General Structure Information
| PDB ID | 1xm9 |
| HGNC Gene Label(s) | PKP1 |
| Structure Name | structure of the armadillo repeat domain of plakophilin 1 |
| Resolution | 2.8Å |
| Reference | AUTH H.J.CHOI,W.I.WEISTITL STRUCTURE OF THE ARMADILLO REPEAT DOMAIN OFTITL 2 PLAKOPHILIN 1.REF J.MOL.BIOL. V. 346 367 2005REFN ISSN 0022-2836PMID 15663951DOI 10.1016/J.JMB.2004.11.048 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 420 |
| Number Of SNVs | 128 |
| Number Of Permutations | 38209 |
| Optimal Distance Threshold | 27.0 |
| K Statistic | 0.386 |
| p-value | 0.085 |
COSMIC
| Number Of Residues | 420 |
| Number Of SNVs | 6 |
| Number Of Permutations | 4760 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.067 |
| p-value | 0.752 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 128 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.086 |
| p-value | 0.352 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:201285715 | T>S | A:246 | (-32.46, 7.26, 28.25) | |
| 1:201285727 | A>S | A:250 | (-28.19, 3.10, 25.41) | |
| 1:201285742 | S>G | A:255 | (-24.77, -4.99, 23.95) | |
| 1:201285754 | E>K | A:259 | (-26.27, -4.08, 13.58) | |
| 1:201285758 | rs142131454 | K>I | A:260 | (-32.21, -0.88, 14.09) |
| 1:201285760 | rs528045800 | Y>H | A:261 | (-32.47, -1.55, 18.26) |
| 1:201285766 | A>T | A:263 | (-26.73, 2.51, 16.19) | |
| 1:201285767 | A>V | A:263 | (-26.73, 2.51, 16.19) | |
| 1:201285769 | I>V | A:264 | (-29.89, 3.78, 18.15) | |
| 1:201285770 | rs369999615 | I>T | A:264 | (-29.89, 3.78, 18.15) |
| 1:201285775 | A>T | A:266 | (-23.71, 5.47, 20.08) | |
| 1:201285776 | A>D | A:266 | (-23.71, 5.47, 20.08) | |
| 1:201285778 | Y>N | A:267 | (-25.26, 7.34, 15.94) | |
| 1:201285796 | C>R | A:273 | (-22.47, 13.06, 25.80) | |
| 1:201285803 | Q>L | A:275 | (-21.93, 21.03, 25.79) | |
| 1:201285805 | rs191741262 | D>Y | A:276 | (-23.06, 17.42, 29.93) |
| 1:201285824 | Q>R | A:282 | (-24.18, 9.09, 33.31) | |
| 1:201286707 | Q>R | A:285 | (-20.39, 6.00, 36.33) | |
| 1:201286719 | I>N | A:289 | (-16.26, 2.89, 27.95) | |
| 1:201286736 | rs150414253 | L>V | A:295 | (-19.34, -1.85, 18.67) |
| 1:201286739 | rs564123317 COSM241151 |
L>F | A:296 | (-15.10, -0.11, 16.44) |
| 1:201286742 | rs368718493 CD066691 |
R>G | A:297 | (-14.10, -5.67, 17.38) |
| 1:201286743 | COSM902156 COSM902155 |
R>H | A:297 | (-14.10, -5.67, 17.38) |
| 1:201286748 | P>S | A:299 | (-19.84, -5.46, 10.33) | |
| 1:201286752 | rs552414505 | N>T | A:300 | (-22.64, -1.45, 9.95) |
| 1:201286767 | Q>L | A:305 | (-20.11, 6.21, 11.49) | |
| 1:201286773 | rs536481505 | A>V | A:307 | (-18.76, 4.37, 18.10) |
| 1:201286775 | rs529199336 | A>P | A:308 | (-16.47, 6.66, 16.91) |
| 1:201286779 | G>E | A:309 | (-17.93, 9.38, 18.14) | |
| 1:201286781 | A>T | A:310 | (-19.28, 8.53, 20.91) | |
| 1:201286785 | L>P | A:311 | (-15.67, 7.03, 21.75) | |
| 1:201286788 | R>H | A:312 | (-14.31, 13.19, 18.47) | |
| 1:201286790 | N>D | A:313 | (-17.91, 13.46, 21.79) | |
| 1:201286805 | S>G | A:318 | (-11.99, 13.68, 30.30) | |
| 1:201286809 | T>N | A:319 | (-8.46, 12.81, 32.36) | |
| 1:201286817 | K>E | A:322 | (-8.80, 10.70, 28.00) | |
| 1:201286829 | R>W | A:326 | (-5.05, 3.40, 28.44) | |
| 1:201286830 | R>Q | A:326 | (-5.05, 3.40, 28.44) | |
| 1:201286847 | rs562755351 | R>C | A:332 | (-6.36, -3.07, 20.14) |
| 1:201286877 | rs375682551 | G>R | A:342 | (-13.18, 4.55, 3.29) |
| 1:201286883 | A>T | A:344 | (-14.66, 9.88, 5.60) | |
| 1:201286886 | E>K | A:345 | (-17.51, 10.67, 9.16) | |
| 1:201286888 | E>D | A:345 | (-17.51, 10.67, 9.16) | |
| 1:201287767 | S>F | A:359 | (-4.18, 16.09, 25.60) | |
| 1:201287770 | T>I | A:360 | (-3.53, 12.83, 27.98) | |
| 1:201287772 | D>N | A:361 | (1.06, 14.53, 29.44) | |
| 1:201287775 | E>K | A:362 | (-0.21, 9.78, 30.54) | |
| 1:201287793 | rs142169193 | I>V | A:368 | (4.19, 7.59, 19.61) |
| 1:201287794 | I>T | A:368 | (4.19, 7.59, 19.61) | |
| 1:201287799 | rs180970899 | D>N | A:370 | (0.48, 1.89, 18.06) |
| 1:201287823 | rs200975137 COSM252721 |
R>C | A:378 | (-4.82, 5.27, 5.25) |
| 1:201287824 | R>H | A:378 | (-4.82, 5.27, 5.25) | |
| 1:201287847 | W>R | A:386 | (7.40, 14.02, -0.36) | |
| 1:201287851 | C>Y | A:387 | (5.17, 11.06, -3.68) | |
| 1:201287908 | A>D | A:406 | (-3.81, 14.30, 12.39) | |
| 1:201289399 | rs370631788 | L>M | A:413 | (2.58, 13.31, 19.82) |
| 1:201289406 | rs151203492 | S>L | A:415 | (5.43, 17.67, 23.16) |
| 1:201289411 | rs141222689 | D>N | A:417 | (11.44, 14.11, 24.80) |
| 1:201289420 | rs146785756 | R>C | A:420 | (11.55, 15.72, 20.04) |
| 1:201289421 | rs569372122 COSM252722 |
R>H | A:420 | (11.55, 15.72, 20.04) |
| 1:201289424 | Q>R | A:421 | (13.81, 11.75, 19.31) | |
| 1:201289432 | rs551980188 | R>C | A:424 | (13.70, 14.88, 14.84) |
| 1:201289433 | rs376870836 COSM902167 COSM902166 |
R>H | A:424 | (13.70, 14.88, 14.84) |
| 1:201289445 | G>E | A:428 | (8.27, 11.65, 5.18) | |
| 1:201289450 | I>V | A:430 | (9.40, 16.45, 8.30) | |
| 1:201289464 | M>I | A:434 | (7.68, 21.30, 4.58) | |
| 1:201289469 | COSM3740914 COSM3740913 |
Y>C | A:436 | (-0.05, 22.02, 4.08) |
| 1:201289483 | V>I | A:441 | (2.87, 29.86, 1.13) | |
| 1:201289487 | rs10920171 | A>V | A:442 | (1.76, 29.56, -2.86) |
| 1:201289489 | rs376318223 | A>S | A:443 | (-1.76, 29.46, -2.48) |
| 1:201289490 | A>V | A:443 | (-1.76, 29.46, -2.48) | |
| 1:201289492 | S>C | A:444 | (-1.96, 32.33, -0.98) | |
| 1:201289496 | rs137968512 | R>H | A:445 | (-5.11, 29.11, 1.59) |
| 1:201289498 | rs78672252 | C>R | A:446 | (-0.77, 31.44, 5.03) |
| 1:201289499 | C>Y | A:446 | (-0.77, 31.44, 5.03) | |
| 1:201289504 | D>N | A:448 | (-4.96, 26.54, 5.22) | |
| 1:201289508 | K>R | A:449 | (-7.92, 23.89, 8.58) | |
| 1:201291109 | V>M | A:451 | (-0.60, 25.77, 8.60) | |
| 1:201291133 | rs371151624 | H>Y | A:459 | (8.36, 25.14, 17.51) |
| 1:201291148 | rs374293363 COSM1730585 COSM1730584 |
R>C | A:464 | (17.79, 19.67, 22.73) |
| 1:201291157 | A>T | A:467 | (21.64, 18.08, 20.43) | |
| 1:201291158 | A>V | A:467 | (21.64, 18.08, 20.43) | |
| 1:201291160 | E>K | A:468 | (18.69, 15.60, 19.42) | |
| 1:201291164 | V>A | A:469 | (20.01, 15.95, 14.70) | |
| 1:201291170 | T>I | A:471 | (24.98, 18.11, 11.24) | |
| 1:201291172 | R>C | A:472 | (26.87, 19.57, 7.46) | |
| 1:201291173 | COSM4026918 COSM4026917 |
R>H | A:472 | (26.87, 19.57, 7.46) |
| 1:201291178 | rs148461275 | R>C | A:474 | (27.31, 17.35, 15.99) |
| 1:201291179 | R>H | A:474 | (27.31, 17.35, 15.99) | |
| 1:201292162 | L>V | A:509 | (32.06, 26.54, 6.43) | |
| 1:201292168 | rs371952348 | E>K | A:511 | (27.31, 22.05, 2.19) |
| 1:201292181 | N>S | A:515 | (19.00, 16.60, -2.00) | |
| 1:201292183 | P>S | A:516 | (16.59, 18.12, 1.59) | |
| 1:201292188 | K>N | A:517 | (14.98, 12.99, 3.66) | |
| 1:201292195 | rs149193673 | G>S | A:520 | (16.76, 18.09, 7.05) |
| 1:201292198 | W>R | A:521 | (13.44, 19.81, 4.09) | |
| 1:201292203 | COSM3711218 COSM3711217 |
L>F | A:522 | (14.03, 21.04, 10.67) |
| 1:201292207 | H>Y | A:524 | (17.27, 23.94, 3.96) | |
| 1:201292222 | R>C | A:529 | (12.56, 30.34, 1.91) | |
| 1:201292223 | rs143362477 | R>H | A:529 | (12.56, 30.34, 1.91) |
| 1:201292241 | M>T | A:535 | (6.62, 35.50, 10.16) | |
| 1:201292244 | G>D | A:536 | (4.24, 38.06, 7.05) | |
| 1:201292246 | K>E | A:537 | (1.07, 37.24, 4.50) | |
| 1:201292247 | K>R | A:537 | (1.07, 37.24, 4.50) | |
| 1:201292268 | L>Q | A:544 | (3.20, 34.49, 14.00) | |
| 1:201292280 | A>V | A:548 | (9.43, 32.33, 15.76) | |
| 1:201293579 | L>F | A:568 | (20.62, 30.98, 6.63) | |
| 1:201293581 | rs202232462 | I>T | A:569 | (17.63, 33.86, 9.53) |
| 1:201293593 | E>G | A:573 | (16.37, 33.92, 3.27) | |
| 1:201293596 | K>R | A:574 | (17.03, 39.54, 3.28) | |
| 1:201293613 | A>T | A:580 | (10.96, 43.24, 14.06) | |
| 1:201293616 | rs377328987 | R>C | A:581 | (6.22, 42.72, 11.12) |
| 1:201293617 | rs142096411 | R>H | A:581 | (6.22, 42.72, 11.12) |
| 1:201293619 | L>I | A:582 | (6.65, 39.74, 15.46) | |
| 1:201293649 | rs138678921 | R>W | A:592 | (8.70, 35.13, 24.01) |
| 1:201293650 | R>Q | A:592 | (8.70, 35.13, 24.01) | |
| 1:201293659 | A>D | A:595 | (13.06, 38.72, 21.20) | |
| 1:201293664 | L>I | A:597 | (14.81, 35.10, 17.27) | |
| 1:201293667 | L>V | A:598 | (16.01, 39.25, 17.73) | |
| 1:201293682 | R>C | A:603 | (24.59, 34.22, 20.49) | |
| 1:201293683 | R>H | A:603 | (24.59, 34.22, 20.49) | |
| 1:201293709 | COSM531855 COSM531854 |
G>W | A:612 | (21.32, 47.70, 13.40) |
| 1:201294071 | N>Y | A:613 | (20.99, 48.69, 9.89) | |
| 1:201294077 | V>L | A:615 | (16.47, 45.65, 15.25) | |
| 1:201294084 | P>L | A:617 | (14.77, 50.73, 16.36) | |
| 1:201294089 | V>M | A:619 | (14.42, 46.59, 20.63) | |
| 1:201294090 | V>A | A:619 | (14.42, 46.59, 20.63) | |
| 1:201294093 | T>I | A:620 | (14.58, 50.68, 22.09) | |
| 1:201294095 | R>G | A:621 | (9.17, 52.01, 20.49) | |
| 1:201294097 | R>S | A:621 | (9.17, 52.01, 20.49) | |
| 1:201294116 | rs373741646 | G>S | A:628 | (8.04, 43.58, 34.31) |
| 1:201294129 | rs200677178 | N>T | A:632 | (5.92, 37.04, 28.93) |
| 1:201294134 | E>K | A:634 | (10.65, 38.97, 33.69) | |
| 1:201294138 | D>V | A:635 | (11.15, 36.67, 29.00) | |
| 1:201294152 | A>S | A:640 | (15.93, 43.39, 24.80) | |
| 1:201294168 | R>K | A:645 | (24.99, 43.28, 26.81) | |
| 1:201294172 | N>K | A:646 | (25.31, 41.33, 22.15) | |
| 1:201294183 | rs200484616 | S>L | A:650 | (29.88, 46.86, 17.77) |
| 1:201294204 | Q>P | A:657 | (21.68, 56.51, 17.03) | |
| 1:201294207 | Y>F | A:658 | (18.21, 54.35, 18.04) | |
| 1:201294213 | S>F | A:660 | (15.63, 57.45, 25.09) | |
| 1:201294216 | S>T | A:661 | (15.40, 59.76, 28.01) | |
| 1:201294249 | rs139909774 | R>Q | A:672 | (16.11, 50.43, 41.70) |
| 1:201294255 | S>N | A:674 | (12.44, 42.69, 43.76) | |
| 1:201294893 | rs146324118 | K>M | A:678 | (14.36, 37.18, 34.28) |
| 1:201294898 | rs553668177 COSM1337825 COSM1337824 |
A>T | A:680 | (17.01, 43.20, 36.65) |
| 1:201294903 | E>D | A:681 | (20.61, 40.00, 36.06) | |
| 1:201294910 | rs61818256 | R>W | A:684 | (22.02, 44.33, 37.31) |
| 1:201294914 | L>R | A:685 | (24.22, 42.78, 33.01) | |
| 1:201294955 | V>I | A:699 | (23.65, 60.17, 27.43) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:201286871 | COSM1337815 | R>G | A:340 | (-8.22, -3.04, 8.05) |
| 1:201289408 | COSM3385611 | A>T | A:416 | (7.49, 14.56, 23.76) |
| 1:201289420 | COSM2212258 | R>C | A:420 | (11.55, 15.72, 20.04) |
| 1:201292203 | COSM3711217 | L>F | A:522 | (14.03, 21.04, 10.67) |
| 1:201293709 | COSM531855 | G>W | A:612 | (21.32, 47.70, 13.40) |
| 1:201294249 | COSM1689604 | R>Q | A:672 | (16.11, 50.43, 41.70) |