General Structure Information
| PDB ID | 4mwt |
| HGNC Gene Label(s) | CTSA |
| Structure Name | crystal structure of human ppca (trigonal crystal form 2) |
| Resolution | 3.85Å |
| Reference | AUTH N.KOLLI,S.C.GARMANTITL PROTEOLYTIC ACTIVATION OF HUMAN CATHEPSIN A.REF J.BIOL.CHEM. V. 289 11592 2014REFN ISSN 0021-9258PMID 24599961DOI 10.1074/JBC.M113.524280 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 413 |
| Number Of SNVs | 100 |
| Number Of Permutations | 48920 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.017 |
| p-value | 0.769 |
ClinVar
| Number Of Residues | 413 |
| Number Of SNVs | 11 |
| Number Of Permutations | 5981 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.109 |
| p-value | 0.06 |
Ripley’s K Analysis Plots
ExACClinVar
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 100 |
| Number Of ClinVar SNVs | 11 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.075 |
| p-value | 0.055 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 20:44520292 | rs376350093 | A>S | A:1 | (19.65, -0.71, -11.86) |
| 20:44520295 | P>A | A:2 | (19.95, -1.08, -8.27) | |
| 20:44520309 | E>D | A:6 | (27.16, -2.43, -8.41) | |
| 20:44520316 | R>G | A:9 | (37.15, -4.62, -6.03) | |
| 20:44520317 | R>P | A:9 | (37.15, -4.62, -6.03) | |
| 20:44520319 | L>V | A:10 | (33.92, -9.90, -4.27) | |
| 20:44520335 | K>R | A:15 | (40.38, -11.86, -12.63) | |
| 20:44520336 | COSM297668 | K>N | A:15 | (40.38, -11.86, -12.63) |
| 20:44520350 | R>H | A:20 | (27.08, -4.88, -15.09) | |
| 20:44520359 | rs538562022 CM961138 |
S>C | A:23 | (23.68, -7.38, -3.51) |
| 20:44520361 | G>S | A:24 | (20.16, -7.13, -2.02) | |
| 20:44520364 | Y>H | A:25 | (17.93, -7.09, 1.04) | |
| 20:44520367 | rs138615064 | L>F | A:26 | (13.87, -8.19, -3.12) |
| 20:44520374 | G>D | A:28 | (7.66, -8.85, 0.17) | |
| 20:44520383 | S>F | A:31 | (8.02, -7.04, 7.04) | |
| 20:44520398 | rs201198067 | Y>C | A:36 | (19.42, -9.00, -4.72) |
| 20:44520569 | Q>R | A:42 | (29.83, -14.14, -18.66) | |
| 20:44520587 | S>N | A:48 | (20.47, -13.21, -21.86) | |
| 20:44520589 | rs137868961 | P>A | A:49 | (17.97, -15.34, -20.29) |
| 20:44520592 | V>M | A:50 | (15.88, -13.99, -16.32) | |
| 20:44520608 | N>S | A:55 | (18.40, -23.77, -3.03) | |
| 20:44520619 | G>C | A:59 | (16.04, -22.99, 5.11) | |
| 20:44520646 | T>A | A:68 | (28.66, -24.82, -4.10) | |
| 20:44520928 | V>A | A:80 | (39.31, -16.97, 1.57) | |
| 20:44521044 | rs199735882 COSM443916 |
N>S | A:94 | (20.69, -12.99, -16.55) |
| 20:44521052 | Y>H | A:97 | (21.88, -17.15, -7.54) | |
| 20:44521067 | rs376642070 | A>T | A:102 | (12.15, -15.21, 5.74) |
| 20:44521073 | rs137854545 | V>M | A:104 | (17.13, -17.84, 4.88) |
| 20:44521089 | S>Y | A:109 | (11.71, -9.75, 9.16) | |
| 20:44521091 | COSM1027320 | D>N | A:110 | (11.04, -5.71, 10.28) |
| 20:44521110 | T>I | A:116 | (6.20, -20.00, 6.89) | |
| 20:44521367 | A>T | A:122 | (4.80, -18.19, -2.88) | |
| 20:44521382 | E>Q | A:127 | (5.11, -9.76, -3.40) | |
| 20:44521385 | A>P | A:128 | (10.08, -10.32, -4.91) | |
| 20:44521386 | rs139760741 | A>V | A:128 | (10.08, -10.32, -4.91) |
| 20:44521404 | rs139920208 | R>H | A:134 | (8.99, -2.63, -8.27) |
| 20:44521413 | P>L | A:137 | (13.31, -2.14, -15.30) | |
| 20:44521421 | K>Q | A:140 | (10.03, -5.82, -17.10) | |
| 20:44521422 | K>R | A:140 | (10.03, -5.82, -17.10) | |
| 20:44521428 | N>S | A:142 | (14.56, -10.46, -20.52) | |
| 20:44521452 | S>T | A:150 | (15.14, -29.68, -3.19) | |
| 20:44521457 | A>S | A:152 | (11.97, -26.21, -4.96) | |
| 20:44521467 | rs376113662 | Y>C | A:155 | (10.07, -23.30, -2.41) |
| 20:44521482 | A>V | A:160 | (4.59, -20.45, -11.42) | |
| 20:44521484 | COSM1027322 | V>M | A:161 | (0.80, -20.67, -10.62) |
| 20:44521510 | M>I | A:169 | (5.97, -11.63, -15.04) | |
| 20:44521872 | G>D | A:177 | (16.33, -30.44, -8.96) | |
| 20:44521884 | S>F | A:181 | (7.12, -33.50, -6.80) | |
| 20:44521886 | S>P | A:182 | (5.51, -36.75, -4.59) | |
| 20:44521905 | N>S | A:188 | (6.76, -45.72, -2.50) | |
| 20:44521937 | rs560144001 | L>I | A:199 | (21.07, -50.50, 1.20) |
| 20:44522666 | N>K | A:216 | (1.37, -55.98, -8.71) | |
| 20:44522679 | rs137854544 | Y>N | A:221 | (2.82, -41.89, 2.00) |
| 20:44522703 | V>M | A:229 | (5.69, -49.15, 10.58) | |
| 20:44523290 | rs145354134 | L>P | A:232 | (9.02, -48.43, 6.63) |
| 20:44523304 | R>C | A:237 | (18.63, -47.62, 10.77) | |
| 20:44523313 | G>S | A:240 | (19.49, -41.68, 7.18) | |
| 20:44523322 | G>R | A:243 | (26.36, -43.15, 7.29) | |
| 20:44523350 | COSM1027325 | P>L | A:252 | (32.04, -39.59, 1.35) |
| 20:44523362 | G>E | A:256 | (31.82, -39.27, 9.83) | |
| 20:44523660 | COSM1202629 | R>C | A:298 | (25.14, -24.88, 12.69) |
| 20:44523661 | rs554534522 COSM1027326 |
R>H | A:298 | (25.14, -24.88, 12.69) |
| 20:44523664 | rs140321228 | M>T | A:299 | (20.18, -27.38, 10.47) |
| 20:44523684 | T>A | A:306 | (28.88, -25.64, 5.74) | |
| 20:44523693 | rs374059459 | A>P | A:309 | (30.72, -20.74, 2.77) |
| 20:44523715 | rs368108194 | P>L | A:316 | (33.22, -8.68, 7.74) |
| 20:44523724 | rs375345060 | R>Q | A:319 | (27.81, -9.13, 6.23) |
| 20:44523727 | K>M | A:320 | (31.09, -4.04, 4.06) | |
| 20:44523728 | rs557995825 | K>N | A:320 | (31.09, -4.04, 4.06) |
| 20:44523732 | L>V | A:322 | (27.24, -8.52, -0.51) | |
| 20:44523742 | rs142302144 | P>L | A:325 | (22.74, -5.09, 6.82) |
| 20:44523757 | rs138549425 | Q>P | A:330 | (25.83, -16.29, 11.87) |
| 20:44523758 | Q>H | A:330 | (25.83, -16.29, 11.87) | |
| 20:44523765 | M>V | A:333 | (23.66, -23.49, 4.15) | |
| 20:44525611 | rs369583698 | V>I | A:338 | (12.77, -21.81, 8.98) |
| 20:44525614 | rs372863499 | N>D | A:339 | (13.11, -26.59, 8.93) |
| 20:44525626 | R>C | A:343 | (2.07, -25.87, 8.69) | |
| 20:44525630 | R>H | A:344 | (6.28, -29.55, 5.18) | |
| 20:44525639 | rs370763298 | R>Q | A:347 | (1.74, -33.66, 0.93) |
| 20:44525644 | rs530752765 | M>V | A:349 | (3.17, -30.22, -7.19) |
| 20:44525645 | M>T | A:349 | (3.17, -30.22, -7.19) | |
| 20:44525646 | M>I | A:349 | (3.17, -30.22, -7.19) | |
| 20:44525678 | Q>R | A:360 | (0.55, -25.75, -24.37) | |
| 20:44526363 | Q>R | A:363 | (10.66, -25.27, -21.74) | |
| 20:44526386 | COSM577597 | V>I | A:371 | (23.35, -41.44, -6.84) |
| 20:44526387 | V>A | A:371 | (23.35, -41.44, -6.84) | |
| 20:44526390 | D>G | A:372 | (19.75, -38.63, -4.46) | |
| 20:44526392 | M>V | A:373 | (19.00, -41.57, -1.13) | |
| 20:44526402 | N>S | A:376 | (14.57, -40.96, -5.96) | |
| 20:44526410 | G>R | A:379 | (10.02, -40.54, -8.51) | |
| 20:44526426 | V>E | A:384 | (6.72, -37.05, -15.21) | |
| 20:44526654 | Q>R | A:394 | (10.90, -42.25, -27.93) | |
| 20:44526656 | R>C | A:395 | (14.32, -43.54, -21.25) | |
| 20:44526657 | R>H | A:395 | (14.32, -43.54, -21.25) | |
| 20:44526660 | R>Q | A:396 | (17.57, -40.09, -25.77) | |
| 20:44526662 | P>T | A:397 | (20.59, -42.03, -24.42) | |
| 20:44526666 | rs370723777 | W>L | A:398 | (22.25, -36.58, -21.54) |
| 20:44526680 | rs375579156 | G>R | A:403 | (38.62, -34.69, -22.45) |
| 20:44526689 | G>R | A:406 | (34.87, -38.17, -25.29) | |
| 20:44526692 | rs368625215 | E>K | A:407 | (30.64, -38.25, -27.08) |
| 20:44526704 | rs137854547 | G>S | A:411 | (22.16, -39.90, -19.36) |
| 20:44526707 | rs137854540 | F>V | A:412 | (19.42, -42.39, -19.77) |
| 20:44526731 | rs144407534 | A>T | A:420 | (11.31, -33.22, -19.55) |
| 20:44526732 | rs185187245 | A>V | A:420 | (11.31, -33.22, -19.55) |
| 20:44527007 | rs373421813 | G>V | A:426 | (26.54, -40.02, -10.92) |
| 20:44527012 | rs200051553 | G>S | A:428 | (23.48, -36.10, -6.91) |
| 20:44527018 | M>V | A:430 | (24.20, -30.82, -5.10) | |
| 20:44527028 | rs149971062 | T>N | A:433 | (28.72, -30.17, -7.42) |
| 20:44527030 | rs145261803 | D>N | A:434 | (28.41, -34.08, -8.24) |
| 20:44527052 | T>I | A:441 | (25.01, -29.31, -21.40) | |
| 20:44527055 | M>T | A:442 | (20.92, -29.58, -18.63) | |
| 20:44527063 | rs147472210 | R>C | A:445 | (21.71, -29.22, -24.78) |
| 20:44527064 | R>H | A:445 | (21.71, -29.22, -24.78) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 20:44520353 | rs137854541 | Q>R | A:21 | (28.01, -8.70, -9.44) |
| 20:44520400 | rs28934603 | W>R | A:37 | (25.17, -12.77, -5.26) |
| 20:44520629 | rs137854542 | S>L | A:62 | (20.27, -19.76, -2.76) |
| 20:44521073 | rs137854545 | V>M | A:104 | (17.13, -17.84, 4.88) |
| 20:44522641 | rs137854546 | L>P | A:208 | (9.08, -54.56, 3.47) |
| 20:44522679 | rs137854544 | Y>N | A:221 | (2.82, -41.89, 2.00) |
| 20:44526375 | rs137854543 | Y>C | A:367 | (17.56, -31.38, -12.87) |
| 20:44526408 | rs137854548 | M>T | A:378 | (12.26, -43.98, -10.02) |
| 20:44526704 | rs137854547 | G>S | A:411 | (22.16, -39.90, -19.36) |
| 20:44526707 | rs137854540 | F>V | A:412 | (19.42, -42.39, -19.77) |
| 20:44526746 | rs137854549 | K>E | A:425 | (25.50, -41.50, -15.18) |