General Structure Information
| PDB ID | 2okn |
| HGNC Gene Label(s) | PEPD |
| Structure Name | crystal strcture of human prolidase |
| Resolution | 2.45Å |
| Reference | AUTH U.MUELLER,F.H.NIESEN,Y.ROSKE,F.GOETZ,J.BEHLKE,K.BUESSOW,AUTH 2 U.HEINEMANNTITL CRYSTAL STRUCTURE OF HUMAN PROLIDASE: THE MOLECULAR BASIS OFTITL 2 PD DISEASE.REF TO BE PUBLISHEDREFN |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 477 |
| Number Of SNVs | 163 |
| Number Of Permutations | 71025 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.073 |
| p-value | 0.415 |
ClinVar
| Number Of Residues | 477 |
| Number Of SNVs | 8 |
| Number Of Permutations | 4876 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | 0.857 |
| p-value | 0.001 |
COSMIC
| Number Of Residues | 477 |
| Number Of SNVs | 8 |
| Number Of Permutations | 3196 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.071 |
| p-value | 0.438 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 163 |
| Number Of ClinVar SNVs | 8 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | 0.59 |
| p-value | 0.002 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 163 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | -0.172 |
| p-value | 0.346 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:34003681 | P>T | A:8 | (106.29, 31.41, 94.23) | |
| 19:34003668 | L>P | A:12 | (101.53, 29.22, 81.07) | |
| 19:34003666 | rs201992066 | G>R | A:13 | (105.72, 29.44, 79.38) |
| 19:34003648 | V>M | A:19 | (102.68, 36.18, 88.18) | |
| 19:34003644 | rs377085952 | P>L | A:20 | (104.46, 37.06, 91.48) |
| 19:34003645 | P>S | A:20 | (104.46, 37.06, 91.48) | |
| 19:34003638 | rs199711203 | A>V | A:22 | (103.35, 38.09, 96.17) |
| 19:34003620 | rs372527759 | R>Q | A:28 | (96.59, 38.14, 101.29) |
| 19:34003614 | R>H | A:30 | (96.41, 46.58, 99.69) | |
| 19:34003612 | L>V | A:31 | (92.02, 43.91, 102.93) | |
| 19:34003602 | rs187269138 | R>Q | A:34 | (91.17, 50.31, 103.81) |
| 19:34003603 | rs61734503 | R>W | A:34 | (91.17, 50.31, 103.81) |
| 19:34003596 | rs200435937 | R>Q | A:36 | (94.40, 46.29, 110.56) |
| 19:34003597 | rs185183225 | R>W | A:36 | (94.40, 46.29, 110.56) |
| 19:34003593 | K>R | A:37 | (92.67, 52.33, 109.95) | |
| 19:34003589 | N>K | A:38 | (86.81, 50.25, 109.90) | |
| 19:34003567 | rs369878645 | I>V | A:46 | (88.10, 35.92, 110.34) |
| 19:34003564 | V>M | A:47 | (88.16, 37.60, 105.89) | |
| 19:34003548 | rs199892951 | G>E | A:52 | (84.51, 28.75, 92.91) |
| 19:34003549 | G>R | A:52 | (84.51, 28.75, 92.91) | |
| 19:34003533 | R>H | A:57 | (76.99, 22.86, 78.31) | |
| 19:34003527 | rs564126763 | C>Y | A:59 | (71.17, 19.00, 82.86) |
| 19:34003522 | D>N | A:61 | (78.34, 15.68, 81.64) | |
| 19:34003516 | G>R | A:63 | (81.91, 21.35, 80.94) | |
| 19:34003513 | V>F | A:64 | (82.07, 25.03, 82.02) | |
| 19:34003503 | R>H | A:67 | (87.41, 33.36, 85.79) | |
| 19:34003504 | rs368995247 COSM377536 |
R>C | A:67 | (87.41, 33.36, 85.79) |
| 19:34003500 | Q>R | A:68 | (88.15, 31.90, 90.50) | |
| 19:34002048 | H>R | A:73 | (92.36, 36.03, 91.40) | |
| 19:34002049 | rs201752816 | H>D | A:73 | (92.36, 36.03, 91.40) |
| 19:34002042 | rs533996123 COSM4076799 |
A>V | A:75 | (93.19, 37.34, 97.42) |
| 19:34002037 | G>S | A:77 | (95.16, 32.88, 92.94) | |
| 19:34002030 | rs186203899 | T>S | A:79 | (93.35, 27.87, 89.60) |
| 19:34002024 | P>L | A:81 | (87.81, 24.19, 91.71) | |
| 19:34002015 | rs376397947 COSM1680879 |
Y>C | A:84 | (85.62, 27.80, 101.15) |
| 19:34001992 | G>R | A:92 | (97.38, 38.04, 108.07) | |
| 19:34001985 | rs375348295 | S>L | A:94 | (96.67, 32.89, 105.11) |
| 19:34001967 | R>M | A:100 | (89.42, 15.54, 102.56) | |
| 19:34001956 | S>G | A:104 | (89.83, 6.53, 94.64) | |
| 19:34001949 | A>V | A:106 | (93.76, 9.31, 90.33) | |
| 19:33991902 | H>R | A:113 | (98.52, 17.55, 94.38) | |
| 19:33991899 | rs570117233 | S>F | A:114 | (99.50, 17.59, 99.29) |
| 19:33991891 | H>Y | A:117 | (101.28, 21.27, 95.98) | |
| 19:33991885 | K>E | A:119 | (101.95, 26.17, 102.35) | |
| 19:33991878 | K>R | A:121 | (100.67, 26.51, 93.98) | |
| 19:33991870 | V>M | A:124 | (99.44, 30.36, 102.01) | |
| 19:33991860 | V>G | A:127 | (96.54, 24.33, 103.83) | |
| 19:33991861 | V>I | A:127 | (96.54, 24.33, 103.83) | |
| 19:33991856 | Q>H | A:128 | (93.59, 22.83, 106.50) | |
| 19:33991852 | V>I | A:130 | (86.59, 22.26, 102.82) | |
| 19:33991849 | rs533413828 | D>Y | A:131 | (85.85, 18.70, 105.50) |
| 19:33984239 | A>D | A:134 | (84.02, 24.79, 111.21) | |
| 19:33984234 | V>I | A:136 | (89.64, 25.41, 111.66) | |
| 19:33984227 | rs188930796 | T>M | A:138 | (85.73, 26.98, 116.19) |
| 19:33984212 | rs375915358 | S>F | A:143 | (84.68, 38.06, 116.77) |
| 19:33984210 | V>I | A:144 | (83.30, 38.62, 113.41) | |
| 19:33980963 | rs61734505 | R>C | A:149 | (75.32, 41.05, 100.44) |
| 19:33980957 | V>I | A:151 | (75.61, 46.17, 94.65) | |
| 19:33980953 | rs368559424 | N>T | A:152 | (78.02, 45.29, 90.44) |
| 19:33980951 | T>A | A:153 | (77.55, 49.49, 89.95) | |
| 19:33980942 | COSM4076797 | G>C | A:156 | (73.01, 44.73, 89.89) |
| 19:33980938 | S>T | A:157 | (74.33, 41.87, 90.84) | |
| 19:33980933 | C>R | A:159 | (77.67, 39.53, 95.87) | |
| 19:33980920 | S>F | A:163 | (78.33, 29.40, 103.06) | |
| 19:33980911 | COSM1524788 | G>D | A:166 | (78.09, 25.77, 110.64) |
| 19:33980905 | rs61734506 | S>N | A:168 | (74.89, 29.26, 112.25) |
| 19:33968991 | rs61748998 | E>V | A:171 | (78.89, 37.24, 115.18) |
| 19:33968992 | E>K | A:171 | (78.89, 37.24, 115.18) | |
| 19:33968989 | rs368784737 | V>L | A:172 | (78.12, 36.81, 110.24) |
| 19:33968985 | N>S | A:173 | (79.45, 41.46, 109.03) | |
| 19:33968964 | E>A | A:180 | (86.93, 48.49, 102.68) | |
| 19:33968962 | I>V | A:181 | (87.63, 44.15, 98.84) | |
| 19:33968952 | rs556625829 | C>Y | A:184 | (91.73, 47.76, 97.43) |
| 19:33954966 | rs121917722 | R>Q | A:185 | (89.27, 44.87, 92.89) |
| 19:33954954 | rs141623136 | T>M | A:189 | (99.84, 46.86, 92.84) |
| 19:33954951 | rs151278946 | D>G | A:190 | (103.79, 48.17, 91.13) |
| 19:33954952 | D>N | A:190 | (103.79, 48.17, 91.13) | |
| 19:33954930 | rs374162516 | R>H | A:197 | (102.63, 47.23, 82.28) |
| 19:33954931 | rs368647287 | R>C | A:197 | (102.63, 47.23, 82.28) |
| 19:33954921 | rs533937837 | N>S | A:200 | (97.58, 45.71, 76.94) |
| 19:33954903 | A>V | A:206 | (96.58, 40.63, 67.98) | |
| 19:33954897 | R>H | A:208 | (100.06, 45.85, 65.50) | |
| 19:33954898 | rs555350937 | R>C | A:208 | (100.06, 45.85, 65.50) |
| 19:33953938 | A>S | A:213 | (94.48, 39.69, 57.93) | |
| 19:33953925 | G>V | A:217 | (85.00, 38.36, 52.51) | |
| 19:33953901 | rs377738544 | S>I | A:225 | (89.59, 32.91, 65.78) |
| 19:33904548 | L>F | A:226 | (93.54, 35.17, 64.45) | |
| 19:33904538 | H>R | A:229 | (95.63, 31.06, 67.76) | |
| 19:33904535 | Y>C | A:230 | (99.04, 36.29, 69.15) | |
| 19:33904524 | rs371953949 | R>W | A:234 | (102.46, 34.10, 70.07) |
| 19:33904511 | rs577079343 | R>H | A:238 | (92.17, 28.16, 78.48) |
| 19:33904512 | R>C | A:238 | (92.17, 28.16, 78.48) | |
| 19:33904494 | C>R | A:244 | (84.85, 39.28, 70.63) | |
| 19:33904485 | rs368547324 | G>S | A:247 | (82.26, 45.00, 63.53) |
| 19:33902653 | G>D | A:249 | (79.62, 48.27, 59.11) | |
| 19:33902645 | rs201572375 | S>T | A:252 | (80.18, 49.57, 63.72) |
| 19:33902641 | A>V | A:253 | (76.84, 50.95, 65.27) | |
| 19:33902639 | rs200450538 | V>M | A:254 | (75.91, 47.55, 67.01) |
| 19:33902629 | Y>C | A:257 | (77.98, 42.68, 66.71) | |
| 19:33902627 | COSM710369 | G>R | A:258 | (78.79, 39.31, 69.23) |
| 19:33902624 | H>D | A:259 | (75.21, 39.22, 70.94) | |
| 19:33902621 | rs370370158 | A>T | A:260 | (74.30, 35.22, 70.45) |
| 19:33902617 | rs376338457 | G>E | A:261 | (72.29, 37.47, 68.33) |
| 19:33902618 | G>R | A:261 | (72.29, 37.47, 68.33) | |
| 19:33902612 | P>S | A:263 | (77.01, 35.87, 65.93) | |
| 19:33902607 | COSM994705 | N>K | A:264 | (80.75, 38.02, 64.93) |
| 19:33902606 | D>N | A:265 | (77.13, 36.45, 61.21) | |
| 19:33902602 | rs200351927 | R>Q | A:266 | (78.68, 41.73, 57.84) |
| 19:33902599 | rs537651471 | T>R | A:267 | (80.38, 39.31, 54.89) |
| 19:33902600 | T>A | A:267 | (80.38, 39.31, 54.89) | |
| 19:33902582 | rs199794147 | M>V | A:273 | (84.57, 51.18, 58.84) |
| 19:33892765 | rs374795227 | M>L | A:278 | (89.22, 42.20, 70.49) |
| 19:33892761 | rs121917723 | G>D | A:279 | (90.59, 41.03, 75.03) |
| 19:33892759 | G>S | A:280 | (92.69, 39.33, 76.78) | |
| 19:33892752 | Y>C | A:282 | (98.19, 35.74, 82.03) | |
| 19:33892753 | rs367902648 | Y>N | A:282 | (98.19, 35.74, 82.03) |
| 19:33892741 | A>T | A:286 | (92.34, 42.35, 81.79) | |
| 19:33892735 | rs201584435 | D>N | A:288 | (89.39, 46.85, 76.82) |
| 19:33892731 | rs139214756 | I>T | A:289 | (92.05, 46.88, 72.96) |
| 19:33892726 | C>R | A:291 | (90.64, 48.81, 66.75) | |
| 19:33892714 | A>T | A:295 | (88.23, 46.84, 55.30) | |
| 19:33892708 | rs370970279 | G>S | A:297 | (92.88, 49.91, 53.86) |
| 19:33892702 | F>V | A:299 | (90.88, 55.65, 56.28) | |
| 19:33892693 | rs574398144 | D>Y | A:302 | (83.49, 60.68, 54.85) |
| 19:33892681 | rs200931112 | V>I | A:306 | (84.76, 60.25, 61.84) |
| 19:33892677 | Y>C | A:307 | (90.06, 57.35, 63.21) | |
| 19:33892662 | rs1063319 COSM1392689 |
R>Q | A:312 | (90.40, 66.64, 68.61) |
| 19:33892663 | COSM1195519 | R>W | A:312 | (90.40, 66.64, 68.61) |
| 19:33892653 | rs201447445 COSM1220193 |
R>H | A:315 | (95.92, 61.33, 70.88) |
| 19:33892654 | rs537473674 | R>C | A:315 | (95.92, 61.33, 70.88) |
| 19:33892645 | M>V | A:318 | (95.23, 60.41, 76.82) | |
| 19:33892633 | K>E | A:322 | (95.95, 65.53, 86.44) | |
| 19:33882380 | rs371556469 | W>R | A:326 | (84.08, 65.33, 87.87) |
| 19:33882368 | rs563348250 | M>V | A:330 | (87.51, 64.35, 80.65) |
| 19:33882349 | R>H | A:336 | (82.83, 71.26, 73.54) | |
| 19:33882350 | rs543374825 | R>C | A:336 | (82.83, 71.26, 73.54) |
| 19:33882337 | E>A | A:340 | (84.59, 71.18, 67.77) | |
| 19:33882322 | M>T | A:345 | (82.49, 66.96, 59.16) | |
| 19:33882302 | rs558843453 COSM1167624 |
V>M | A:352 | (79.34, 74.06, 70.04) |
| 19:33882296 | A>T | A:354 | (74.21, 75.06, 72.21) | |
| 19:33882291 | rs372210606 | M>I | A:355 | (75.53, 71.88, 69.98) |
| 19:33882292 | M>T | A:355 | (75.53, 71.88, 69.98) | |
| 19:33882287 | Q>K | A:357 | (73.32, 74.36, 76.49) | |
| 19:33882274 | rs201089253 | G>E | A:361 | (76.70, 64.18, 72.10) |
| 19:33882269 | V>M | A:363 | (73.21, 61.71, 69.49) | |
| 19:33882259 | rs200183031 | P>L | A:366 | (75.73, 56.71, 73.63) |
| 19:33882227 | rs374603111 | V>M | A:377 | (86.49, 44.70, 81.86) |
| 19:33882223 | H>R | A:378 | (83.15, 46.69, 82.83) | |
| 19:33882224 | H>N | A:378 | (83.15, 46.69, 82.83) | |
| 19:33882221 | rs367841505 COSM3771000 |
D>N | A:379 | (86.87, 46.77, 87.84) |
| 19:33882218 | V>M | A:380 | (85.10, 47.08, 91.09) | |
| 19:33878977 | rs76199755 | R>H | A:389 | (74.88, 56.95, 87.74) |
| 19:33878978 | R>C | A:389 | (74.88, 56.95, 87.74) | |
| 19:33878972 | rs377199331 | D>N | A:391 | (70.07, 62.42, 85.26) |
| 19:33878956 | rs561611888 | R>Q | A:396 | (72.03, 58.78, 82.06) |
| 19:33878938 | R>Q | A:402 | (85.95, 57.70, 91.86) | |
| 19:33878939 | R>W | A:402 | (85.95, 57.70, 91.86) | |
| 19:33878917 | V>A | A:409 | (93.33, 51.26, 85.53) | |
| 19:33878909 | rs544921062 | V>M | A:412 | (90.28, 56.08, 77.01) |
| 19:33878902 | P>L | A:414 | (86.46, 57.59, 72.57) | |
| 19:33878896 | rs575962845 | I>N | A:416 | (81.54, 59.02, 66.50) |
| 19:33878883 | D>E | A:420 | (69.08, 55.33, 62.80) | |
| 19:33878884 | rs142070498 | D>G | A:420 | (69.08, 55.33, 62.80) |
| 19:33878860 | A>V | A:428 | (61.99, 65.51, 66.24) | |
| 19:33878848 | COSM3692617 | R>H | A:432 | (67.94, 67.55, 69.82) |
| 19:33878849 | R>C | A:432 | (67.94, 67.55, 69.82) | |
| 19:33878846 | rs149042427 | A>T | A:433 | (67.11, 69.78, 64.60) |
| 19:33878836 | L>P | A:436 | (71.35, 67.86, 62.85) | |
| 19:33878837 | rs17570 | L>F | A:436 | (71.35, 67.86, 62.85) |
| 19:33878830 | rs373297406 | R>H | A:438 | (67.62, 67.05, 58.11) |
| 19:33878831 | rs376372688 COSM710370 |
R>C | A:438 | (67.62, 67.05, 58.11) |
| 19:33878828 | rs376211407 | E>K | A:439 | (72.18, 67.91, 53.37) |
| 19:33878815 | rs568774163 | R>H | A:443 | (77.47, 61.93, 53.10) |
| 19:33878816 | rs537755422 | R>C | A:443 | (77.47, 61.93, 53.10) |
| 19:33878809 | rs371934154 | R>H | A:445 | (71.38, 57.82, 58.32) |
| 19:33878798 | rs121917724 | G>R | A:449 | (81.49, 53.39, 63.66) |
| 19:33878381 | rs377685056 | I>V | A:452 | (89.74, 55.04, 69.49) |
| 19:33878373 | E>D | A:454 | (93.79, 53.50, 74.30) | |
| 19:33878371 | D>V | A:455 | (93.99, 50.32, 78.33) | |
| 19:33878369 | V>I | A:456 | (95.30, 54.24, 80.96) | |
| 19:33878365 | V>A | A:457 | (97.92, 54.00, 84.50) | |
| 19:33878366 | rs189549581 | V>M | A:457 | (97.92, 54.00, 84.50) |
| 19:33878359 | T>I | A:459 | (100.54, 58.70, 87.10) | |
| 19:33878360 | T>P | A:459 | (100.54, 58.70, 87.10) | |
| 19:33878347 | rs201222933 | I>T | A:463 | (98.70, 59.04, 81.59) |
| 19:33878345 | E>Q | A:464 | (101.49, 54.22, 81.87) | |
| 19:33878330 | V>M | A:469 | (97.80, 49.95, 68.57) | |
| 19:33878323 | COSM1261948 | R>H | A:471 | (95.16, 54.04, 67.44) |
| 19:33878324 | R>C | A:471 | (95.16, 54.04, 67.44) | |
| 19:33878320 | T>I | A:472 | (97.73, 57.26, 62.68) | |
| 19:33878318 | rs200072143 | V>M | A:473 | (95.36, 57.26, 58.94) |
| 19:33878297 | M>V | A:480 | (95.77, 47.06, 56.72) | |
| 19:33878290 | rs144944440 | G>V | A:482 | (102.19, 44.91, 54.90) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:33954966 | rs121917722 | R>Q | A:185 | (89.27, 44.87, 92.89) |
| 19:33954912 | rs267606943 | S>F | A:203 | (96.02, 42.24, 72.85) |
| 19:33953938 | rs747700126 | A>S | A:213 | (94.48, 39.69, 57.93) |
| 19:33892768 | rs121917721 | D>N | A:277 | (86.17, 45.45, 71.28) |
| 19:33892761 | rs121917723 | G>D | A:279 | (90.59, 41.03, 75.03) |
| 19:33882250 | rs797045185 | L>R | A:369 | (85.05, 58.33, 78.06) |
| 19:33878906 | rs267606944 | E>K | A:413 | (85.89, 53.73, 75.56) |
| 19:33878798 | rs121917724 | G>R | A:449 | (81.49, 53.39, 63.66) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:34003534 | COSM994709 | R>C | A:57 | (76.99, 22.86, 78.31) |
| 19:34002057 | COSM1641121 | S>Y | A:70 | (87.15, 38.11, 90.91) |
| 19:34002042 | COSM4076799 | A>V | A:75 | (93.19, 37.34, 97.42) |
| 19:33991894 | COSM1750808 | E>Q | A:116 | (103.25, 21.54, 101.84) |
| 19:33892648 | COSM1680877 | V>F | A:317 | (91.22, 62.63, 77.36) |
| 19:33878848 | COSM3692617 | R>H | A:432 | (67.94, 67.55, 69.82) |
| 19:33878837 | COSM3756628 | L>F | A:436 | (71.35, 67.86, 62.85) |
| 19:33878323 | COSM1261948 | R>H | A:471 | (95.16, 54.04, 67.44) |