General Structure Information
| PDB ID | 2fh7 |
| HGNC Gene Label(s) | PTPRS |
| Structure Name | crystal structure of the phosphatase domains of human ptp sigma |
| Resolution | 2.0Å |
| Reference | AUTH S.C.ALMO,J.B.BONANNO,J.M.SAUDER,S.EMTAGE,AUTH 2 T.P.DILORENZO,V.MALASHKEVICH,S.R.WASSERMAN,AUTH 3 S.SWAMINATHAN,S.ESWARAMOORTHY,R.AGARWAL,D.KUMARAN,AUTH 4 M.MADEGOWDA,S.RAGUMANI,Y.PATSKOVSKY,J.ALVARADO,AUTH 5 U.A.RAMAGOPAL,J.FABER-BARATA,M.R.CHANCE,A.SALI,AUTH 6 A.FISER,Z.Y.ZHANG,D.S.LAWRENCE,S.K.BURLEYTITL STRUCTURAL GENOMICS OF PROTEIN PHOSPHATASES.REF 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 | 568 |
| Number Of SNVs | 135 |
| Number Of Permutations | 37546 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.007 |
| p-value | 0.914 |
COSMIC
| Number Of Residues | 568 |
| Number Of SNVs | 11 |
| Number Of Permutations | 11688 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.091 |
| p-value | 0.673 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 135 |
| Number Of COSMIC SNVs | 11 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.032 |
| p-value | 0.933 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:5215591 | COSM4080672 COSM4080671 |
P>L | A:1371 | (25.59, 94.34, 19.94) |
| 19:5215588 | P>L | A:1372 | (24.87, 90.61, 20.83) | |
| 19:5215577 | rs200850387 COSM1000154 |
A>T | A:1376 | (13.87, 89.38, 24.70) |
| 19:5215567 | rs373247829 | A>V | A:1379 | (11.06, 92.37, 18.78) |
| 19:5215558 | rs558948003 COSM1394773 |
T>M | A:1382 | (13.16, 93.63, 14.33) |
| 19:5215556 | E>K | A:1383 | (9.56, 97.38, 15.63) | |
| 19:5215552 | rs114166264 | R>Q | A:1384 | (15.76, 99.63, 16.05) |
| 19:5215538 | rs267605547 COSM142766 |
D>N | A:1389 | (10.91, 101.89, 4.70) |
| 19:5215526 | rs369098162 | L>F | A:1393 | (17.74, 96.96, 7.86) |
| 19:5215417 | rs374920205 | D>N | A:1401 | (33.41, 95.00, 6.08) |
| 19:5215383 | rs201183797 | N>S | A:1412 | (39.07, 84.01, -12.93) |
| 19:5215365 | rs530579519 | P>L | A:1418 | (33.13, 77.55, -17.94) |
| 19:5215345 | V>I | A:1425 | (29.43, 84.43, -8.30) | |
| 19:5215308 | rs190342971 | P>L | A:1437 | (43.21, 65.96, -8.88) |
| 19:5215305 | I>T | A:1438 | (41.13, 64.33, -12.95) | |
| 19:5214739 | G>S | A:1443 | (41.02, 72.18, -13.22) | |
| 19:5214712 | rs192807174 | V>M | A:1452 | (30.24, 78.40, 5.47) |
| 19:5214699 | R>Q | A:1456 | (30.50, 77.64, 19.47) | |
| 19:5214700 | rs373940938 | R>W | A:1456 | (30.50, 77.64, 19.47) |
| 19:5214696 | rs369756620 | C>Y | A:1457 | (28.24, 74.05, 14.96) |
| 19:5214697 | rs4807697 | C>R | A:1457 | (28.24, 74.05, 14.96) |
| 19:5214687 | A>V | A:1460 | (29.07, 73.30, 8.50) | |
| 19:5214688 | rs189135288 | A>T | A:1460 | (29.07, 73.30, 8.50) |
| 19:5214669 | G>A | A:1466 | (23.91, 75.54, -9.31) | |
| 19:5214666 | rs116660613 | P>L | A:1467 | (24.43, 72.53, -10.46) |
| 19:5214637 | R>C | A:1477 | (34.69, 64.67, -7.70) | |
| 19:5214631 | V>M | A:1479 | (29.06, 64.96, -2.21) | |
| 19:5214618 | R>Q | A:1483 | (33.91, 61.93, 3.75) | |
| 19:5214615 | S>L | A:1484 | (28.35, 64.85, 2.39) | |
| 19:5214612 | rs139132124 | A>V | A:1485 | (24.58, 63.47, 3.74) |
| 19:5214613 | A>T | A:1485 | (24.58, 63.47, 3.74) | |
| 19:5214604 | rs116515629 | V>I | A:1488 | (19.95, 72.16, 1.06) |
| 19:5214600 | M>T | A:1489 | (17.49, 72.72, -3.82) | |
| 19:5214594 | T>M | A:1491 | (15.65, 76.47, -5.93) | |
| 19:5214591 | COSM1304981 | R>Q | A:1492 | (11.02, 76.93, -8.17) |
| 19:5214592 | rs369295620 COSM1394769 COSM4080664 |
R>W | A:1492 | (11.02, 76.93, -8.17) |
| 19:5214490 | I>S | A:1499 | (17.10, 78.00, -15.87) | |
| 19:5214479 | rs368562196 | Q>E | A:1503 | (17.63, 67.58, -13.16) |
| 19:5214461 | G>S | A:1509 | (17.63, 55.45, -10.89) | |
| 19:5214457 | rs147152459 | T>M | A:1510 | (21.33, 54.72, -11.92) |
| 19:5214448 | Y>F | A:1513 | (25.87, 62.20, -12.60) | |
| 19:5214446 | rs116099658 | G>S | A:1514 | (31.49, 60.65, -13.87) |
| 19:5214440 | rs540902322 | I>V | A:1516 | (29.88, 59.30, -8.78) |
| 19:5214430 | T>M | A:1519 | (20.67, 55.57, -7.22) | |
| 19:5214413 | E>K | A:1525 | (5.83, 65.98, -4.34) | |
| 19:5214395 | COSM1222687 | V>I | A:1531 | (12.66, 64.60, 0.20) |
| 19:5214385 | rs527477754 | F>S | A:1534 | (19.71, 60.40, -4.05) |
| 19:5214386 | rs143481159 | F>L | A:1534 | (19.71, 60.40, -4.05) |
| 19:5214377 | H>D | A:1537 | (29.29, 52.96, -6.33) | |
| 19:5214374 | K>E | A:1538 | (33.89, 56.17, -6.74) | |
| 19:5212483 | R>H | A:1545 | (29.14, 57.32, 0.64) | |
| 19:5212481 | COSM713120 | E>K | A:1546 | (22.35, 56.88, 1.58) |
| 19:5212474 | COSM4080656 COSM4080655 |
R>H | A:1548 | (18.26, 61.60, 2.85) |
| 19:5212475 | rs369058883 | R>C | A:1548 | (18.26, 61.60, 2.85) |
| 19:5212472 | Q>K | A:1549 | (17.63, 66.55, -2.48) | |
| 19:5212459 | rs182037655 | T>M | A:1553 | (9.40, 74.48, -3.64) |
| 19:5212439 | rs150241840 | V>M | A:1560 | (11.23, 87.51, 0.36) |
| 19:5212433 | E>K | A:1562 | (4.13, 87.30, 2.96) | |
| 19:5212424 | T>A | A:1565 | (5.92, 79.20, 8.54) | |
| 19:5212402 | R>Q | A:1572 | (10.96, 72.11, 11.67) | |
| 19:5212372 | A>V | A:1582 | (28.87, 63.98, 8.56) | |
| 19:5212370 | G>S | A:1583 | (29.75, 66.26, 6.50) | |
| 19:5212361 | rs140472977 | V>M | A:1586 | (25.59, 70.78, 0.41) |
| 19:5212257 | rs571743236 | G>S | A:1592 | (25.02, 80.55, -3.52) |
| 19:5212248 | R>C | A:1595 | (16.96, 81.72, -2.35) | |
| 19:5212230 | rs367918810 | V>I | A:1601 | (22.01, 82.71, 9.03) |
| 19:5212224 | rs151279682 | D>N | A:1603 | (20.68, 76.53, 11.09) |
| 19:5212208 | rs148739536 | R>Q | A:1608 | (24.15, 82.13, 19.28) |
| 19:5212209 | rs142364974 | R>W | A:1608 | (24.15, 82.13, 19.28) |
| 19:5212166 | T>M | A:1622 | (30.48, 89.74, 8.83) | |
| 19:5212164 | L>F | A:1623 | (32.05, 85.05, 9.48) | |
| 19:5212145 | N>S | A:1629 | (30.93, 86.12, -2.91) | |
| 19:5212109 | I>T | A:1641 | (17.15, 86.34, 8.46) | |
| 19:5212107 | H>Y | A:1642 | (16.18, 89.65, 11.44) | |
| 19:5212104 | E>K | A:1643 | (10.87, 88.27, 9.35) | |
| 19:5212098 | L>V | A:1645 | (15.16, 84.15, 13.99) | |
| 19:5212086 | rs139009302 | V>M | A:1649 | (11.82, 82.53, 19.46) |
| 19:5212073 | N>S | A:1653 | (8.83, 70.95, 19.76) | |
| 19:5212062 | P>S | A:1657 | (5.90, 61.01, 17.78) | |
| 19:5212055 | COSM440126 | R>H | A:1659 | (5.91, 55.42, 19.85) |
| 19:5212047 | Y>H | A:1662 | (-2.68, 58.98, 25.65) | |
| 19:5212043 | rs575673773 | A>G | A:1663 | (1.28, 61.68, 26.28) |
| 19:5212026 | A>P | A:1669 | (-4.76, 68.38, 29.88) | |
| 19:5212006 | E>D | A:1675 | (0.04, 77.88, 34.96) | |
| 19:5212008 | E>K | A:1675 | (0.04, 77.88, 34.96) | |
| 19:5212002 | rs549449179 | V>I | A:1677 | (-4.75, 77.56, 31.98) |
| 19:5211991 | M>I | A:1680 | (-4.39, 72.42, 24.72) | |
| 19:5211778 | rs370553812 | R>Q | A:1686 | (2.10, 79.51, 22.11) |
| 19:5211779 | rs544687640 | R>W | A:1686 | (2.10, 79.51, 22.11) |
| 19:5211773 | A>T | A:1688 | (-0.29, 84.84, 18.16) | |
| 19:5211742 | I>T | A:1698 | (-6.52, 96.60, -0.43) | |
| 19:5211743 | I>V | A:1698 | (-6.52, 96.60, -0.43) | |
| 19:5211714 | F>L | A:1707 | (-21.67, 94.19, -0.67) | |
| 19:5211706 | R>H | A:1710 | (-21.55, 86.52, 6.35) | |
| 19:5211707 | rs145108936 | R>C | A:1710 | (-21.55, 86.52, 6.35) |
| 19:5211701 | V>M | A:1712 | (-15.97, 93.49, 9.10) | |
| 19:5211692 | M>V | A:1715 | (-10.92, 90.50, 5.68) | |
| 19:5211673 | R>Q | A:1721 | (-7.78, 87.93, -3.57) | |
| 19:5211667 | C>F | A:1723 | (-8.95, 86.44, -7.97) | |
| 19:5211658 | P>L | A:1726 | (-12.56, 91.01, -14.31) | |
| 19:5211652 | rs369364998 | R>Q | A:1728 | (-15.94, 94.86, -20.03) |
| 19:5211640 | G>A | A:1732 | (-15.01, 94.35, -7.74) | |
| 19:5211641 | G>S | A:1732 | (-15.01, 94.35, -7.74) | |
| 19:5211637 | S>F | A:1733 | (-15.76, 91.93, -10.13) | |
| 19:5211629 | I>L | A:1736 | (-14.69, 86.23, -3.39) | |
| 19:5211613 | I>T | A:1741 | (-5.48, 77.09, 1.68) | |
| 19:5210796 | COSM1394767 | A>V | A:1752 | (-11.33, 79.28, 2.17) |
| 19:5210797 | rs145869121 | A>T | A:1752 | (-11.33, 79.28, 2.17) |
| 19:5210793 | T>K | A:1753 | (-15.11, 80.61, 1.71) | |
| 19:5210784 | P>L | A:1756 | (-22.62, 82.05, 0.73) | |
| 19:5210778 | rs374377699 | A>V | A:1758 | (-27.48, 86.51, -1.54) |
| 19:5210774 | E>D | A:1759 | (-26.05, 89.74, -1.45) | |
| 19:5210776 | E>K | A:1759 | (-26.05, 89.74, -1.45) | |
| 19:5210769 | COSM3389278 | T>M | A:1761 | (-24.64, 83.37, -4.65) |
| 19:5210770 | T>A | A:1761 | (-24.64, 83.37, -4.65) | |
| 19:5210754 | R>H | A:1766 | (-17.56, 84.20, -11.47) | |
| 19:5210752 | M>L | A:1767 | (-15.15, 80.74, -6.98) | |
| 19:5210733 | COSM1000117 | S>L | A:1773 | (-14.16, 73.84, -7.74) |
| 19:5210725 | rs116345982 | V>M | A:1776 | (-18.51, 72.13, -1.99) |
| 19:5210710 | K>E | A:1781 | (-27.10, 73.53, 10.35) | |
| 19:5210703 | R>Q | A:1783 | (-31.65, 79.20, 10.72) | |
| 19:5210704 | R>W | A:1783 | (-31.65, 79.20, 10.72) | |
| 19:5210694 | G>D | A:1786 | (-31.89, 80.98, 15.41) | |
| 19:5210589 | Y>F | A:1793 | (-25.04, 77.84, -1.84) | |
| 19:5210571 | S>F | A:1799 | (-33.32, 74.72, -12.51) | |
| 19:5210565 | R>H | A:1801 | (-29.75, 82.61, -14.67) | |
| 19:5210566 | COSM1000113 | R>C | A:1801 | (-29.75, 82.61, -14.67) |
| 19:5210550 | V>A | A:1806 | (-27.52, 76.80, -15.37) | |
| 19:5210533 | E>K | A:1812 | (-30.78, 65.52, -1.56) | |
| 19:5210511 | rs529235837 | I>T | A:1819 | (-26.49, 66.28, 3.22) |
| 19:5210505 | R>Q | A:1821 | (-26.87, 68.73, -1.36) | |
| 19:5210481 | R>Q | A:1829 | (-20.44, 82.39, -20.87) | |
| 19:5210482 | rs147647579 | R>W | A:1829 | (-20.44, 82.39, -20.87) |
| 19:5208389 | COSM4080643 COSM4080642 |
R>Q | A:1834 | (-17.59, 72.16, -14.95) |
| 19:5208384 | V>L | A:1836 | (-20.80, 70.20, -8.46) | |
| 19:5208347 | G>A | A:1848 | (-19.16, 73.38, 20.19) | |
| 19:5208345 | rs560052043 | V>M | A:1849 | (-16.95, 70.41, 19.72) |
| 19:5208335 | rs148478353 | S>L | A:1852 | (-16.58, 61.85, 18.48) |
| 19:5208257 | V>G | A:1878 | (-14.14, 74.81, 2.59) | |
| 19:5208064 | G>S | A:1883 | (-14.32, 80.54, 7.08) | |
| 19:5208061 | COSM1394761 | V>M | A:1884 | (-12.26, 80.68, 9.97) |
| 19:5208046 | rs142977438 | V>I | A:1889 | (-11.03, 71.90, 11.85) |
| 19:5208036 | T>M | A:1892 | (-6.01, 71.05, 10.22) | |
| 19:5208033 | L>H | A:1893 | (-7.99, 67.12, 10.70) | |
| 19:5208025 | V>M | A:1896 | (-2.79, 66.03, 10.42) | |
| 19:5208009 | R>Q | A:1901 | (-2.07, 56.30, 6.44) | |
| 19:5207998 | V>M | A:1905 | (4.48, 62.76, 12.55) | |
| 19:5207979 | rs115470613 | T>M | A:1911 | (-0.89, 72.91, 10.71) |
| 19:5207969 | M>I | A:1914 | (1.05, 77.37, 7.53) | |
| 19:5207970 | M>T | A:1914 | (1.05, 77.37, 7.53) | |
| 19:5207947 | M>V | A:1922 | (-7.92, 79.33, 10.09) | |
| 19:5206842 | rs199713079 COSM3371450 |
Q>H | A:1930 | (-8.97, 69.88, 22.64) |
| 19:5206837 | C>S | A:1932 | (-7.72, 68.61, 16.16) | |
| 19:5206820 | E>K | A:1938 | (-10.50, 59.19, 17.73) | |
| 19:5206811 | rs200187372 | G>R | A:1941 | (-6.74, 53.79, 16.99) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:5215591 | COSM4080671 | P>L | A:1371 | (25.59, 94.34, 19.94) |
| 19:5215583 | COSM1711634 | P>S | A:1374 | (18.86, 89.63, 23.72) |
| 19:5215577 | COSM1000154 | A>T | A:1376 | (13.87, 89.38, 24.70) |
| 19:5215358 | COSM4781074 | N>K | A:1420 | (31.62, 79.86, -12.94) |
| 19:5215344 | COSM4286070 | V>D | A:1425 | (29.43, 84.43, -8.30) |
| 19:5214592 | COSM4080664 | R>W | A:1492 | (11.02, 76.93, -8.17) |
| 19:5212257 | COSM4286042 | G>S | A:1592 | (25.02, 80.55, -3.52) |
| 19:5212247 | COSM4080651 | R>H | A:1595 | (16.96, 81.72, -2.35) |
| 19:5210755 | COSM1000119 | R>C | A:1766 | (-17.56, 84.20, -11.47) |
| 19:5210733 | COSM1000117 | S>L | A:1773 | (-14.16, 73.84, -7.74) |
| 19:5210566 | COSM1000113 | R>C | A:1801 | (-29.75, 82.61, -14.67) |
| 19:5208061 | COSM4781235 | V>M | A:1884 | (-12.26, 80.68, 9.97) |
| 19:5208015 | COSM4783049 | R>Q | A:1899 | (2.71, 64.89, 8.70) |