -12.83, 34.43)
17:39921277		I>V	B:318	(-29.66, -12.19, 34.37)
17:39921270	COSM979311	R>H	B:320	(-35.05, -8.69, 31.57)
17:39921271		R>C	B:320	(-35.05, -8.69, 31.57)
17:39921265		Y>H	B:322	(-29.14, -8.94, 38.31)
17:39921262		S>G	B:323	(-26.52, -3.75, 37.14)
17:39921259		Y>N	B:324	(-21.88, -7.45, 38.90)
17:39921256	COSM3889679	E>K	B:325	(-19.89, -5.50, 34.13)
17:39921240		T>N	B:330	(-20.45, -13.53, 32.16)
17:39921231		R>H	B:333	(-18.55, -14.76, 27.65)
17:39921232		R>C	B:333	(-18.55, -14.76, 27.65)
17:39921229	rs201434935	V>M	B:334	(-23.51, -17.57, 27.68)
17:39921194	rs150194093	K>N	B:345	(-30.94, -18.55, 16.94)
17:39921193		P>S	B:346	(-35.47, -19.39, 18.59)
17:39921190		A>T	B:347	(-35.48, -19.14, 22.60)
17:39921183		V>A	B:349	(-35.90, -14.03, 20.25)
17:39921181		E>Q	B:350	(-39.52, -16.88, 21.66)
17:39921050		G>D	B:358	(-30.20, -3.63, 23.51)
17:39921027		P>T	B:366	(-16.75, -1.87, 25.91)
17:39921023		R>H	B:367	(-16.24, -6.56, 28.92)
17:39921003		W>G	B:374	(-19.87, -10.48, 17.95)
17:39920993	rs200433530	R>H	B:377	(-23.88, -10.62, 13.78)
17:39920994	rs368564000	R>S	B:377	(-23.88, -10.62, 13.78)
17:39919562		E>D	B:390	(-38.56, 0.49, 18.03)
17:39919560	rs199826380	S>N	B:391	(-34.45, 1.20, 20.64)
17:39919558		V>M	B:392	(-32.32, -1.67, 18.98)
17:39919528		V>M	B:402	(-18.92, 3.79, 15.73)
17:39919519	rs200019016	V>I	B:405	(-14.45, -2.14, 12.70)
17:39919515	COSM1737173	N>S	B:406	(-15.67, -5.39, 15.12)
17:39919513	rs370913228 CM107149	V>I	B:407	(-19.31, -2.11, 16.16)
17:39919510		L>F	B:408	(-19.39, -0.66, 11.49)
17:39919497		T>M	B:412	(-23.96, -3.65, 9.03)
17:39919476		T>I	B:419	(-34.37, -5.00, 7.10)
17:39919474		C>R	B:420	(-35.78, -9.17, 5.92)
17:39919470		N>S	B:421	(-39.39, -9.42, 4.24)
17:39919452		T>M	B:427	(-40.07, 2.69, 7.72)
17:39919443		T>K	B:430	(-35.61, 5.21, 6.35)
17:39919424		E>D	B:436	(-28.32, 8.70, 4.95)
17:39919413		H>R	B:440	(-21.57, 7.93, 5.18)
17:39919408	rs142213474	I>F	B:442	(-20.34, 1.52, 1.68)
17:39919401	rs369507567 COSM1211308	R>H	B:444	(-15.95, 4.04, 7.53)
17:39919402		R>C	B:444	(-15.95, 4.04, 7.53)
17:39919399		A>P	B:445	(-15.11, 0.03, 3.79)
17:39919396		G>C	B:446	(-14.77, -0.63, 0.61)
17:39919389	rs573614651	K>R	B:448	(-13.74, -4.21, 4.48)
17:39919384		D>N	B:450	(-17.03, -8.21, 5.99)
17:39919377		T>M	B:452	(-19.98, -3.98, 1.57)
17:39919373		E>D	B:453	(-22.63, -8.52, 1.60)
17:39919372		P>S	B:454	(-24.09, -6.32, 4.70)
17:39919366	rs78437817	V>I	B:456	(-25.82, -3.55, -0.39)
17:39919360	rs139559495	A>T	B:458	(-29.90, -2.97, 3.63)
17:39919353	rs397517296	R>H	B:460	(-31.58, -5.49, -1.70)
17:39919354		R>C	B:460	(-31.58, -5.49, -1.70)
17:39919348		L>F	B:462	(-34.32, 0.37, 3.08)
17:39919338	rs369486398	R>H	B:465	(-40.79, -5.27, -1.23)
17:39919339		R>C	B:465	(-40.79, -5.27, -1.23)
17:39919332	COSM3672447	P>L	B:467	(-44.16, 2.83, 3.22)
17:39919302		R>H	B:477	(-30.35, 10.59, -6.10)
17:39919293		Y>C	B:480	(-23.62, 12.29, -3.67)
17:39919276		V>M	B:486	(-22.04, 0.98, -9.47)
17:39919267		L>F	B:489	(-20.93, -4.24, -10.06)
17:39919254		N>S	B:493	(-13.71, -14.09, -5.89)
17:39919237		K>Q	B:499	(-27.08, -11.65, -6.11)
17:39915113	rs376051686	G>S	B:503	(-30.79, -5.44, -6.84)
17:39915094		A>D	B:509	(-34.45, 1.90, -11.30)
17:39915092		L>V	B:510	(-37.98, 1.45, -9.43)
17:39915044		R>C	B:526	(-19.94, -4.98, -15.36)
17:39915038	rs368271628	V>I	B:528	(-24.48, -6.57, -20.54)
17:39915014		Q>E	B:536	(-21.78, -18.19, -22.29)
17:39915001	rs376881608	R>H	B:540	(-20.39, -23.94, -19.56)
17:39915002		R>C	B:540	(-20.39, -23.94, -19.56)
17:39914998		H>P	B:541	(-24.35, -26.25, -17.56)
17:39914766		G>D	B:553	(-23.98, -19.81, -3.64)
17:39914757		M>T	B:556	(-24.44, -17.80, -12.50)
17:39914736	rs142006878	C>Y	B:563	(-28.88, -8.47, -15.09)
17:39914719	rs370101446	I>F	B:569	(-36.39, -1.52, -14.53)
17:39914709		R>Q	B:572	(-39.00, 1.68, -16.61)
17:39914710		R>W	B:572	(-39.00, 1.68, -16.61)
17:39914695		R>C	B:577	(-35.16, 2.37, -24.47)
17:39914680		R>W	B:582	(-26.88, 0.79, -30.55)
17:39914671		T>A	B:585	(-28.75, -7.13, -26.00)
17:39914664		P>L	B:587	(-29.87, -11.34, -29.63)
17:39914026	COSM1610251	S>L	B:595	(-35.96, -20.22, -20.20)
17:39914006	COSM979291	R>C	B:602	(-41.05, -11.21, -15.47)
17:39913999		A>D	B:604	(-37.05, -11.11, -20.91)
17:39913960		A>V	B:617	(-35.60, -2.41, -31.92)
17:39913948		I>T	B:621	(-37.03, -8.07, -31.67)
17:39913942		A>G	B:623	(-35.37, -10.78, -37.20)
17:39913934		A>T	B:626	(-39.18, -13.51, -31.40)
17:39913930		S>L	B:627	(-42.10, -14.07, -33.54)
17:39913928		A>T	B:628	(-42.55, -17.38, -31.83)
17:39913909		L>P	B:634	(-49.52, -15.69, -24.99)
17:39913906		H>R	B:635	(-50.62, -20.26, -23.66)
17:39913900	rs142095597	R>H	B:637	(-48.26, -20.90, -14.04)
17:39913901		R>C	B:637	(-48.26, -20.90, -14.04)
17:39913898		N>H	B:638	(-46.77, -15.45, -14.86)
17:39913780		A>T	B:645	(-45.57, -11.35, -24.67)
17:39913771	rs143043662	V>I	B:648	(-43.50, -7.78, -27.80)
17:39913761	rs201649512	R>H	B:651	(-44.79, -2.74, -28.57)
17:39913726		R>C	B:663	(-51.90, -13.59, -39.50)
17:39913723		V>M	B:664	(-51.09, -11.70, -33.19)

3IFQ.B | JUP.

3IFQ.B | JUP

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
17:39925732	rs782392706	D>N	B:136	(2.98, -26.06, 60.27)
17:39923767	rs794729052	E>G	B:258	(-7.96, -29.62, 30.89)
17:39923746	rs782440692	R>H	B:265	(-19.96, -31.75, 29.08)
17:39923722	rs782091454	M>T	B:273	(-25.19, -25.25, 36.84)
17:39914722	rs794729048	H>Y	B:568	(-37.64, -4.63, -17.18)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:39925321	COSM48459	R>C	B:203	(-20.71, -26.12, 56.18)
17:39923762	COSM979315	A>T	B:260	(-13.40, -31.28, 33.16)
17:39919515	COSM1737173	N>S	B:406	(-15.67, -5.39, 15.12)
17:39914695	COSM4393708	R>C	B:577	(-35.16, 2.37, -24.47)
17:39914026	COSM1610251	S>L	B:595	(-35.96, -20.22, -20.20)
17:39913930	COSM4835963	S>L	B:627	(-42.10, -14.07, -33.54)