General Structure Information
| PDB ID | 2nlk |
| HGNC Gene Label(s) | PTPRG |
| Structure Name | crystal structure of d1 and d2 catalytic domains of human protein tyrosine phosphatase gamma (d1+d2 ptprg) |
| Resolution | 2.4Å |
| Reference | AUTH A.J.BARR,E.UGOCHUKWU,W.H.LEE,O.N.KING,P.FILIPPAKOPOULOS,AUTH 2 I.ALFANO,P.SAVITSKY,N.A.BURGESS-BROWN,S.MULLER,S.KNAPPTITL LARGE-SCALE STRUCTURAL ANALYSIS OF THE CLASSICAL HUMANTITL 2 PROTEIN TYROSINE PHOSPHATOME.REF CELL(CAMBRIDGE,MASS.) V. 136 352 2009REFN ISSN 0092-8674PMID 19167335DOI 10.1016/J.CELL.2008.11.038 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 553 |
| Number Of SNVs | 139 |
| Number Of Permutations | 30645 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.07 |
| p-value | 0.517 |
COSMIC
| Number Of Residues | 553 |
| Number Of SNVs | 8 |
| Number Of Permutations | 7138 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.036 |
| p-value | 0.897 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 139 |
| Number Of COSMIC SNVs | 8 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.022 |
| p-value | 1.0 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:62240825 | Q>E | A:832 | (14.83, 8.16, 42.79) | |
| 3:62240826 | rs201604042 | Q>R | A:832 | (14.83, 8.16, 42.79) |
| 3:62240841 | I>S | A:837 | (24.23, 8.41, 40.40) | |
| 3:62240843 | rs72878145 | G>S | A:838 | (23.80, 8.40, 37.01) |
| 3:62240853 | Y>C | A:841 | (29.08, 8.43, 37.87) | |
| 3:62240862 | N>I | A:844 | (32.73, 13.89, 32.20) | |
| 3:62240863 | rs570891194 | N>K | A:844 | (32.73, 13.89, 32.20) |
| 3:62240867 | rs556748617 | H>Y | A:846 | (28.77, 18.66, 35.08) |
| 3:62240880 | E>G | A:850 | (28.70, 21.65, 39.22) | |
| 3:62240886 | F>S | A:852 | (33.48, 18.83, 45.85) | |
| 3:62248482 | COSM1047894 | R>C | A:857 | (33.89, 28.37, 47.32) |
| 3:62248483 | rs561653746 COSM397771 |
R>H | A:857 | (33.89, 28.37, 47.32) |
| 3:62248485 | C>R | A:858 | (29.43, 26.83, 50.82) | |
| 3:62248489 | rs369989465 | T>S | A:859 | (31.66, 28.50, 53.58) |
| 3:62248494 | D>N | A:861 | (30.39, 34.37, 51.25) | |
| 3:62248497 | M>V | A:862 | (29.63, 32.08, 55.89) | |
| 3:62248501 | N>S | A:863 | (33.58, 35.55, 56.57) | |
| 3:62248503 | rs146787787 | I>F | A:864 | (33.93, 30.87, 59.10) |
| 3:62248506 | T>A | A:865 | (36.70, 32.85, 62.30) | |
| 3:62248522 | N>S | A:870 | (45.81, 31.17, 63.23) | |
| 3:62248543 | K>T | A:877 | (48.62, 23.09, 69.92) | |
| 3:62248554 | I>V | A:881 | (49.77, 25.89, 58.40) | |
| 3:62248557 | N>H | A:882 | (46.45, 24.06, 55.99) | |
| 3:62248569 | rs556570148 | Y>N | A:886 | (36.01, 26.82, 61.23) |
| 3:62253090 | H>Y | A:888 | (31.69, 28.20, 65.17) | |
| 3:62253093 | rs149158341 | S>G | A:889 | (32.91, 24.59, 66.33) |
| 3:62253141 | rs200045412 | D>N | A:905 | (41.26, 26.54, 75.25) |
| 3:62253162 | V>I | A:912 | (30.36, 17.58, 63.64) | |
| 3:62253367 | rs146998290 | N>S | A:916 | (19.16, 13.63, 64.44) |
| 3:62253378 | A>T | A:920 | (27.73, 13.51, 67.18) | |
| 3:62253382 | Y>F | A:921 | (29.98, 12.76, 64.61) | |
| 3:62253384 | I>V | A:922 | (34.83, 15.33, 68.28) | |
| 3:62253414 | F>L | A:932 | (49.72, 12.39, 72.80) | |
| 3:62253425 | rs147139816 | F>L | A:935 | (43.10, 12.93, 72.21) |
| 3:62253427 | rs139531452 | W>S | A:936 | (43.35, 10.01, 75.73) |
| 3:62253443 | E>D | A:941 | (36.69, 17.39, 79.46) | |
| 3:62253444 | rs148757915 | Q>E | A:942 | (33.44, 16.23, 75.83) |
| 3:62253457 | I>T | A:946 | (33.71, 5.60, 70.48) | |
| 3:62253480 | V>L | A:954 | (53.54, 5.43, 58.98) | |
| 3:62253487 | K>T | A:956 | (54.21, 6.60, 50.72) | |
| 3:62254719 | D>H | A:962 | (51.86, 10.71, 66.62) | |
| 3:62254748 | E>D | A:971 | (51.43, 5.70, 79.20) | |
| 3:62254765 | rs145097172 | I>T | A:977 | (46.10, 6.35, 83.50) |
| 3:62254771 | rs201115216 | T>M | A:979 | (44.94, 0.58, 80.15) |
| 3:62254809 | COSM169007 | R>C | A:992 | (43.30, -0.92, 69.46) |
| 3:62254810 | COSM193601 | R>H | A:992 | (43.30, -0.92, 69.46) |
| 3:62254812 | R>C | A:993 | (37.79, -2.88, 75.51) | |
| 3:62254813 | R>H | A:993 | (37.79, -2.88, 75.51) | |
| 3:62254827 | N>Y | A:998 | (40.81, 11.06, 85.94) | |
| 3:62257080 | G>A | A:1011 | (31.70, 1.26, 88.71) | |
| 3:62257083 | COSM1471635 | R>H | A:1012 | (36.87, 2.44, 90.61) |
| 3:62257091 | E>Q | A:1015 | (37.71, 3.75, 86.01) | |
| 3:62257104 | I>S | A:1019 | (36.02, 1.12, 72.05) | |
| 3:62257121 | rs151031619 | Q>E | A:1025 | (43.78, -1.70, 54.56) |
| 3:62257127 | P>S | A:1027 | (44.23, 4.05, 50.72) | |
| 3:62257145 | E>K | A:1033 | (38.82, -0.32, 44.71) | |
| 3:62257154 | L>V | A:1036 | (31.84, -4.36, 51.16) | |
| 3:62257167 | rs373945707 | T>S | A:1040 | (31.57, -3.54, 57.80) |
| 3:62257185 | COSM446950 | S>L | A:1046 | (27.99, 3.27, 64.70) |
| 3:62257193 | R>W | A:1049 | (27.02, 6.47, 69.25) | |
| 3:62257194 | rs150212631 | R>Q | A:1049 | (27.02, 6.47, 69.25) |
| 3:62257196 | rs146981409 | M>V | A:1050 | (26.37, 3.10, 73.80) |
| 3:62257206 | T>M | A:1053 | (27.53, 8.98, 75.07) | |
| 3:62257217 | L>V | A:1057 | (36.86, 10.95, 68.37) | |
| 3:62257228 | C>W | A:1060 | (42.71, 11.28, 60.31) | |
| 3:62258628 | V>M | A:1064 | (39.18, 16.81, 57.06) | |
| 3:62258646 | Y>H | A:1070 | (32.79, 7.43, 59.73) | |
| 3:62258647 | Y>C | A:1070 | (32.79, 7.43, 59.73) | |
| 3:62258649 | rs138240632 | I>V | A:1071 | (30.82, 12.01, 59.46) |
| 3:62258650 | I>T | A:1071 | (30.82, 12.01, 59.46) | |
| 3:62258652 | V>L | A:1072 | (28.60, 11.58, 55.30) | |
| 3:62258681 | K>N | A:1081 | (17.98, 2.36, 59.33) | |
| 3:62258682 | D>H | A:1082 | (14.56, 6.93, 60.04) | |
| 3:62258700 | rs148186037 | V>I | A:1088 | (25.09, 13.88, 50.53) |
| 3:62258709 | F>I | A:1091 | (25.03, 16.23, 56.34) | |
| 3:62258719 | H>R | A:1094 | (25.26, 21.81, 58.30) | |
| 3:62258733 | R>C | A:1099 | (36.89, 20.67, 60.76) | |
| 3:62258734 | COSM1263478 | R>H | A:1099 | (36.89, 20.67, 60.76) |
| 3:62258740 | Y>C | A:1101 | (39.48, 22.18, 54.02) | |
| 3:62258742 | L>F | A:1102 | (34.63, 18.39, 56.05) | |
| 3:62259389 | I>T | A:1112 | (30.12, 9.24, 49.93) | |
| 3:62259394 | D>N | A:1114 | (30.01, 4.77, 44.99) | |
| 3:62259409 | A>S | A:1119 | (24.06, -0.20, 50.68) | |
| 3:62259422 | K>T | A:1123 | (21.35, -5.66, 51.63) | |
| 3:62259430 | E>Q | A:1126 | (26.53, -10.28, 59.30) | |
| 3:62259433 | rs373896623 | V>L | A:1127 | (23.81, -14.24, 59.61) |
| 3:62259442 | rs141205324 | N>H | A:1130 | (21.49, -19.22, 66.63) |
| 3:62259447 | Q>H | A:1131 | (19.55, -15.85, 62.66) | |
| 3:62259455 | rs142191522 | S>N | A:1134 | (16.15, -19.62, 58.94) |
| 3:62259458 | Y>C | A:1135 | (19.65, -16.10, 55.61) | |
| 3:62259471 | I>M | A:1139 | (18.12, -17.62, 50.87) | |
| 3:62259476 | rs377021023 | I>T | A:1141 | (12.18, -19.61, 49.37) |
| 3:62259518 | K>R | A:1155 | (24.05, -11.55, 40.34) | |
| 3:62261552 | rs548790891 | V>A | A:1157 | (28.93, -12.51, 43.71) |
| 3:62261561 | C>Y | A:1160 | (33.09, -9.72, 38.17) | |
| 3:62261597 | K>T | A:1172 | (45.27, -8.51, 28.94) | |
| 3:62261611 | E>Q | A:1177 | (51.34, -17.41, 25.89) | |
| 3:62261613 | rs199721492 | E>D | A:1177 | (51.34, -17.41, 25.89) |
| 3:62261614 | K>Q | A:1178 | (52.45, -15.83, 31.58) | |
| 3:62261624 | N>S | A:1181 | (41.51, -19.74, 31.72) | |
| 3:62262652 | R>C | A:1189 | (43.96, -3.83, 43.02) | |
| 3:62262653 | rs148705310 | R>H | A:1189 | (43.96, -3.83, 43.02) |
| 3:62262655 | A>T | A:1190 | (44.92, -7.98, 43.17) | |
| 3:62262656 | A>G | A:1190 | (44.92, -7.98, 43.17) | |
| 3:62262659 | rs141644107 | R>Q | A:1191 | (48.97, -7.58, 39.19) |
| 3:62262668 | L>P | A:1194 | (56.98, -10.76, 39.73) | |
| 3:62262705 | I>M | A:1206 | (52.06, -14.14, 38.18) | |
| 3:62262713 | S>F | A:1209 | (45.30, -13.10, 43.20) | |
| 3:62262716 | rs375459395 | Y>C | A:1210 | (47.67, -10.14, 46.49) |
| 3:62263245 | E>A | A:1219 | (45.52, -14.42, 54.96) | |
| 3:62263248 | F>C | A:1220 | (44.69, -16.49, 51.60) | |
| 3:62263250 | I>L | A:1221 | (48.40, -15.72, 46.82) | |
| 3:62263253 | I>V | A:1222 | (44.21, -17.49, 44.49) | |
| 3:62263268 | L>V | A:1227 | (52.52, -23.46, 33.10) | |
| 3:62263271 | P>A | A:1228 | (56.30, -25.42, 32.41) | |
| 3:62263296 | R>Q | A:1236 | (60.38, -14.38, 40.26) | |
| 3:62263311 | rs147611132 | H>R | A:1241 | (55.26, -12.06, 48.05) |
| 3:62263312 | H>Q | A:1241 | (55.26, -12.06, 48.05) | |
| 3:62263317 | A>V | A:1243 | (55.91, -17.63, 51.24) | |
| 3:62263322 | I>F | A:1245 | (52.04, -22.15, 53.18) | |
| 3:62263328 | V>I | A:1247 | (47.86, -25.30, 49.18) | |
| 3:62263331 | M>L | A:1248 | (48.60, -28.84, 45.07) | |
| 3:62267272 | E>A | A:1267 | (69.19, -34.40, 42.69) | |
| 3:62267293 | rs201725005 | A>V | A:1274 | (68.08, -14.80, 43.34) |
| 3:62267301 | rs143489755 | V>I | A:1277 | (64.56, -24.32, 45.17) |
| 3:62267335 | S>F | A:1288 | (39.23, -39.50, 57.77) | |
| 3:62267338 | N>S | A:1289 | (38.11, -41.30, 54.74) | |
| 3:62267356 | I>S | A:1295 | (54.37, -32.71, 53.13) | |
| 3:62267362 | D>G | A:1297 | (59.79, -29.26, 53.43) | |
| 3:62267364 | F>V | A:1298 | (60.80, -27.25, 49.13) | |
| 3:62267379 | T>A | A:1303 | (72.36, -16.22, 45.19) | |
| 3:62268411 | V>L | A:1308 | (66.92, -19.13, 54.15) | |
| 3:62268423 | R>W | A:1312 | (55.50, -27.47, 55.02) | |
| 3:62268472 | S>N | A:1328 | (34.75, -33.22, 56.77) | |
| 3:62268487 | rs199516750 | I>T | A:1333 | (40.32, -25.63, 56.48) |
| 3:62268493 | V>D | A:1335 | (45.66, -28.85, 58.69) | |
| 3:62268503 | E>D | A:1338 | (46.92, -25.01, 63.27) | |
| 3:62268508 | A>G | A:1340 | (49.77, -20.69, 59.55) | |
| 3:62268522 | G>R | A:1345 | (53.03, -14.86, 55.06) | |
| 3:62268528 | rs199914909 | T>A | A:1347 | (48.78, -18.94, 51.96) |
| 3:62268538 | H>L | A:1350 | (47.84, -24.42, 43.26) | |
| 3:62278103 | A>T | A:1355 | (39.29, -21.53, 40.84) | |
| 3:62278116 | G>A | A:1359 | (38.38, -20.34, 46.97) | |
| 3:62278124 | C>G | A:1362 | (39.99, -19.06, 50.95) | |
| 3:62278133 | rs137949763 | T>A | A:1365 | (39.41, -20.27, 56.10) |
| 3:62278154 | E>K | A:1372 | (36.27, -19.20, 65.85) | |
| 3:62278158 | N>S | A:1373 | (36.37, -15.07, 66.17) | |
| 3:62278159 | N>K | A:1373 | (36.37, -15.07, 66.17) | |
| 3:62278170 | V>E | A:1377 | (28.46, -15.78, 58.73) | |
| 3:62278211 | COSM276954 | P>S | A:1391 | (37.69, -12.50, 38.07) |
| 3:62278220 | F>L | A:1394 | (33.27, -18.35, 43.65) | |
| 3:62278229 | I>L | A:1397 | (24.17, -21.01, 42.33) | |
| 3:62278855 | Y>F | A:1404 | (25.10, -19.84, 52.51) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:62240819 | COSM1617981 | V>F | A:830 | (16.20, 5.33, 48.60) |
| 3:62240846 | COSM1263476 | E>K | A:839 | (21.31, 11.80, 36.85) |
| 3:62254741 | COSM3737243 | N>S | A:969 | (50.48, -2.66, 79.54) |
| 3:62254809 | COSM169007 | R>C | A:992 | (43.30, -0.92, 69.46) |
| 3:62254810 | COSM193601 | R>H | A:992 | (43.30, -0.92, 69.46) |
| 3:62258677 | COSM249683 | I>R | A:1080 | (18.75, 5.32, 54.48) |
| 3:62258734 | COSM1263478 | R>H | A:1099 | (36.89, 20.67, 60.76) |
| 3:62263230 | COSM2783008 | Y>S | A:1214 | (38.53, -12.74, 60.55) |
| 3:62267340 | COSM480517 | E>K | A:1290 | (42.92, -44.18, 55.34) |