2I1Y.B | PTPRN

General Structure Information

PDB ID	2i1y
HGNC Gene Label(s)	PTPRN
Structure Name	crystal structure of the phosphatase domain of human ptp ia-2
Resolution	2.23Å
Reference	AUTH S.C.ALMO,J.B.BONANNO,J.M.SAUDER,S.EMTAGE,T.P.DILORENZO,AUTH 2 V.MALASHKEVICH,S.R.WASSERMAN,S.SWAMINATHAN,S.ESWARAMOORTHY,AUTH 3 R.AGARWAL,D.KUMARAN,M.MADEGOWDA,S.RAGUMANI,Y.PATSKOVSKY,AUTH 4 J.ALVARADO,U.A.RAMAGOPAL,J.FABER-BARATA,M.R.CHANCE,A.SALI,AUTH 5 A.FISER,Z.Y.ZHANG,D.S.LAWRENCE,S.K.BURLEYTITL STRUCTURAL GENOMICS OF PROTEIN PHOSPHATASESREF J.STRUCT.FUNCT.GENOM. V. 8 121 2007REFN ISSN 1345-711XPMID 18058037DOI 10.1007/S10969-007-9036-1

Variant Set Distributions

ExAC Variants

Number Of Residues	290
Number Of SNVs	73
Number Of Permutations	35495
Optimal Distance Threshold	16.0
K Statistic	0.218
p-value	0.666

COSMIC

Number Of Residues	290
Number Of SNVs	9
Number Of Permutations	2590
Optimal Distance Threshold	14.0
K Statistic	0.306
p-value	0.498

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	73
Number Of COSMIC SNVs	7
Optimal Distance Threshold	14.0
K Statistic	0.228
p-value	0.611

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:220161983		M>T	B:687	(95.98, 74.23, -12.67)
2:220161971	rs542436411	T>M	B:691	(92.95, 70.67, -15.95)
2:220161969		G>R	B:692	(89.63, 72.44, -14.32)
2:220161841		D>V	B:701	(80.21, 62.85, -9.34)
2:220161832	rs147632050	R>Q	B:704	(74.54, 65.42, -6.99)
2:220161826		R>Q	B:706	(74.85, 61.81, -0.33)
2:220161827		R>W	B:706	(74.85, 61.81, -0.33)
2:220161820	rs370564509	R>H	B:708	(82.81, 59.17, -2.45)
2:220161785	rs200950374	Q>E	B:720	(93.47, 57.04, 15.90)
2:220161764		A>T	B:727	(99.30, 64.92, 28.07)
2:220161758		A>T	B:729	(96.84, 69.47, 27.68)
2:220161751	COSM142786	G>E	B:731	(97.08, 68.73, 32.75)
2:220161752		G>R	B:731	(97.08, 68.73, 32.75)
2:220161749	rs201942873	E>K	B:732	(97.38, 70.29, 37.20)
2:220161740		I>F	B:735	(92.31, 72.23, 33.14)
2:220161736		K>I	B:736	(91.02, 77.12, 34.11)
2:220161727	rs369186246 COSM719891	R>Q	B:739	(86.69, 77.78, 25.36)
2:220161728		R>W	B:739	(86.69, 77.78, 25.36)
2:220161532		R>H	B:750	(102.74, 72.16, 22.48)
2:220161530		I>V	B:751	(102.35, 76.53, 19.88)
2:220161520	rs559253599	K>R	B:754	(109.57, 82.46, 24.56)
2:220161502	rs139505738	S>F	B:760	(102.52, 81.83, 34.19)
2:220161499	COSM3391488	R>Q	B:761	(107.21, 82.49, 34.31)
2:220161500	rs142317962	R>W	B:761	(107.21, 82.49, 34.31)
2:220161496	rs142244541	S>N	B:762	(103.86, 78.48, 30.96)
2:220161488		I>V	B:765	(98.57, 77.94, 23.91)
2:220161482	COSM3991089	A>T	B:767	(97.88, 75.62, 19.82)
2:220161473	rs562356106	I>V	B:770	(98.75, 73.26, 10.62)
2:220161231		H>R	B:773	(105.06, 70.65, 0.70)
2:220161222	rs534579452 COSM303054	R>Q	B:776	(111.44, 74.43, 6.39)
2:220161204	rs150127850	A>V	B:782	(95.14, 76.16, 15.17)
2:220161201	COSM288844	T>M	B:783	(93.57, 78.42, 18.14)
2:220161192		P>L	B:786	(90.46, 83.45, 23.25)
2:220161184	rs141059049	H>D	B:789	(93.31, 82.64, 32.50)
2:220161180		T>I	B:790	(94.05, 82.81, 27.59)
2:220161166		W>G	B:795	(97.47, 89.56, 21.39)
2:220161052	rs141500290	G>S	B:802	(104.87, 86.85, 13.42)
2:220161043	rs536328542	V>I	B:805	(96.93, 87.33, 9.59)
2:220161037	rs201885534 COSM1263502	V>I	B:807	(91.06, 84.10, 10.80)
2:220161024		P>L	B:811	(80.36, 84.92, 16.79)
2:220160993		D>E	B:821	(86.39, 85.86, 25.59)
2:220160992		R>C	B:822	(86.56, 92.13, 23.78)
2:220160986		W>R	B:824	(88.62, 92.43, 19.79)
2:220160982		P>L	B:825	(90.50, 96.92, 21.19)
2:220160956	rs199963736	V>I	B:834	(103.94, 93.59, 27.23)
2:220159850	rs371070609	S>W	B:841	(90.75, 100.22, 10.96)
2:220159845		H>D	B:843	(85.91, 97.99, 5.90)
2:220159841		I>T	B:844	(81.66, 96.90, 8.08)
2:220159796	rs151230230	V>G	B:859	(105.63, 98.09, 26.14)
2:220159797	rs373906567	V>L	B:859	(105.63, 98.09, 26.14)
2:220159790		T>N	B:861	(111.02, 95.92, 23.15)
2:220159785	COSM3364587	E>K	B:863	(109.83, 95.56, 18.98)
2:220159758		F>L	B:872	(82.62, 84.95, 8.68)
2:220159739	rs376114976	E>G	B:878	(74.61, 73.21, 14.92)
2:220159737	rs548633041 COSM476949	G>S	B:879	(75.96, 73.91, 10.86)
2:220159728		A>T	B:882	(73.59, 78.43, 2.82)
2:220159716	rs530183269	P>T	B:886	(80.15, 84.77, 1.66)
2:220159700		R>H	B:891	(90.18, 82.22, 0.48)
2:220156240		V>G	B:894	(92.66, 86.56, 4.04)
2:220156225	rs200458438	R>Q	B:899	(100.55, 85.78, 4.35)
2:220156222		G>D	B:900	(104.78, 87.92, 6.09)
2:220156219		R>H	B:901	(109.80, 87.23, 4.95)
2:220156220	rs142153156	R>C	B:901	(109.80, 87.23, 4.95)
2:220156205		I>V	B:906	(96.32, 82.93, 13.86)
2:220156202	COSM1530850	V>M	B:907	(92.81, 80.11, 12.35)
2:220156196	rs536833144	C>R	B:909	(86.78, 79.32, 16.60)
2:220155611		D>N	B:911	(86.54, 74.33, 19.13)
2:220155589		T>I	B:918	(86.24, 73.72, 7.62)
2:220155584		I>V	B:920	(92.48, 75.05, 7.46)
2:220155575	COSM1222671	D>N	B:923	(92.90, 77.60, 2.18)
2:220155559	COSM1016713	R>H	B:928	(97.38, 71.08, -1.86)
2:220155560		R>C	B:928	(97.38, 71.08, -1.86)
2:220155316	rs146180532	I>V	B:938	(88.81, 66.47, 0.63)
2:220155267	rs372873328 COSM1405622	R>H	B:954	(83.00, 68.98, 15.79)
2:220155004		A>S	B:962	(84.23, 72.09, 2.01)
2:220155001		L>V	B:963	(83.56, 69.45, -1.54)
2:220154997		T>R	B:964	(80.49, 72.99, -1.88)
2:220154998		T>S	B:964	(80.49, 72.99, -1.88)
2:220154991		V>A	B:966	(86.46, 73.81, -3.37)
2:220154992	rs139964061	V>M	B:966	(86.46, 73.81, -3.37)
2:220154988		A>V	B:967	(83.53, 73.83, -6.29)
2:220154979	rs201261677	V>A	B:970	(86.91, 76.09, -9.37)

2I1Y.B | PTPRN.

2I1Y.B | PTPRN

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:220161981	COSM109389	D>N	B:688	(95.38, 74.34, -17.18)
2:220161732	COSM1669777	K>N	B:737	(95.27, 77.29, 30.19)
2:220161722	COSM356485	P>S	B:741	(87.76, 69.12, 27.09)
2:220161499	COSM3391488	R>Q	B:761	(107.21, 82.49, 34.31)
2:220161491	COSM1614393	Y>H	B:764	(99.00, 75.03, 27.12)
2:220161222	COSM303054	R>Q	B:776	(111.44, 74.43, 6.39)
2:220161201	COSM288844	T>M	B:783	(93.57, 78.42, 18.14)
2:220161175	COSM395235	A>T	B:792	(98.02, 87.13, 27.20)
2:220159737	COSM476949	G>S	B:879	(75.96, 73.91, 10.86)