General Structure Information
| PDB ID | 2v5y |
| HGNC Gene Label(s) | PTPRM |
| Structure Name | crystal structure of the receptor protein tyrosine phosphatase mu ectodomain |
| Resolution | 3.1Å |
| Reference | AUTH A.R.ARICESCU,C.SIEBOLD,K.CHOUDHURI,V.T.CHANG,W.LU,S.J.DAVIS,AUTH 2 P.A.VAN DER MERWE,E.Y.JONESTITL STRUCTURE OF A TYROSINE PHOSPHATASE ADHESIVE INTERACTIONTITL 2 REVEALS A SPACER-CLAMP MECHANISM.REF SCIENCE V. 317 1217 2007REFN ISSN 0036-8075PMID 17761881DOI 10.1126/SCIENCE.1144646 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 564 |
| Number Of SNVs | 125 |
| Number Of Permutations | 69641 |
| Optimal Distance Threshold | 67.0 |
| K Statistic | 0.52 |
| p-value | 0.645 |
COSMIC
| Number Of Residues | 564 |
| Number Of SNVs | 7 |
| Number Of Permutations | 13450 |
| Optimal Distance Threshold | 26.0 |
| K Statistic | 0.048 |
| p-value | 0.655 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 125 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 24.0 |
| K Statistic | -0.197 |
| p-value | 0.605 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 18:7567881 | T>K | A:2 | (211.61, 76.51, -9.88) | |
| 18:7774160 | rs373506007 | F>L | A:9 | (221.94, 71.53, 4.97) |
| 18:7774168 | P>L | A:12 | (224.48, 78.60, 4.56) | |
| 18:7774190 | rs35224276 | S>R | A:19 | (214.43, 79.30, 10.14) |
| 18:7774206 | D>N | A:25 | (213.73, 75.54, 24.54) | |
| 18:7774213 | N>S | A:27 | (218.82, 76.70, 18.21) | |
| 18:7774237 | T>N | A:35 | (235.61, 71.14, 6.70) | |
| 18:7774242 | P>S | A:37 | (237.40, 67.13, 11.05) | |
| 18:7774243 | P>L | A:37 | (237.40, 67.13, 11.05) | |
| 18:7774261 | rs151278836 | M>K | A:43 | (229.23, 62.43, 14.43) |
| 18:7774266 | S>P | A:45 | (230.28, 62.32, 7.01) | |
| 18:7888114 | rs374726087 | M>I | A:49 | (221.20, 70.77, 10.52) |
| 18:7888115 | rs113099035 | L>M | A:50 | (223.26, 68.38, 14.74) |
| 18:7888116 | L>R | A:50 | (223.26, 68.38, 14.74) | |
| 18:7888124 | A>T | A:53 | (220.98, 65.89, 23.30) | |
| 18:7888128 | S>F | A:54 | (224.25, 65.90, 24.70) | |
| 18:7888149 | rs139956933 | R>K | A:61 | (210.12, 71.16, 22.67) |
| 18:7888155 | H>R | A:63 | (211.03, 73.99, 16.69) | |
| 18:7888181 | N>Y | A:72 | (200.29, 75.41, -8.58) | |
| 18:7888199 | D>N | A:78 | (212.94, 64.21, -0.08) | |
| 18:7888202 | F>I | A:79 | (213.45, 63.95, 5.19) | |
| 18:7888221 | S>N | A:85 | (223.34, 56.71, 20.99) | |
| 18:7888223 | rs183539758 | K>Q | A:86 | (226.56, 57.67, 23.92) |
| 18:7888224 | K>R | A:86 | (226.56, 57.67, 23.92) | |
| 18:7888239 | P>L | A:91 | (218.23, 61.05, 21.79) | |
| 18:7888251 | rs147625334 | N>S | A:95 | (208.13, 65.63, 15.59) |
| 18:7888268 | rs188245197 | N>H | A:101 | (197.32, 79.29, 5.66) |
| 18:7888274 | rs140491606 | G>R | A:103 | (198.56, 78.75, 11.61) |
| 18:7888294 | I>M | A:109 | (202.69, 64.85, 9.53) | |
| 18:7888296 | rs371315590 | W>S | A:110 | (208.00, 61.63, 10.14) |
| 18:7888301 | I>V | A:112 | (211.29, 58.92, 14.51) | |
| 18:7888305 | S>C | A:113 | (211.11, 57.34, 18.74) | |
| 18:7888314 | COSM708797 | P>Q | A:116 | (219.46, 54.53, 17.94) |
| 18:7888317 | T>K | A:117 | (220.34, 53.37, 13.49) | |
| 18:7888329 | rs560144418 | N>S | A:121 | (216.79, 56.77, 7.06) |
| 18:7888366 | rs147856783 | N>K | A:133 | (196.39, 77.88, 0.21) |
| 18:7888367 | F>L | A:134 | (200.52, 79.56, 3.06) | |
| 18:7888374 | Q>R | A:136 | (206.09, 76.40, 7.57) | |
| 18:7906522 | T>I | A:143 | (214.89, 66.20, 24.58) | |
| 18:7906540 | Y>C | A:149 | (224.98, 63.28, 18.55) | |
| 18:7906545 | COSM1389896 | A>T | A:151 | (220.11, 64.43, 11.88) |
| 18:7906548 | I>V | A:152 | (218.33, 66.66, 9.06) | |
| 18:7906551 | D>N | A:153 | (221.74, 65.67, 5.00) | |
| 18:7906563 | V>L | A:157 | (211.39, 70.41, -2.96) | |
| 18:7926625 | T>A | A:183 | (181.91, 60.60, 5.87) | |
| 18:7926655 | V>M | A:193 | (200.40, 48.64, 1.16) | |
| 18:7949191 | rs199848221 | R>G | A:206 | (187.84, 63.61, 19.56) |
| 18:7949212 | I>V | A:213 | (190.37, 50.94, 1.64) | |
| 18:7949231 | R>L | A:219 | (197.74, 55.59, -10.90) | |
| 18:7949234 | R>H | A:220 | (193.40, 56.43, -9.09) | |
| 18:7949254 | V>I | A:227 | (183.04, 61.64, 12.70) | |
| 18:7949267 | T>I | A:231 | (178.63, 67.35, 18.80) | |
| 18:7949273 | rs372350305 | R>Q | A:233 | (181.91, 70.80, 22.21) |
| 18:7949275 | D>N | A:234 | (183.10, 67.02, 16.90) | |
| 18:7949279 | A>D | A:235 | (183.52, 71.12, 14.86) | |
| 18:7949290 | R>C | A:239 | (195.39, 67.23, 7.91) | |
| 18:7949298 | M>I | A:241 | (196.85, 61.21, 7.42) | |
| 18:7949302 | rs140369696 | R>C | A:243 | (203.62, 56.65, 8.46) |
| 18:7949303 | R>H | A:243 | (203.62, 56.65, 8.46) | |
| 18:7949305 | T>P | A:244 | (204.06, 54.68, 3.85) | |
| 18:7949306 | T>N | A:244 | (204.06, 54.68, 3.85) | |
| 18:7949333 | rs61737159 | Y>C | A:253 | (193.61, 70.97, 7.45) |
| 18:7949339 | E>A | A:255 | (185.53, 73.16, 8.07) | |
| 18:7949345 | V>G | A:257 | (179.78, 72.11, 9.69) | |
| 18:7955127 | rs148967648 | V>I | A:263 | (163.21, 72.48, 17.81) |
| 18:7955151 | rs368960026 | A>T | A:271 | (142.81, 80.06, 15.89) |
| 18:7955154 | S>T | A:272 | (139.73, 78.19, 15.45) | |
| 18:7955183 | Q>H | A:281 | (149.06, 80.11, 14.00) | |
| 18:7955203 | rs202158284 | N>S | A:288 | (165.97, 75.87, 19.90) |
| 18:7955218 | I>T | A:293 | (163.42, 75.42, 7.55) | |
| 18:7955224 | A>G | A:295 | (160.32, 71.10, 6.01) | |
| 18:7955227 | COSM3147711 COSM3362611 |
R>Q | A:296 | (157.20, 74.22, 8.13) |
| 18:7955241 | C>R | A:301 | (147.63, 62.89, 19.08) | |
| 18:7955245 | COSM1389897 | T>M | A:302 | (144.21, 61.13, 20.22) |
| 18:7955274 | rs373015243 | P>T | A:312 | (152.71, 67.87, 5.37) |
| 18:7955287 | rs150274533 | T>M | A:316 | (151.64, 79.95, 9.20) |
| 18:7955289 | S>C | A:317 | (147.81, 79.38, 8.72) | |
| 18:7955290 | S>N | A:317 | (147.81, 79.38, 8.72) | |
| 18:7955322 | rs145090404 | E>K | A:328 | (141.88, 66.06, 24.51) |
| 18:7955359 | E>V | A:340 | (170.31, 61.43, 7.26) | |
| 18:7955368 | T>I | A:343 | (163.68, 66.54, 11.18) | |
| 18:8069689 | M>V | A:360 | (123.34, 62.32, 12.94) | |
| 18:8069690 | rs147623982 | M>T | A:360 | (123.34, 62.32, 12.94) |
| 18:8069695 | G>S | A:362 | (117.15, 60.82, 15.99) | |
| 18:8069708 | rs377050800 | L>P | A:366 | (109.74, 54.79, 18.21) |
| 18:8069722 | V>F | A:371 | (99.20, 49.34, 25.03) | |
| 18:8069726 | K>R | A:372 | (98.50, 48.84, 29.89) | |
| 18:8069731 | COSM990150 COSM3422348 |
R>W | A:374 | (96.23, 54.68, 34.19) |
| 18:8069732 | R>Q | A:374 | (96.23, 54.68, 34.19) | |
| 18:8069736 | Q>H | A:375 | (100.88, 51.93, 31.39) | |
| 18:8069743 | rs148379127 | I>V | A:378 | (108.29, 53.34, 24.34) |
| 18:8069747 | rs141549150 | R>L | A:379 | (111.34, 49.05, 21.44) |
| 18:8069809 | rs139024463 | C>R | A:400 | (100.68, 65.08, 23.63) |
| 18:8069815 | rs201218602 | Q>K | A:402 | (93.82, 65.99, 24.42) |
| 18:8069824 | G>R | A:405 | (89.58, 69.54, 27.27) | |
| 18:8069827 | Q>K | A:406 | (92.14, 70.54, 29.85) | |
| 18:8069835 | Q>H | A:408 | (97.79, 67.20, 29.72) | |
| 18:8069857 | D>N | A:416 | (118.41, 53.64, 29.26) | |
| 18:8069860 | T>A | A:417 | (123.17, 55.81, 28.40) | |
| 18:8069881 | H>Y | A:424 | (110.38, 55.27, 29.18) | |
| 18:8069882 | H>R | A:424 | (110.38, 55.27, 29.18) | |
| 18:8069887 | I>L | A:426 | (104.70, 56.62, 29.59) | |
| 18:8069900 | S>L | A:430 | (93.88, 58.93, 29.70) | |
| 18:8069912 | N>S | A:434 | (95.18, 59.75, 20.80) | |
| 18:8069926 | L>M | A:439 | (112.47, 60.17, 21.42) | |
| 18:8069941 | P>S | A:444 | (125.34, 71.27, 24.28) | |
| 18:8069963 | Q>P | A:451 | (109.64, 59.21, 13.11) | |
| 18:8069991 | D>E | A:460 | (88.96, 50.71, 31.27) | |
| 18:8069992 | rs375793330 | L>F | A:461 | (85.85, 49.24, 33.14) |
| 18:8076459 | G>V | A:463 | (81.18, 54.41, 34.75) | |
| 18:8076464 | V>L | A:465 | (74.55, 55.63, 34.90) | |
| 18:8076477 | S>C | A:469 | (69.57, 60.05, 34.83) | |
| 18:8076485 | G>R | A:472 | (60.55, 57.14, 34.58) | |
| 18:8076488 | S>G | A:473 | (57.65, 56.61, 32.46) | |
| 18:8076508 | rs149407641 | I>M | A:479 | (58.09, 50.96, 33.02) |
| 18:8076509 | rs369526421 | F>L | A:480 | (60.49, 54.99, 28.76) |
| 18:8076531 | T>I | A:487 | (80.34, 61.11, 33.78) | |
| 18:8076537 | T>I | A:489 | (83.25, 56.53, 29.24) | |
| 18:8076545 | V>I | A:492 | (83.04, 53.13, 23.13) | |
| 18:8076558 | Y>F | A:496 | (73.89, 50.94, 28.41) | |
| 18:8085672 | rs548529823 | T>A | A:499 | (68.41, 44.28, 35.89) |
| 18:8085676 | Y>C | A:500 | (63.26, 43.07, 35.08) | |
| 18:8085679 | K>R | A:501 | (64.42, 42.70, 40.38) | |
| 18:8085685 | V>A | A:503 | (59.84, 44.75, 45.02) | |
| 18:8085688 | rs568430278 | S>T | A:504 | (56.05, 45.41, 45.60) |
| 18:8085727 | G>V | A:517 | (65.17, 40.24, 34.48) | |
| 18:8085730 | R>T | A:518 | (69.70, 39.94, 32.75) | |
| 18:8085757 | H>R | A:527 | (65.74, 53.87, 25.28) | |
| 18:8085765 | F>L | A:530 | (61.17, 47.64, 30.77) | |
| 18:8085766 | F>C | A:530 | (61.17, 47.64, 30.77) | |
| 18:8085808 | COSM125688 | R>Q | A:544 | (76.25, 46.37, 34.75) |
| 18:8085844 | T>K | A:556 | (69.89, 51.70, 41.05) | |
| 18:8085856 | T>I | A:560 | (55.50, 52.36, 40.59) | |
| 18:8088753 | S>C | A:567 | (37.33, 46.07, 33.39) | |
| 18:8088755 | M>V | A:568 | (33.59, 45.56, 33.94) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 18:7906516 | COSM1389894 | V>A | A:141 | (213.90, 67.63, 18.44) |
| 18:7949192 | COSM4916839 | R>Q | A:206 | (187.84, 63.61, 19.56) |
| 18:7955127 | COSM4276946 | V>I | A:263 | (163.21, 72.48, 17.81) |
| 18:7955244 | COSM4276949 | T>A | A:302 | (144.21, 61.13, 20.22) |
| 18:8069731 | COSM990150 | R>W | A:374 | (96.23, 54.68, 34.19) |
| 18:8069752 | COSM3147714 | E>K | A:381 | (118.23, 52.06, 17.16) |
| 18:8085711 | COSM990166 | L>V | A:512 | (55.24, 34.84, 44.11) |
| 18:8085745 | COSM139088 | G>E | A:523 | (74.84, 52.41, 23.42) |