General Structure Information
| PDB ID | 3lgg |
| HGNC Gene Label(s) | CECR1 |
| Structure Name | crystal structure of human adenosine deaminase growth factor, adenosine deaminase type 2 (ada2) complexed with transition state analogue, coformycin |
| Resolution | 2.5Å |
| Reference | AUTH A.V.ZAVIALOV,X.YU,D.SPILLMANN,G.LAUVAU,A.V.ZAVIALOVTITL STRUCTURAL BASIS FOR THE GROWTH FACTOR ACTIVITY OF HUMANTITL 2 ADENOSINE DEAMINASE ADA2.REF J.BIOL.CHEM. V. 285 12367 2010REFN ISSN 0021-9258PMID 20147294DOI 10.1074/JBC.M109.083527 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 482 |
| Number Of SNVs | 142 |
| Number Of Permutations | 43160 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.008 |
| p-value | 0.54 |
ClinVar
| Number Of Residues | 482 |
| Number Of SNVs | 7 |
| Number Of Permutations | 1857 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.048 |
| p-value | 0.513 |
COSMIC
| Number Of Residues | 482 |
| Number Of SNVs | 9 |
| Number Of Permutations | 7970 |
| Optimal Distance Threshold | 21.0 |
| K Statistic | 0.167 |
| p-value | 0.45 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 142 |
| Number Of ClinVar SNVs | 7 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.033 |
| p-value | 0.657 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 142 |
| Number Of COSMIC SNVs | 9 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | -0.066 |
| p-value | 0.515 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 22:17690470 | T>I | A:7 | (-18.81, -22.45, 6.56) | |
| 22:17690471 | rs558427920 | T>A | A:7 | (-18.81, -22.45, 6.56) |
| 22:17690467 | R>P | A:8 | (-20.79, -16.42, 5.50) | |
| 22:17690468 | R>W | A:8 | (-20.79, -16.42, 5.50) | |
| 22:17690464 | rs151283756 | A>V | A:9 | (-20.21, -18.00, 10.18) |
| 22:17690453 | rs538213260 | L>M | A:13 | (-16.42, -16.21, 14.82) |
| 22:17690450 | K>E | A:14 | (-11.44, -18.00, 12.47) | |
| 22:17690439 | M>I | A:17 | (-12.25, -14.13, 17.74) | |
| 22:17690441 | M>L | A:17 | (-12.25, -14.13, 17.74) | |
| 22:17690434 | rs571235882 COSM4102400 |
R>Q | A:19 | (-10.34, -8.98, 14.46) |
| 22:17690435 | R>W | A:19 | (-10.34, -8.98, 14.46) | |
| 22:17690414 | L>V | A:26 | (-16.57, -6.10, 26.60) | |
| 22:17690404 | K>R | A:29 | (-21.08, 0.34, 31.46) | |
| 22:17690378 | M>V | A:38 | (-18.81, 1.24, 16.27) | |
| 22:17690374 | rs61747288 | T>M | A:39 | (-23.02, 4.13, 15.44) |
| 22:17690363 | rs374965869 | A>T | A:43 | (-21.58, 6.86, 9.69) |
| 22:17690355 | M>I | A:45 | (-16.66, 4.40, 7.04) | |
| 22:17690353 | K>R | A:46 | (-21.51, 4.13, 5.13) | |
| 22:17690341 | R>K | A:50 | (-21.81, 10.09, -0.31) | |
| 22:17690331 | I>M | A:53 | (-14.08, 12.85, 1.56) | |
| 22:17690320 | S>T | A:57 | (-7.04, 8.23, 1.97) | |
| 22:17690316 | M>I | A:58 | (-6.79, 12.07, 2.56) | |
| 22:17690318 | rs143853882 | M>V | A:58 | (-6.79, 12.07, 2.56) |
| 22:17690314 | H>R | A:59 | (-0.88, 13.88, 3.11) | |
| 22:17690302 | rs548766340 | A>V | A:63 | (-6.84, 15.41, 6.69) |
| 22:17690296 | rs149466386 | H>R | A:65 | (-9.45, 19.89, 7.84) |
| 22:17690290 | I>T | A:67 | (-9.20, 14.07, 11.65) | |
| 22:17690286 | E>D | A:68 | (-9.44, 18.46, 13.98) | |
| 22:17690282 | S>G | A:70 | (-14.36, 13.40, 14.10) | |
| 22:17690279 | rs370709874 COSM478703 |
Q>E | A:71 | (-17.86, 13.06, 16.66) |
| 22:17690276 | V>M | A:72 | (-14.23, 9.00, 16.17) | |
| 22:17690263 | L>P | A:76 | (-9.88, 8.52, 20.08) | |
| 22:17690252 | P>S | A:80 | (-7.36, 6.20, 28.23) | |
| 22:17688174 | A>V | A:84 | (4.42, 6.70, 24.43) | |
| 22:17688167 | rs587777241 | H>Q | A:86 | (8.71, 5.38, 18.34) |
| 22:17688169 | H>Y | A:86 | (8.71, 5.38, 18.34) | |
| 22:17688147 | rs200935979 | V>G | A:93 | (6.69, 20.16, 21.30) |
| 22:17688148 | V>M | A:93 | (6.69, 20.16, 21.30) | |
| 22:17688144 | T>I | A:94 | (3.54, 22.22, 19.26) | |
| 22:17688145 | T>P | A:94 | (3.54, 22.22, 19.26) | |
| 22:17688140 | M>I | A:95 | (6.91, 23.75, 16.44) | |
| 22:17688141 | rs189403607 | M>T | A:95 | (6.91, 23.75, 16.44) |
| 22:17688142 | M>V | A:95 | (6.91, 23.75, 16.44) | |
| 22:17688130 | V>M | A:99 | (7.81, 30.63, 17.25) | |
| 22:17688122 | N>K | A:101 | (7.68, 31.24, 24.16) | |
| 22:17688087 | T>I | A:113 | (24.21, 28.67, 6.31) | |
| 22:17688080 | R>S | A:115 | (24.53, 25.44, 1.58) | |
| 22:17688081 | R>K | A:115 | (24.53, 25.44, 1.58) | |
| 22:17688075 | I>T | A:117 | (20.37, 26.31, 6.34) | |
| 22:17688068 | Q>H | A:119 | (21.63, 28.57, 12.47) | |
| 22:17688057 | rs201701549 | A>V | A:123 | (23.93, 34.50, 23.42) |
| 22:17688042 | rs545602214 | R>H | A:128 | (33.86, 36.71, 17.69) |
| 22:17688043 | rs200153182 | R>C | A:128 | (33.86, 36.71, 17.69) |
| 22:17688040 | P>T | A:129 | (31.78, 35.86, 13.62) | |
| 22:17688033 | E>A | A:131 | (33.11, 28.78, 8.36) | |
| 22:17688027 | C>Y | A:133 | (27.93, 32.22, 10.86) | |
| 22:17688024 | S>F | A:134 | (28.90, 35.57, 8.79) | |
| 22:17688003 | D>G | A:141 | (17.26, 43.58, 16.59) | |
| 22:17687998 | R>G | A:143 | (10.79, 39.56, 15.73) | |
| 22:17687992 | rs115986203 | R>W | A:145 | (16.09, 45.41, 11.39) |
| 22:17684655 | R>K | A:158 | (5.61, 28.87, 6.68) | |
| 22:17684647 | T>P | A:161 | (6.78, 22.08, 9.92) | |
| 22:17684643 | L>P | A:162 | (7.27, 18.70, 6.82) | |
| 22:17684644 | L>V | A:162 | (7.27, 18.70, 6.82) | |
| 22:17684633 | Q>H | A:165 | (-1.00, 23.69, 0.34) | |
| 22:17684619 | rs538708563 | I>T | A:170 | (6.94, 20.35, -2.24) |
| 22:17684596 | W>R | A:178 | (14.44, 11.24, 5.92) | |
| 22:17684592 | rs369306297 COSM3972851 |
S>L | A:179 | (16.42, 16.74, 3.23) |
| 22:17684580 | T>I | A:183 | (16.95, 20.72, 7.67) | |
| 22:17684577 | rs376482971 COSM3551954 |
I>T | A:184 | (13.34, 20.77, 10.50) |
| 22:17684574 | rs373928007 | F>Y | A:185 | (15.23, 17.35, 13.40) |
| 22:17684565 | rs369510859 | I>T | A:188 | (14.74, 23.13, 15.94) |
| 22:17684566 | I>V | A:188 | (14.74, 23.13, 15.94) | |
| 22:17684559 | G>V | A:190 | (19.43, 25.82, 19.15) | |
| 22:17684539 | V>M | A:197 | (14.52, 26.03, 26.43) | |
| 22:17684532 | R>K | A:199 | (15.71, 23.19, 32.14) | |
| 22:17684517 | rs186116639 | R>Q | A:204 | (4.64, 22.66, 26.43) |
| 22:17684499 | rs145966045 | Y>C | A:210 | (-1.78, 14.68, 31.83) |
| 22:17684497 | E>K | A:211 | (-4.11, 17.40, 26.82) | |
| 22:17684487 | V>A | A:214 | (-0.59, 9.90, 27.48) | |
| 22:17684477 | rs151014930 | M>I | A:217 | (6.76, 9.59, 27.89) |
| 22:17684475 | E>A | A:218 | (9.78, 4.90, 26.51) | |
| 22:17684466 | A>V | A:221 | (17.87, 10.51, 22.75) | |
| 22:17684454 | rs148936893 | P>L | A:225 | (25.44, 19.13, 23.45) |
| 22:17672686 | S>R | A:230 | (28.61, 31.09, 28.73) | |
| 22:17672676 | H>Y | A:234 | (26.11, 20.96, 30.14) | |
| 22:17672670 | rs551968547 | E>K | A:236 | (26.18, 12.75, 27.46) |
| 22:17672646 | rs149787245 | Q>E | A:244 | (15.70, 11.79, 36.72) |
| 22:17672598 | I>V | A:260 | (10.42, 10.08, 31.25) | |
| 22:17672576 | H>R | A:267 | (22.32, 9.82, 13.38) | |
| 22:17672574 | R>G | A:268 | (21.29, 3.99, 10.48) | |
| 22:17670915 | COSM1031843 COSM1592844 |
D>Y | A:271 | (32.03, 5.60, 10.95) |
| 22:17670908 | COSM1714130 COSM1714131 |
A>V | A:273 | (33.95, 3.54, 15.49) |
| 22:17670890 | I>T | A:279 | (27.55, 1.08, 22.35) | |
| 22:17670887 | COSM1031842 COSM1592845 |
R>Q | A:280 | (32.20, 1.28, 24.75) |
| 22:17670885 | M>V | A:281 | (28.09, 6.69, 26.53) | |
| 22:17670877 | rs146597836 | M>I | A:283 | (27.43, 0.26, 28.40) |
| 22:17670872 | L>R | A:285 | (24.34, 6.29, 30.53) | |
| 22:17670869 | R>Q | A:286 | (21.31, 0.58, 31.65) | |
| 22:17670865 | rs144415615 | I>M | A:287 | (25.84, 1.47, 35.20) |
| 22:17670854 | rs146788085 | T>M | A:291 | (15.70, 4.18, 36.67) |
| 22:17669337 | rs374130382 | V>M | A:299 | (18.41, 6.90, 14.24) |
| 22:17669333 | COSM4135114 COSM4135115 |
G>E | A:300 | (17.55, 7.49, 10.43) |
| 22:17669334 | G>R | A:300 | (17.55, 7.49, 10.43) | |
| 22:17669325 | rs369716341 | D>N | A:303 | (16.76, 3.27, 2.58) |
| 22:17669318 | G>D | A:305 | (22.51, 3.81, 5.53) | |
| 22:17669303 | rs377213003 | D>G | A:310 | (27.17, -2.78, 8.26) |
| 22:17669301 | Y>H | A:311 | (26.78, -0.24, 12.56) | |
| 22:17669297 | rs573337330 | K>R | A:312 | (28.49, -7.82, 13.70) |
| 22:17669288 | rs142508522 | L>P | A:315 | (25.78, -3.76, 17.86) |
| 22:17669277 | COSM1580694 COSM1580695 |
A>T | A:319 | (28.30, -9.54, 24.73) |
| 22:17669267 | rs191772679 | G>D | A:322 | (28.74, -9.47, 29.67) |
| 22:17669265 | rs74317375 | V>I | A:323 | (26.86, -6.50, 29.39) |
| 22:17669250 | rs373498904 | F>L | A:328 | (14.70, -0.42, 22.36) |
| 22:17669245 | rs116020027 | F>L | A:329 | (17.62, -1.89, 16.91) |
| 22:17669240 | A>V | A:331 | (13.34, -1.82, 11.42) | |
| 22:17669238 | rs45511697 | G>R | A:332 | (11.96, -1.68, 8.00) |
| 22:17669235 | E>K | A:333 | (11.49, 3.03, 8.00) | |
| 22:17669232 | T>A | A:334 | (11.48, -0.04, 3.59) | |
| 22:17663634 | I>L | A:341 | (17.19, -2.09, 4.00) | |
| 22:17663627 | R>K | A:343 | (18.05, -8.67, 4.88) | |
| 22:17663628 | R>G | A:343 | (18.05, -8.67, 4.88) | |
| 22:17663615 | rs375443506 | D>V | A:347 | (19.84, -8.63, 11.89) |
| 22:17663613 | A>T | A:348 | (17.06, -7.04, 15.41) | |
| 22:17663594 | T>I | A:354 | (12.84, -5.17, 23.49) | |
| 22:17663590 | R>S | A:355 | (10.31, -1.79, 21.95) | |
| 22:17663586 | G>S | A:357 | (10.71, 0.03, 14.69) | |
| 22:17663569 | L>F | A:362 | (7.22, -7.96, 9.40) | |
| 22:17663560 | H>Q | A:365 | (10.03, -10.87, 5.58) | |
| 22:17663561 | H>R | A:365 | (10.03, -10.87, 5.58) | |
| 22:17663562 | rs372341852 | H>Y | A:365 | (10.03, -10.87, 5.58) |
| 22:17663556 | A>T | A:367 | (9.54, -16.26, 9.33) | |
| 22:17663538 | W>G | A:373 | (3.23, -15.10, 17.72) | |
| 22:17663519 | I>K | A:379 | (5.64, -3.65, 15.70) | |
| 22:17663510 | C>Y | A:382 | (4.14, 5.29, 13.25) | |
| 22:17663508 | P>S | A:383 | (0.72, 5.95, 11.20) | |
| 22:17662900 | rs142726959 | V>L | A:392 | (2.02, 4.74, 2.39) |
| 22:17662851 | H>L | A:408 | (1.78, -9.15, 15.54) | |
| 22:17662849 | rs186147069 | P>A | A:409 | (2.66, -8.25, 18.60) |
| 22:17662845 | M>T | A:410 | (0.88, -4.01, 17.67) | |
| 22:17662846 | M>L | A:410 | (0.88, -4.01, 17.67) | |
| 22:17662837 | S>G | A:413 | (3.31, 6.05, 18.38) | |
| 22:17662825 | P>S | A:417 | (4.21, 14.64, 16.41) | |
| 22:17662818 | COSM1580690 COSM1580691 |
M>T | A:419 | (7.80, 17.63, 12.58) |
| 22:17662797 | S>C | A:426 | (-5.08, 10.89, 19.14) | |
| 22:17662794 | rs376785840 | Y>C | A:427 | (-4.24, 13.69, 15.54) |
| 22:17662785 | Y>C | A:430 | (-8.82, 8.74, 12.80) | |
| 22:17662779 | V>G | A:432 | (-5.03, 2.59, 13.49) | |
| 22:17662772 | M>I | A:434 | (-11.17, 4.84, 10.99) | |
| 22:17662767 | rs61744537 | I>T | A:436 | (-4.69, 0.50, 9.45) |
| 22:17662764 | G>E | A:437 | (-8.42, -1.73, 10.80) | |
| 22:17662758 | M>R | A:439 | (-15.93, -1.02, 9.30) | |
| 22:17662722 | rs369910191 | M>T | A:451 | (-3.69, -3.18, 27.66) |
| 22:17662714 | rs372585593 | I>V | A:454 | (1.29, -0.84, 29.99) |
| 22:17662465 | COSM4102386 COSM4102387 |
Y>H | A:456 | (4.70, -5.17, 24.77) |
| 22:17662461 | S>I | A:457 | (7.01, -1.13, 28.88) | |
| 22:17662445 | rs372617067 | S>R | A:462 | (5.70, -3.41, 40.03) |
| 22:17662435 | T>A | A:466 | (0.80, 0.85, 39.52) | |
| 22:17662408 | W>R | A:475 | (-11.16, 1.93, 29.46) | |
| 22:17662404 | D>G | A:476 | (-13.83, 2.56, 34.13) | |
| 22:17662387 | V>M | A:482 | (-18.90, 6.98, 25.59) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 22:17690428 | rs200930463 | G>V | A:21 | (-8.89, -8.01, 20.76) |
| 22:17690429 | rs202134424 | G>W | A:21 | (-8.89, -8.01, 20.76) |
| 22:17688167 | rs587777241 | H>Q | A:86 | (8.71, 5.38, 18.34) |
| 22:17687997 | rs77563738 | R>Q | A:143 | (10.79, 39.56, 15.73) |
| 22:17684454 | rs148936893 | P>L | A:225 | (25.44, 19.13, 23.45) |
| 22:17669232 | rs775440641 | T>A | A:334 | (11.48, -0.04, 3.59) |
| 22:17663586 | rs770689762 | G>S | A:357 | (10.71, 0.03, 14.69) |
| 22:17662794 | rs376785840 | Y>C | A:427 | (-4.24, 13.69, 15.54) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 22:17690464 | COSM167403 | A>V | A:9 | (-20.21, -18.00, 10.18) |
| 22:17688129 | COSM1130510 | V>G | A:99 | (7.81, 30.63, 17.25) |
| 22:17684517 | COSM1580696 | R>Q | A:204 | (4.64, 22.66, 26.43) |
| 22:17672671 | COSM1751709 | D>E | A:235 | (27.61, 15.76, 29.87) |
| 22:17672573 | COSM1682098 | R>I | A:268 | (21.29, 3.99, 10.48) |
| 22:17670887 | COSM1031842 | R>Q | A:280 | (32.20, 1.28, 24.75) |
| 22:17669306 | COSM4002080 | H>R | A:309 | (25.74, -7.33, 9.04) |
| 22:17662876 | COSM1580692 | V>L | A:400 | (-0.05, -3.10, 10.02) |
| 22:17662787 | COSM1592846 | F>L | A:429 | (-4.70, 5.43, 18.80) |