General Structure Information
| PDB ID | 2jjd |
| HGNC Gene Label(s) | PTPRE |
| Structure Name | protein tyrosine phosphatase, receptor type, e isoform |
| Resolution | 3.2Å |
| Reference | AUTH A.J.BARR,E.UGOCHUKWU,W.H.LEE,O.N.F.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 | 541 |
| Number Of SNVs | 127 |
| Number Of Permutations | 36406 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.135 |
| p-value | 0.012 |
COSMIC
| Number Of Residues | 541 |
| Number Of SNVs | 6 |
| Number Of Permutations | 765 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.067 |
| p-value | 0.926 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 127 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.058 |
| p-value | 0.19 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:129847850 | rs369714622 | P>S | C:114 | (-27.31, -33.30, -77.35) |
| 10:129847856 | P>S | C:116 | (-25.93, -31.78, -83.62) | |
| 10:129847862 | E>Q | C:118 | (-25.10, -29.69, -88.19) | |
| 10:129847880 | rs373652260 | I>F | C:124 | (-28.53, -20.25, -82.23) |
| 10:129847883 | R>C | C:125 | (-32.15, -18.94, -84.37) | |
| 10:129847884 | rs200125787 | R>H | C:125 | (-32.15, -18.94, -84.37) |
| 10:129847893 | S>Y | C:128 | (-34.31, -15.99, -80.43) | |
| 10:129847916 | rs201268537 COSM1703239 COSM1703240 |
R>W | C:136 | (-34.06, -16.85, -71.21) |
| 10:129847925 | F>L | C:139 | (-29.72, -19.65, -67.37) | |
| 10:129847926 | F>Y | C:139 | (-29.72, -19.65, -67.37) | |
| 10:129847929 | rs146821168 | N>S | C:140 | (-34.08, -20.04, -66.00) |
| 10:129854397 | S>C | C:144 | (-28.13, -24.37, -58.19) | |
| 10:129854405 | rs576763520 | I>V | C:147 | (-29.58, -29.23, -53.36) |
| 10:129854412 | rs375764437 COSM3435616 COSM3435617 |
G>E | C:149 | (-23.80, -29.89, -51.11) |
| 10:129854414 | rs78752313 | T>S | C:150 | (-21.18, -29.73, -48.21) |
| 10:129854427 | A>E | C:154 | (-16.72, -22.05, -45.94) | |
| 10:129854433 | K>T | C:156 | (-15.57, -21.83, -40.57) | |
| 10:129854468 | rs145455270 | I>V | C:168 | (-20.12, -17.01, -54.20) |
| 10:129859228 | COSM916048 COSM916049 |
S>R | C:179 | (-1.10, -26.61, -46.59) |
| 10:129859232 | L>V | C:181 | (0.05, -23.26, -41.77) | |
| 10:129859245 | rs575682606 | P>L | C:185 | (-5.79, -21.51, -36.90) |
| 10:129859247 | C>R | C:186 | (-7.94, -22.27, -40.49) | |
| 10:129859253 | rs201812647 | D>N | C:188 | (-7.45, -25.11, -44.47) |
| 10:129859259 | I>L | C:190 | (-8.58, -20.98, -50.85) | |
| 10:129859950 | K>T | C:199 | (-11.82, -35.56, -70.67) | |
| 10:129859956 | rs138058188 | K>R | C:201 | (-9.64, -34.30, -64.26) |
| 10:129859967 | I>V | C:205 | (-8.24, -23.91, -60.05) | |
| 10:129859974 | A>V | C:207 | (-10.78, -18.75, -58.27) | |
| 10:129861362 | T>M | C:214 | (-6.36, -13.82, -49.70) | |
| 10:129861370 | D>N | C:217 | (-3.05, -17.87, -50.08) | |
| 10:129861379 | R>G | C:220 | (-0.09, -21.38, -49.60) | |
| 10:129861403 | rs143202687 | A>T | C:228 | (1.79, -22.37, -65.01) |
| 10:129861412 | rs367833771 | V>I | C:231 | (-6.75, -16.97, -66.42) |
| 10:129864355 | Y>C | C:247 | (-2.41, -11.32, -58.22) | |
| 10:129864393 | R>W | C:260 | (8.98, -14.73, -54.43) | |
| 10:129864394 | R>Q | C:260 | (8.98, -14.73, -54.43) | |
| 10:129864402 | rs141160831 | V>M | C:263 | (8.08, -8.95, -63.21) |
| 10:129864408 | D>N | C:265 | (7.26, -9.79, -68.65) | |
| 10:129864409 | D>V | C:265 | (7.26, -9.79, -68.65) | |
| 10:129864414 | rs147368772 | V>M | C:267 | (2.87, -8.16, -73.47) |
| 10:129864438 | R>W | C:275 | (1.17, -9.62, -66.63) | |
| 10:129864450 | I>V | C:279 | (7.17, -18.21, -58.56) | |
| 10:129866412 | P>L | C:290 | (13.01, -21.68, -59.77) | |
| 10:129866448 | P>L | C:302 | (-17.54, -5.78, -70.87) | |
| 10:129866456 | rs376893332 | G>R | C:305 | (-21.56, -8.10, -70.22) |
| 10:129866471 | P>S | C:310 | (-16.36, -14.20, -80.35) | |
| 10:129866472 | rs566201147 | P>L | C:310 | (-16.36, -14.20, -80.35) |
| 10:129866505 | K>R | C:321 | (-3.10, -23.58, -74.90) | |
| 10:129866508 | rs145419797 | T>M | C:322 | (0.22, -21.94, -76.38) |
| 10:129866526 | rs548229621 | A>V | C:328 | (1.29, -28.71, -65.62) |
| 10:129866534 | rs143600735 | I>V | C:331 | (-5.41, -23.60, -65.61) |
| 10:129867957 | A>T | C:337 | (-16.54, -14.71, -57.64) | |
| 10:129867993 | D>N | C:349 | (-12.99, -25.15, -73.66) | |
| 10:129868001 | rs41282868 | M>I | C:351 | (-17.85, -27.63, -75.33) |
| 10:129868004 | rs551149385 | M>I | C:352 | (-13.55, -25.80, -78.38) |
| 10:129868018 | A>V | C:357 | (-14.38, -35.25, -80.76) | |
| 10:129868053 | R>G | C:369 | (-21.39, -30.78, -64.03) | |
| 10:129868575 | rs140608471 | T>M | C:385 | (-25.98, -16.76, -75.16) |
| 10:129868583 | Y>H | C:388 | (-24.83, -22.15, -77.28) | |
| 10:129868600 | E>D | C:393 | (-17.40, -17.49, -84.74) | |
| 10:129868613 | rs568266268 | G>R | C:398 | (-12.27, -21.12, -87.19) |
| 10:129868620 | T>R | C:400 | (-8.69, -18.99, -90.71) | |
| 10:129868634 | S>P | C:405 | (5.65, -22.09, -91.66) | |
| 10:129869082 | N>S | C:435 | (-22.43, -13.24, -96.08) | |
| 10:129869088 | R>Q | C:437 | (-24.52, -8.72, -91.53) | |
| 10:129869094 | M>T | C:439 | (-26.22, -2.94, -89.16) | |
| 10:129869111 | rs137950388 | T>A | C:445 | (-26.43, 9.01, -86.94) |
| 10:129869112 | COSM203780 COSM203781 |
T>M | C:445 | (-26.43, 9.01, -86.94) |
| 10:129869144 | R>G | C:456 | (-17.44, 11.69, -100.79) | |
| 10:129870406 | D>E | C:464 | (-23.22, 4.44, -83.79) | |
| 10:129870414 | R>Q | C:467 | (-20.18, 8.54, -83.93) | |
| 10:129870428 | rs147174284 | M>V | C:472 | (-21.44, 21.15, -80.51) |
| 10:129870449 | T>A | C:479 | (-22.10, 19.76, -85.26) | |
| 10:129870458 | I>V | C:482 | (-17.12, 13.14, -88.99) | |
| 10:129870467 | S>T | C:485 | (-14.79, 4.88, -87.66) | |
| 10:129870474 | rs547109451 | I>R | C:487 | (-10.75, 1.04, -86.23) |
| 10:129871608 | rs141953510 | R>Q | C:491 | (0.49, -3.85, -79.48) |
| 10:129871620 | Y>C | C:495 | (-3.48, 3.07, -83.44) | |
| 10:129871628 | A>T | C:498 | (-11.62, 5.54, -90.42) | |
| 10:129871649 | rs150682477 | H>Y | C:505 | (-19.51, 20.11, -97.16) |
| 10:129871653 | T>M | C:506 | (-16.18, 18.33, -94.57) | |
| 10:129871671 | R>K | C:512 | (-14.14, 20.11, -85.42) | |
| 10:129871703 | V>M | C:523 | (-2.54, 7.71, -94.15) | |
| 10:129871713 | rs371426050 | T>M | C:526 | (-6.47, 9.00, -102.66) |
| 10:129871723 | Q>H | C:529 | (-8.22, 13.34, -108.96) | |
| 10:129871725 | E>G | C:530 | (-9.61, 10.03, -110.25) | |
| 10:129874894 | E>K | C:543 | (2.61, 26.84, -99.85) | |
| 10:129874897 | rs143949800 | G>C | C:544 | (1.53, 27.76, -96.67) |
| 10:129874907 | T>S | C:547 | (-7.82, 28.75, -92.28) | |
| 10:129874909 | H>Y | C:548 | (-9.75, 25.12, -93.19) | |
| 10:129874924 | I>F | C:553 | (-2.81, 24.24, -91.62) | |
| 10:129874929 | rs148469523 | E>D | C:554 | (1.47, 25.44, -91.85) |
| 10:129874932 | I>M | C:555 | (3.76, 23.44, -95.19) | |
| 10:129874939 | D>Y | C:558 | (7.85, 18.69, -98.47) | |
| 10:129874943 | T>I | C:559 | (9.33, 15.04, -99.24) | |
| 10:129874967 | R>Q | C:567 | (2.83, 16.43, -97.58) | |
| 10:129874988 | N>S | C:574 | (-7.43, 30.06, -83.03) | |
| 10:129875897 | E>G | C:581 | (-0.03, 25.80, -74.69) | |
| 10:129875899 | E>K | C:582 | (-2.22, 23.46, -76.15) | |
| 10:129875903 | Q>R | C:583 | (-2.63, 27.31, -79.39) | |
| 10:129875905 | V>I | C:584 | (0.86, 24.14, -81.22) | |
| 10:129875909 | COSM427239 COSM427240 |
R>Q | C:585 | (-1.31, 19.82, -81.83) |
| 10:129875912 | rs370247861 | V>A | C:586 | (3.54, 18.79, -85.44) |
| 10:129875918 | R>H | C:588 | (4.91, 13.35, -90.85) | |
| 10:129875923 | F>L | C:590 | (2.77, 9.44, -94.11) | |
| 10:129875935 | COSM1346758 COSM1346759 |
G>S | C:594 | (0.67, 3.36, -105.28) |
| 10:129875945 | E>G | C:597 | (-6.93, 4.00, -110.76) | |
| 10:129875947 | rs555685240 | I>V | C:598 | (-7.43, 0.61, -111.67) |
| 10:129875950 | G>R | C:599 | (-6.88, -1.40, -108.81) | |
| 10:129875956 | P>S | C:601 | (-1.14, -2.49, -106.01) | |
| 10:129875959 | A>T | C:602 | (1.76, -4.72, -108.45) | |
| 10:129875962 | rs376366402 COSM333745 COSM333746 |
E>K | C:603 | (3.87, -4.81, -105.81) |
| 10:129875971 | G>S | C:606 | (5.11, 0.12, -100.82) | |
| 10:129875980 | D>Y | C:609 | (7.15, 1.11, -96.83) | |
| 10:129875983 | L>F | C:610 | (3.28, 3.46, -96.14) | |
| 10:129875989 | rs530962130 | A>T | C:612 | (7.00, 1.23, -91.74) |
| 10:129875993 | A>D | C:613 | (6.82, 4.74, -91.90) | |
| 10:129875995 | rs141432047 | V>M | C:614 | (3.35, 5.20, -90.21) |
| 10:129876047 | S>N | C:631 | (-13.12, 8.47, -100.82) | |
| 10:129877828 | G>R | C:633 | (-13.56, 5.04, -96.18) | |
| 10:129877838 | COSM1703243 COSM1703244 |
R>Q | C:636 | (-7.75, 2.46, -101.60) |
| 10:129877877 | rs199816020 | R>Q | C:649 | (-0.96, -11.79, -85.15) |
| 10:129877882 | K>E | C:651 | (6.16, -10.00, -86.10) | |
| 10:129877888 | E>K | C:653 | (1.88, -13.73, -82.38) | |
| 10:129877892 | rs371709759 | G>E | C:654 | (3.72, -15.94, -86.20) |
| 10:129877897 | rs374983935 | L>I | C:656 | (-1.51, -15.19, -91.01) |
| 10:129877903 | V>L | C:658 | (-6.20, -12.32, -93.43) | |
| 10:129877904 | V>A | C:658 | (-6.20, -12.32, -93.43) | |
| 10:129877928 | R>Q | C:666 | (-16.65, -6.26, -93.62) | |
| 10:129877942 | H>D | C:671 | (-18.75, -2.06, -97.35) | |
| 10:129877953 | Q>H | C:674 | (-15.16, -2.72, -100.93) | |
| 10:129881103 | Y>C | C:679 | (-9.14, -11.13, -98.81) | |
| 10:129881120 | V>M | C:685 | (1.62, -7.91, -98.89) | |
| 10:129881129 | COSM916074 COSM916075 |
D>Y | C:688 | (6.25, -10.14, -99.49) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:129859952 | COSM4408782 | E>K | C:200 | (-8.58, -32.96, -68.13) |
| 10:129867964 | COSM1675657 | V>A | C:339 | (-18.64, -17.77, -60.45) |
| 10:129868069 | COSM1222632 | R>H | C:374 | (-17.44, -22.90, -57.69) |
| 10:129868596 | COSM1603147 | L>R | C:392 | (-21.48, -20.66, -84.32) |
| 10:129869087 | COSM3435632 | R>W | C:437 | (-24.52, -8.72, -91.53) |
| 10:129869112 | COSM203781 | T>M | C:445 | (-26.43, 9.01, -86.94) |
| 10:129871629 | COSM4423695 | A>V | C:498 | (-11.62, 5.54, -90.42) |
| 10:129877885 | COSM916072 | A>S | C:652 | (4.94, -10.88, -82.81) |