General Structure Information
| PDB ID | 2pfn |
| HGNC Gene Label(s) | POLL |
| Structure Name | na in the active site of dna polymerase lambda |
| Resolution | 1.9Å |
| Reference | AUTH M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,L.C.PEDERSEN,AUTH 2 T.A.KUNKELTITL ROLE OF THE CATALYTIC METAL DURING POLYMERIZATIONTITL 2 BY DNA POLYMERASE LAMBDA.REF DNA REPAIR V. 6 1333 2007REFN ISSN 1568-7864PMID 17475573DOI 10.1016/J.DNAREP.2007.03.005 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 325 |
| Number Of SNVs | 104 |
| Number Of Permutations | 15186 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.076 |
| p-value | 0.157 |
COSMIC
| Number Of Residues | 325 |
| Number Of SNVs | 3 |
| Number Of Permutations | 7 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.333 |
| p-value | 0.948 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 104 |
| Number Of COSMIC SNVs | 3 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | -0.153 |
| p-value | 1.0 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:103344490 | L>F | A:254 | (29.95, 4.72, 23.47) | |
| 10:103344484 | I>V | A:256 | (26.38, 1.59, 23.59) | |
| 10:103344471 | L>R | A:260 | (21.57, 1.78, 20.73) | |
| 10:103344450 | Y>C | A:267 | (13.19, 0.61, 15.37) | |
| 10:103344438 | G>E | A:271 | (7.90, 4.54, 11.79) | |
| 10:103344425 | R>S | A:275 | (10.09, 0.60, 19.57) | |
| 10:103344421 | rs372482299 | L>M | A:277 | (11.15, 8.29, 21.72) |
| 10:103344415 | Y>H | A:279 | (16.04, 2.28, 21.28) | |
| 10:103344403 | rs140868797 | I>V | A:283 | (20.94, 6.83, 23.23) |
| 10:103344399 | N>S | A:284 | (20.23, 11.14, 25.74) | |
| 10:103344384 | F>S | A:289 | (26.06, 7.98, 33.24) | |
| 10:103344376 | P>S | A:292 | (30.50, 2.88, 32.85) | |
| 10:103344369 | T>I | A:294 | (28.42, -3.11, 34.81) | |
| 10:103344366 | rs368623787 | S>L | A:295 | (25.02, -3.68, 35.98) |
| 10:103343434 | A>V | A:299 | (20.73, 0.02, 33.89) | |
| 10:103343435 | A>T | A:299 | (20.73, 0.02, 33.89) | |
| 10:103343427 | rs529724242 | S>R | A:301 | (19.14, 2.74, 37.27) |
| 10:103343426 | I>V | A:302 | (18.95, 4.58, 34.37) | |
| 10:103343422 | P>L | A:303 | (16.79, 7.29, 33.86) | |
| 10:103343407 | R>Q | A:308 | (13.32, -5.05, 26.26) | |
| 10:103343408 | rs376114934 | R>W | A:308 | (13.32, -5.05, 26.26) |
| 10:103343404 | M>K | A:309 | (17.56, -0.99, 26.50) | |
| 10:103343372 | rs565324718 | G>R | A:320 | (30.27, -6.75, 21.78) |
| 10:103343366 | rs201742864 | L>V | A:322 | (23.15, -5.82, 19.45) |
| 10:103343362 | rs373803211 | R>Q | A:323 | (22.26, -9.24, 17.15) |
| 10:103343363 | R>W | A:323 | (22.26, -9.24, 17.15) | |
| 10:103343340 | rs368773624 | E>D | A:330 | (17.80, -4.65, 2.39) |
| 10:103343336 | V>L | A:332 | (17.03, 1.20, 6.61) | |
| 10:103343325 | L>F | A:335 | (13.94, 4.18, 4.15) | |
| 10:103343314 | rs146197224 | S>F | A:339 | (14.01, 10.58, 4.78) |
| 10:103343312 | N>D | A:340 | (17.52, 12.65, 4.57) | |
| 10:103343307 | I>M | A:341 | (14.34, 14.19, 0.71) | |
| 10:103343308 | I>T | A:341 | (14.34, 14.19, 0.71) | |
| 10:103343309 | rs554844269 | I>V | A:341 | (14.34, 14.19, 0.71) |
| 10:103343284 | A>V | A:349 | (10.00, 6.37, 1.92) | |
| 10:103343277 | rs542569736 | M>I | A:351 | (5.52, 5.14, -1.42) |
| 10:103343265 | rs143224710 | Q>H | A:355 | (6.82, 2.59, -5.85) |
| 10:103342647 | G>D | A:356 | (11.58, 0.46, -6.37) | |
| 10:103342648 | rs139871590 | G>S | A:356 | (11.58, 0.46, -6.37) |
| 10:103342623 | rs146112511 | R>H | A:364 | (16.13, 12.60, -11.64) |
| 10:103342620 | S>N | A:365 | (13.58, 9.83, -12.92) | |
| 10:103342616 | rs370590358 | Q>H | A:366 | (11.09, 7.10, -12.17) |
| 10:103342614 | rs575920065 | A>V | A:367 | (9.24, 10.41, -8.71) |
| 10:103342588 | rs200623399 | G>S | A:376 | (15.33, 18.90, -1.42) |
| 10:103342557 | rs369790337 COSM308118 |
R>H | A:386 | (25.35, 21.58, 10.93) |
| 10:103340172 | V>D | A:399 | (16.77, 38.72, 7.92) | |
| 10:103340173 | V>L | A:399 | (16.77, 38.72, 7.92) | |
| 10:103340160 | A>V | A:403 | (13.39, 44.02, 8.55) | |
| 10:103340128 | rs543893064 | A>T | A:414 | (18.83, 33.84, 16.50) |
| 10:103340125 | C>R | A:415 | (17.06, 30.96, 17.68) | |
| 10:103340112 | rs368168568 | R>Q | A:419 | (19.32, 31.69, 22.30) |
| 10:103340109 | R>Q | A:420 | (21.00, 25.60, 21.66) | |
| 10:103340110 | rs374718867 COSM369793 |
R>W | A:420 | (21.00, 25.60, 21.66) |
| 10:103340100 | rs142388822 | A>V | A:423 | (29.55, 25.72, 16.30) |
| 10:103340097 | T>I | A:424 | (27.57, 24.03, 13.87) | |
| 10:103340094 | C>Y | A:425 | (24.10, 25.63, 12.41) | |
| 10:103340083 | D>N | A:429 | (16.25, 29.28, 13.51) | |
| 10:103340070 | rs201665669 | T>I | A:433 | (8.82, 40.75, 17.43) |
| 10:103340062 | D>Y | A:436 | (4.37, 47.66, 19.08) | |
| 10:103340056 | rs3730477 | R>W | A:438 | (1.31, 45.33, 16.31) |
| 10:103340047 | rs371348876 | R>W | A:441 | (1.25, 42.49, 11.27) |
| 10:103340044 | G>R | A:442 | (1.96, 41.63, 7.94) | |
| 10:103340031 | R>H | A:446 | (7.65, 42.61, 2.90) | |
| 10:103340032 | R>C | A:446 | (7.65, 42.61, 2.90) | |
| 10:103340029 | L>F | A:447 | (10.74, 40.21, 5.03) | |
| 10:103340020 | rs145030649 | S>G | A:450 | (13.05, 42.04, 0.40) |
| 10:103340013 | R>Q | A:452 | (11.33, 36.76, -2.49) | |
| 10:103340014 | rs200281533 | R>W | A:452 | (11.33, 36.76, -2.49) |
| 10:103340009 | Q>H | A:453 | (15.03, 41.25, -4.47) | |
| 10:103339565 | rs80066411 | T>I | A:458 | (16.54, 30.35, -3.41) |
| 10:103339562 | D>G | A:459 | (14.00, 27.91, -2.79) | |
| 10:103339545 | E>Q | A:465 | (2.83, 34.44, 1.21) | |
| 10:103339540 | E>D | A:466 | (-2.34, 32.79, 1.15) | |
| 10:103339535 | rs149956893 | G>D | A:468 | (-2.16, 37.11, 7.42) |
| 10:103339531 | rs377575684 COSM914041 |
Q>H | A:469 | (-2.98, 35.47, 10.45) |
| 10:103339517 | L>W | A:474 | (9.93, 27.14, 6.29) | |
| 10:103339518 | L>M | A:474 | (9.93, 27.14, 6.29) | |
| 10:103339505 | R>Q | A:478 | (23.26, 31.16, -2.57) | |
| 10:103339493 | P>L | A:482 | (32.47, 32.82, -3.58) | |
| 10:103339487 | rs200705693 | R>Q | A:484 | (28.73, 31.54, 0.65) |
| 10:103339488 | rs370380523 | R>W | A:484 | (28.73, 31.54, 0.65) |
| 10:103339484 | rs146653325 | R>Q | A:485 | (26.83, 25.57, -0.75) |
| 10:103339485 | rs140396238 | R>W | A:485 | (26.83, 25.57, -0.75) |
| 10:103339482 | H>Y | A:486 | (21.86, 26.89, -1.50) | |
| 10:103339478 | R>Q | A:487 | (23.27, 27.05, 4.07) | |
| 10:103339476 | R>C | A:488 | (16.33, 25.41, 5.85) | |
| 10:103339467 | rs138242344 | I>V | A:491 | (11.36, 33.27, 9.43) |
| 10:103339451 | Y>S | A:496 | (6.74, 41.76, 22.91) | |
| 10:103339446 | rs377327286 | E>K | A:498 | (2.97, 34.98, 21.91) |
| 10:103339440 | rs150453080 | A>T | A:500 | (8.80, 34.15, 25.72) |
| 10:103339430 | L>R | A:503 | (12.65, 32.87, 22.65) | |
| 10:103339424 | rs142581169 | Y>S | A:505 | (9.41, 26.69, 19.50) |
| 10:103339406 | H>R | A:511 | (14.66, 16.37, 24.75) | |
| 10:103339407 | H>Y | A:511 | (14.66, 16.37, 24.75) | |
| 10:103339400 | N>S | A:513 | (10.78, 22.27, 24.04) | |
| 10:103339397 | R>H | A:514 | (9.29, 16.41, 23.13) | |
| 10:103339398 | R>C | A:514 | (9.29, 16.41, 23.13) | |
| 10:103339391 | rs373253236 | M>T | A:516 | (9.60, 22.34, 29.61) |
| 10:103339392 | rs202015609 | M>V | A:516 | (9.60, 22.34, 29.61) |
| 10:103339370 | K>R | A:523 | (2.73, 21.02, 37.09) | |
| 10:103339365 | M>V | A:525 | (0.40, 23.96, 33.32) | |
| 10:103339353 | E>K | A:529 | (4.65, 27.69, 20.24) | |
| 10:103339350 | H>Y | A:530 | (1.29, 30.63, 20.67) | |
| 10:103339334 | A>V | A:535 | (-6.45, 25.32, 34.19) | |
| 10:103339332 | rs544757979 | V>M | A:536 | (-5.63, 22.94, 31.14) |
| 10:103339328 | V>D | A:537 | (-9.46, 20.81, 31.07) | |
| 10:103339325 | rs202232099 | R>Q | A:538 | (-5.40, 18.18, 29.94) |
| 10:103339326 | R>W | A:538 | (-5.40, 18.18, 29.94) | |
| 10:103339319 | T>I | A:540 | (-8.26, 9.90, 30.33) | |
| 10:103339316 | rs148557018 | H>R | A:541 | (-7.50, 9.84, 26.28) |
| 10:103339292 | R>Q | A:549 | (-6.02, 30.58, 33.76) | |
| 10:103339289 | V>A | A:550 | (-3.00, 32.58, 29.56) | |
| 10:103339280 | T>I | A:553 | (5.04, 34.77, 30.16) | |
| 10:103339277 | P>R | A:554 | (7.20, 38.40, 30.52) | |
| 10:103339274 | T>I | A:555 | (10.42, 36.47, 30.81) | |
| 10:103339264 | D>E | A:558 | (8.52, 34.30, 34.00) | |
| 10:103339262 | V>A | A:559 | (8.23, 29.89, 31.83) | |
| 10:103339260 | F>I | A:560 | (12.22, 28.10, 33.26) | |
| 10:103339235 | rs573888152 | R>Q | A:568 | (18.19, 25.34, 32.29) |
| 10:103339232 | COSM426957 | E>G | A:569 | (21.33, 30.44, 30.12) |
| 10:103339221 | rs555309980 | R>W | A:573 | (17.66, 26.09, 27.01) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:103342641 | COSM3665446 | R>Q | A:358 | (15.65, 0.76, -4.05) |
| 10:103340110 | COSM369793 | R>W | A:420 | (21.00, 25.60, 21.66) |
| 10:103339473 | COSM1675504 | L>M | A:489 | (15.76, 30.51, 6.51) |