1YGR.B | PTPRC

General Structure Information

PDB ID	1ygr
HGNC Gene Label(s)	PTPRC
Structure Name	crystal structure of the tandem phosphatase domain of rptp cd45
Resolution	2.9Å
Reference	AUTH H.J.NAM,F.POY,H.SAITO,C.A.FREDERICKTITL STRUCTURAL BASIS FOR THE FUNCTION AND REGULATIONTITL 2 OF THE RECEPTOR PROTEIN TYROSINE PHOSPHATASE CD45.REF J.EXP.MED. V. 201 441 2005REFN ISSN 0022-1007PMID 15684325DOI 10.1084/JEM.20041890

Variant Set Distributions

ExAC Variants

Number Of Residues	561
Number Of SNVs	135
Number Of Permutations	40540
Optimal Distance Threshold	30.0
K Statistic	0.415
p-value	0.616

COSMIC

Number Of Residues	561
Number Of SNVs	11
Number Of Permutations	13391
Optimal Distance Threshold	30.0
K Statistic	0.509
p-value	0.512

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	135
Number Of COSMIC SNVs	12
Optimal Distance Threshold	6.0
K Statistic	0.023
p-value	0.544

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
1:198700757		Q>K	B:601	(-0.36, 50.82, 117.69)
1:198700818		I>T	B:621	(5.93, 37.47, 134.91)
1:198700828		E>D	B:624	(4.35, 43.28, 138.38)
1:198700839		F>C	B:628	(1.72, 39.97, 130.55)
1:198701436	COSM1639671	P>L	B:636	(-9.02, 48.67, 122.86)
1:198701459		I>L	B:644	(-23.50, 51.57, 120.53)
1:198701472	COSM2125954	R>Q	B:648	(-26.33, 54.84, 123.51)
1:198701488		Q>H	B:653	(-31.33, 54.25, 129.42)
1:198701490		N>T	B:654	(-34.20, 51.98, 133.03)
1:198701496		N>S	B:656	(-28.71, 49.24, 130.96)
1:198701504	rs147515054	V>I	B:659	(-23.70, 53.90, 131.41)
1:198701621		R>L	B:668	(-28.98, 43.85, 119.74)
1:198701623		V>I	B:669	(-29.18, 39.49, 122.01)
1:198701632		S>A	B:672	(-39.75, 38.62, 120.45)
1:198701643	rs200818686 COSM121680	N>K	B:675	(-47.03, 44.72, 119.19)
1:198701647	rs372940886	D>N	B:677	(-43.53, 47.44, 124.12)
1:198701665		I>V	B:683	(-31.40, 42.32, 126.34)
1:198701675		S>N	B:686	(-23.64, 39.88, 123.49)
1:198703352		A>S	B:699	(-22.36, 37.89, 127.05)
1:198703475		V>A	B:708	(-36.13, 39.43, 135.84)
1:198703481	rs201711547	D>V	B:710	(-36.66, 40.49, 129.48)
1:198703485	rs139089055	F>L	B:711	(-32.00, 36.50, 131.79)
1:198703546		G>R	B:732	(-20.46, 45.17, 149.17)
1:198704278		P>L	B:742	(-36.17, 29.32, 142.28)
1:198704281		S>L	B:743	(-35.96, 28.85, 146.49)
1:198704287		E>G	B:745	(-37.52, 26.11, 149.88)
1:198704298	rs200672643	R>W	B:749	(-40.79, 32.51, 141.51)
1:198704308		G>E	B:752	(-43.87, 35.51, 133.38)
1:198704313	rs146726593	V>I	B:754	(-40.99, 31.66, 131.93)
1:198704319		V>L	B:756	(-38.57, 28.35, 136.79)
1:198704325		I>F	B:758	(-35.32, 23.79, 141.56)
1:198704334		H>Y	B:761	(-29.01, 23.28, 145.51)
1:198704341	COSM1720180	R>T	B:763	(-24.64, 23.61, 148.69)
1:198704350		D>G	B:766	(-15.88, 26.85, 144.68)
1:198704353	COSM901878	Y>C	B:767	(-18.73, 24.36, 141.89)
1:198704361		Q>E	B:770	(-29.16, 25.23, 140.44)
1:198704377		V>G	B:775	(-42.05, 25.70, 130.81)
1:198710998		K>E	B:777	(-47.67, 26.46, 129.89)
1:198711005	rs570434674	E>G	B:779	(-45.34, 28.53, 123.74)
1:198711025		V>L	B:786	(-31.67, 24.19, 132.80)
1:198711029	rs369548767	T>I	B:787	(-27.47, 23.55, 133.87)
1:198711032	rs534640068	H>L	B:788	(-27.46, 27.96, 137.55)
1:198711053		P>Q	B:795	(-13.47, 38.36, 143.19)
1:198711062		G>E	B:798	(-10.74, 40.13, 140.08)
1:198711084	rs146402228	L>F	B:805	(-10.64, 27.08, 141.23)
1:198711110		N>S	B:814	(-17.12, 21.56, 129.00)
1:198711113		A>V	B:815	(-19.99, 18.29, 130.95)
1:198711122	rs143328050	N>S	B:818	(-26.50, 22.09, 124.34)
1:198711137		P>L	B:823	(-26.43, 29.65, 123.29)
1:198711139		I>V	B:824	(-23.06, 28.99, 126.60)
1:198711142		V>M	B:825	(-25.46, 32.05, 129.33)
1:198711369		V>A	B:832	(-17.44, 42.43, 130.66)
1:198711375	COSM334232	R>H	B:834	(-16.52, 38.32, 137.06)
1:198711384		T>S	B:837	(-11.98, 35.91, 131.86)
1:198711393		G>E	B:840	(-10.86, 32.62, 127.30)
1:198711423		A>V	B:850	(-5.64, 22.19, 118.64)
1:198711425		E>K	B:851	(-3.41, 25.01, 116.88)
1:198711429		N>S	B:852	(0.02, 22.77, 120.42)
1:198711432		K>T	B:853	(-1.04, 27.46, 118.25)
1:198711446		G>S	B:858	(-6.22, 38.19, 120.02)
1:198711453	rs552482393	V>A	B:860	(-8.63, 39.58, 124.04)
1:198711468		R>Q	B:865	(-12.56, 43.64, 117.41)
1:198711494	COSM424965	E>K	B:874	(-4.69, 44.16, 134.73)
1:198713192		I>L	B:878	(-1.84, 37.80, 134.17)
1:198713207		A>T	B:883	(-4.50, 28.69, 132.98)
1:198713223	rs532932175	N>S	B:888	(1.12, 23.40, 130.01)
1:198713263	rs373417813	H>Q	B:901	(-9.60, 0.67, 142.59)
1:198713264	rs376357337	P>A	B:902	(-8.83, 1.53, 137.60)
1:198713268		Y>C	B:903	(-5.54, 6.65, 137.23)
1:198713271		L>R	B:904	(-3.99, 3.57, 141.15)
1:198713274		H>P	B:905	(-3.26, -1.64, 138.61)
1:198713278	rs149625776	N>K	B:906	(-2.69, 0.94, 135.32)
1:198713332		Q>H	B:924	(9.02, 14.09, 140.13)
1:198717250		Y>H	B:929	(6.03, 25.57, 145.83)
1:198717259		W>R	B:932	(5.81, 30.29, 147.48)
1:198717260		W>L	B:932	(5.81, 30.29, 147.48)
1:198717275		I>T	B:937	(8.76, 36.21, 161.35)
1:198717311	rs115365240	N>S	B:949	(13.12, 21.96, 162.25)
1:198717322		I>L	B:953	(10.12, 28.19, 159.40)
1:198717326	rs3208670 COSM3736585	P>L	B:954	(6.35, 29.30, 159.26)
1:198718554		N>S	B:958	(0.84, 30.96, 156.67)
1:198718558		R>S	B:959	(2.83, 34.33, 161.26)
1:198718649		S>G	B:990	(2.17, 40.14, 167.36)
1:198718673		I>V	B:998	(-3.85, 24.50, 156.28)
1:198719624		Y>H	B:1001	(-13.65, 20.51, 149.98)
1:198719649		A>V	B:1009	(-0.35, 22.89, 161.06)
1:198719668		K>N	B:1015	(10.67, 21.93, 177.79)
1:198719673	rs200078132	T>N	B:1017	(6.47, 26.87, 173.49)
1:198719678	rs535347024	G>S	B:1019	(2.31, 28.24, 176.49)
1:198719692	rs376600221	Q>H	B:1023	(-1.71, 31.19, 174.57)
1:198719711		V>F	B:1030	(-9.11, 24.78, 169.10)
1:198719715		K>T	B:1031	(-13.65, 21.58, 169.80)
1:198719716		K>N	B:1031	(-13.65, 21.58, 169.80)
1:198719729		L>M	B:1036	(0.08, 12.26, 164.67)
1:198719733		T>R	B:1037	(3.45, 12.14, 168.12)
1:198721381		I>L	B:1046	(9.20, 13.35, 169.48)
1:198721391	COSM4026738	Q>R	B:1049	(3.71, 16.26, 178.59)
1:198721392	rs190241405	Q>H	B:1049	(3.71, 16.26, 178.59)
1:198721427		I>T	B:1061	(-4.31, 29.84, 180.14)
1:198721444	rs368690279 COSM1337658	D>H	B:1067	(-11.67, 12.70, 180.96)
1:198721454	rs140384318	K>I	B:1070	(-5.67, 3.97, 176.23)
1:198721466		Y>C	B:1074	(-8.15, 6.42, 169.67)
1:198721471		L>F	B:1076	(-9.88, 11.00, 174.33)
1:198721475	COSM531603	R>H	B:1077	(-5.57, 13.01, 176.54)
1:198721727		K>R	B:1087	(-17.60, 30.84, 186.49)
1:198721736	COSM901884	R>Q	B:1090	(-12.91, 27.14, 175.61)
1:198721741		V>L	B:1092	(-10.53, 20.83, 174.47)
1:198721745		Y>C	B:1093	(-13.09, 16.98, 172.79)
1:198721759		T>A	B:1098	(0.03, 5.56, 168.32)
1:198721768	rs112867533	S>R	B:1101	(6.63, 6.08, 163.57)
1:198721771		V>M	B:1102	(8.64, 9.44, 162.06)
1:198721780		L>F	B:1105	(3.62, 4.95, 156.05)
1:198721796	rs369268728	K>T	B:1110	(-7.91, -0.28, 158.72)
1:198721808	rs549131091 COSM1263385	S>F	B:1114	(-11.60, 5.35, 162.09)
1:198721817		Q>P	B:1117	(-15.42, 9.15, 160.63)
1:198721819		V>I	B:1118	(-14.06, 10.06, 165.59)
1:198721820	COSM1500546	V>D	B:1118	(-14.06, 10.06, 165.59)
1:198721822	rs139041596	V>I	B:1119	(-12.18, 13.53, 164.74)
1:198721837		P>A	B:1124	(-18.94, 21.61, 163.83)
1:198721880	rs372398436	T>I	B:1138	(-9.26, 27.33, 163.69)
1:198723400	rs199826421	D>A	B:1146	(7.65, 19.01, 161.64)
1:198723401		D>E	B:1146	(7.65, 19.01, 161.64)
1:198723405		S>A	B:1148	(4.94, 18.62, 158.03)
1:198723415		T>M	B:1151	(0.74, 16.86, 159.62)
1:198723433	rs114970039	L>S	B:1157	(-6.44, 11.75, 153.99)
1:198723439		N>T	B:1159	(-9.12, 17.74, 152.16)
1:198723447		E>Q	B:1162	(-15.17, 16.32, 153.00)
1:198723454	COSM1222601	A>V	B:1164	(-15.17, 11.71, 148.28)
1:198723458	rs115935364	E>D	B:1165	(-18.32, 11.87, 150.75)
1:198723466	rs113148246	E>A	B:1168	(-18.76, 10.70, 143.79)
1:198723469		V>A	B:1169	(-14.02, 13.53, 142.79)
1:198723495	COSM463707	A>S	B:1178	(-1.60, 23.38, 148.26)
1:198723498	rs141995021	L>V	B:1179	(-0.32, 21.08, 151.32)
1:198723501	rs377490765	R>C	B:1180	(4.73, 20.32, 148.24)
1:198723502		R>H	B:1180	(4.73, 20.32, 148.24)
1:198723531		F>L	B:1190	(6.31, 8.01, 145.49)
1:198725042		Y>C	B:1193	(1.66, 11.56, 145.63)
1:198725044		Q>K	B:1194	(2.03, 5.62, 146.76)
1:198725059	rs150672767	V>I	B:1199	(-5.66, 5.16, 151.69)
1:198725062		I>V	B:1200	(-8.46, 7.35, 148.99)
1:198725063		I>T	B:1200	(-8.46, 7.35, 148.99)
1:198725075		Y>C	B:1204	(-13.97, 5.37, 149.53)

1YGR.B | PTPRC.

1YGR.B | PTPRC

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
1:198700809	COSM3705386	K>M	B:618	(8.73, 32.93, 134.04)
1:198701436	COSM1639671	P>L	B:636	(-9.02, 48.67, 122.86)
1:198701456	COSM3481193	P>S	B:643	(-22.41, 50.91, 115.81)
1:198701472	COSM2125954	R>Q	B:648	(-26.33, 54.84, 123.51)
1:198701611	COSM3664966	D>Y	B:665	(-26.15, 47.60, 117.44)
1:198704341	COSM1720180	R>K	B:763	(-24.64, 23.61, 148.69)
1:198711374	COSM1222602	R>C	B:834	(-16.52, 38.32, 137.06)
1:198711383	COSM2125976	T>A	B:837	(-11.98, 35.91, 131.86)
1:198711392	COSM33494	G>R	B:840	(-10.86, 32.62, 127.30)
1:198721378	COSM1689568	E>K	B:1045	(11.84, 15.78, 173.57)
1:198721380	COSM4622374	E>D	B:1045	(11.84, 15.78, 173.57)
1:198721736	COSM901884	R>Q	B:1090	(-12.91, 27.14, 175.61)
1:198723454	COSM1222601	A>V	B:1164	(-15.17, 11.71, 148.28)