General Structure Information
| PDB ID | 1x9n |
| HGNC Gene Label(s) | LIG1 |
| Structure Name | crystal structure of human dna ligase i bound to 5-adenylated, nicked dna |
| Resolution | 3.0Å |
| Reference | AUTH J.M.PASCAL,P.J.OBRIEN,A.E.TOMKINSON,T.ELLENBERGERTITL HUMAN DNA LIGASE I COMPLETELY ENCIRCLES AND PARTIALLYTITL 2 UNWINDS NICKED DNA.REF NATURE V. 432 473 2004REFN ISSN 0028-0836PMID 15565146DOI 10.1038/NATURE03082 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 626 |
| Number Of SNVs | 176 |
| Number Of Permutations | 28041 |
| Optimal Distance Threshold | 19.0 |
| K Statistic | 0.132 |
| p-value | 0.048 |
COSMIC
| Number Of Residues | 626 |
| Number Of SNVs | 6 |
| Number Of Permutations | 792 |
| Optimal Distance Threshold | 19.0 |
| K Statistic | 0.067 |
| p-value | 0.927 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 176 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 37.0 |
| K Statistic | 0.453 |
| p-value | 0.307 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:48647203 | rs180771242 | G>V | A:265 | (50.71, 35.41, 80.94) |
| 19:48647197 | rs3730933 | N>S | A:267 | (52.80, 40.45, 77.88) |
| 19:48647192 | rs201846395 | A>T | A:269 | (53.10, 43.89, 75.00) |
| 19:48647184 | N>K | A:271 | (56.87, 48.01, 78.77) | |
| 19:48647185 | N>S | A:271 | (56.87, 48.01, 78.77) | |
| 19:48647179 | rs367887927 | Y>C | A:273 | (60.07, 41.21, 76.40) |
| 19:48647177 | H>Y | A:274 | (63.05, 41.76, 80.20) | |
| 19:48647164 | D>G | A:278 | (59.48, 38.71, 80.03) | |
| 19:48647158 | C>Y | A:280 | (56.70, 31.42, 78.94) | |
| 19:48647149 | rs574879811 | P>L | A:283 | (65.67, 27.27, 78.37) |
| 19:48647140 | K>T | A:286 | (59.29, 22.67, 72.13) | |
| 19:48646843 | A>S | A:291 | (52.66, 31.90, 73.22) | |
| 19:48646837 | rs528238142 | A>S | A:293 | (48.28, 33.17, 70.91) |
| 19:48646833 | R>Q | A:294 | (47.72, 35.01, 75.35) | |
| 19:48646834 | R>W | A:294 | (47.72, 35.01, 75.35) | |
| 19:48646813 | COSM712112 | E>K | A:301 | (44.63, 43.91, 72.06) |
| 19:48646801 | R>W | A:305 | (51.68, 49.01, 60.57) | |
| 19:48643396 | R>W | A:307 | (53.72, 47.60, 70.05) | |
| 19:48643383 | T>M | A:311 | (54.70, 42.44, 69.98) | |
| 19:48643377 | S>N | A:313 | (59.96, 41.19, 68.08) | |
| 19:48643370 | L>F | A:315 | (57.66, 35.69, 70.31) | |
| 19:48643365 | R>L | A:317 | (63.92, 39.81, 71.34) | |
| 19:48643366 | R>C | A:317 | (63.92, 39.81, 71.34) | |
| 19:48643360 | V>M | A:319 | (62.30, 32.04, 69.68) | |
| 19:48643353 | A>V | A:321 | (67.28, 33.11, 72.73) | |
| 19:48643347 | COSM3536445 | S>L | A:323 | (64.13, 28.06, 71.05) |
| 19:48643341 | rs368085245 | P>R | A:325 | (64.85, 25.53, 66.48) |
| 19:48643323 | L>P | A:331 | (58.04, 32.86, 61.19) | |
| 19:48643312 | rs144552403 | L>F | A:335 | (52.98, 34.32, 57.61) |
| 19:48643308 | N>S | A:336 | (48.60, 31.22, 57.93) | |
| 19:48643305 | rs201228692 | H>R | A:337 | (51.64, 30.74, 54.63) |
| 19:48643294 | P>T | A:341 | (55.90, 29.06, 47.55) | |
| 19:48643270 | rs3730947 | V>M | A:349 | (40.37, 22.49, 54.56) |
| 19:48643263 | D>A | A:351 | (34.62, 26.99, 55.21) | |
| 19:48643252 | rs202150273 | L>F | A:355 | (32.22, 24.25, 59.71) |
| 19:48643245 | A>G | A:357 | (35.03, 19.79, 62.72) | |
| 19:48640942 | R>Q | A:364 | (27.41, 23.53, 68.76) | |
| 19:48640928 | rs3730966 | V>I | A:369 | (28.03, 25.82, 64.27) |
| 19:48640924 | R>Q | A:370 | (27.14, 26.29, 58.52) | |
| 19:48640925 | R>W | A:370 | (27.14, 26.29, 58.52) | |
| 19:48640915 | A>V | A:373 | (29.78, 31.67, 61.78) | |
| 19:48640903 | G>D | A:377 | (32.20, 36.18, 60.96) | |
| 19:48640898 | V>M | A:379 | (34.97, 30.32, 62.77) | |
| 19:48640883 | rs530117495 | E>K | A:384 | (36.43, 28.80, 72.17) |
| 19:48640852 | L>R | A:394 | (42.73, 13.48, 80.53) | |
| 19:48640849 | COSM1213361 | P>L | A:395 | (43.24, 17.06, 78.88) |
| 19:48640843 | P>H | A:397 | (49.55, 17.39, 76.37) | |
| 19:48640840 | P>L | A:398 | (50.37, 21.32, 76.37) | |
| 19:48640834 | T>I | A:400 | (53.76, 22.81, 70.53) | |
| 19:48640826 | G>R | A:403 | (53.09, 20.94, 66.25) | |
| 19:48640807 | rs4987068 | R>H | A:409 | (53.45, 20.58, 56.68) |
| 19:48640808 | rs201504571 | R>C | A:409 | (53.45, 20.58, 56.68) |
| 19:48640799 | rs368941216 | A>T | A:412 | (47.99, 18.98, 53.54) |
| 19:48640794 | rs148171804 | R>S | A:413 | (51.59, 16.08, 54.30) |
| 19:48640781 | COSM312505 | A>S | A:418 | (38.85, 9.59, 52.29) |
| 19:48640324 | I>M | A:424 | (37.93, 16.12, 59.92) | |
| 19:48640325 | rs143797790 | I>T | A:424 | (37.93, 16.12, 59.92) |
| 19:48640326 | I>V | A:424 | (37.93, 16.12, 59.92) | |
| 19:48640319 | I>S | A:426 | (44.07, 16.13, 62.59) | |
| 19:48640316 | I>T | A:427 | (40.90, 19.76, 62.81) | |
| 19:48640310 | G>V | A:429 | (42.23, 17.41, 68.18) | |
| 19:48640301 | V>A | A:432 | (40.31, 18.59, 72.26) | |
| 19:48640292 | R>H | A:435 | (45.33, 24.08, 77.67) | |
| 19:48640293 | rs367665775 | R>C | A:435 | (45.33, 24.08, 77.67) |
| 19:48640287 | S>P | A:437 | (42.76, 31.39, 72.91) | |
| 19:48640277 | R>Q | A:440 | (40.18, 32.46, 69.65) | |
| 19:48640272 | I>L | A:442 | (43.85, 26.88, 65.57) | |
| 19:48640269 | rs374979607 | A>T | A:443 | (40.19, 28.32, 63.50) |
| 19:48639372 | rs139908769 | G>R | A:448 | (42.03, 31.51, 56.19) |
| 19:48639368 | R>Q | A:449 | (39.10, 34.31, 56.73) | |
| 19:48639369 | R>W | A:449 | (39.10, 34.31, 56.73) | |
| 19:48639363 | R>C | A:451 | (40.87, 39.52, 61.35) | |
| 19:48639344 | Q>R | A:457 | (56.54, 43.44, 54.53) | |
| 19:48639305 | rs372266709 | T>M | A:470 | (68.35, 39.42, 70.49) |
| 19:48639296 | rs533897830 | G>D | A:473 | (74.81, 32.67, 68.78) |
| 19:48639033 | F>S | A:476 | (71.18, 30.77, 77.98) | |
| 19:48639030 | P>L | A:477 | (72.35, 33.53, 79.19) | |
| 19:48639000 | rs112555243 | K>R | A:487 | (70.27, 53.77, 69.70) |
| 19:48639001 | rs576097809 | K>E | A:487 | (70.27, 53.77, 69.70) |
| 19:48638979 | rs150334649 | T>M | A:494 | (66.96, 54.58, 61.46) |
| 19:48637292 | rs201483928 | V>L | A:519 | (71.48, 31.35, 56.69) |
| 19:48637277 | rs141215260 | G>S | A:524 | (73.49, 36.73, 60.28) |
| 19:48637267 | R>H | A:527 | (78.77, 38.40, 57.38) | |
| 19:48637262 | P>S | A:529 | (73.63, 38.63, 51.96) | |
| 19:48637243 | S>N | A:535 | (69.49, 30.87, 41.65) | |
| 19:48636349 | P>S | A:539 | (61.53, 31.39, 42.86) | |
| 19:48636330 | rs199848958 | A>G | A:545 | (52.20, 48.11, 39.69) |
| 19:48636315 | G>D | A:550 | (47.14, 59.27, 33.70) | |
| 19:48636301 | L>V | A:555 | (54.55, 62.92, 32.51) | |
| 19:48636294 | COSM998873 | R>H | A:557 | (54.31, 59.60, 39.98) |
| 19:48636295 | rs372831646 COSM4079802 |
R>C | A:557 | (54.31, 59.60, 39.98) |
| 19:48636285 | E>A | A:560 | (63.56, 64.93, 36.62) | |
| 19:48636259 | Y>H | A:569 | (51.18, 42.38, 26.20) | |
| 19:48636249 | Q>R | A:572 | (50.06, 33.86, 33.16) | |
| 19:48634421 | rs538601239 | A>G | A:578 | (67.71, 28.83, 32.58) |
| 19:48634422 | rs375683198 | A>T | A:578 | (67.71, 28.83, 32.58) |
| 19:48634409 | G>E | A:582 | (69.30, 23.05, 30.83) | |
| 19:48634410 | G>R | A:582 | (69.30, 23.05, 30.83) | |
| 19:48634404 | V>M | A:584 | (63.46, 24.92, 32.19) | |
| 19:48634382 | Q>R | A:591 | (56.59, 32.64, 44.05) | |
| 19:48634358 | P>L | A:599 | (54.93, 21.88, 27.75) | |
| 19:48634343 | R>H | A:604 | (59.06, 27.75, 21.89) | |
| 19:48634344 | rs570025325 | R>C | A:604 | (59.06, 27.75, 21.89) |
| 19:48634337 | P>R | A:606 | (66.15, 26.35, 22.58) | |
| 19:48634334 | K>R | A:607 | (63.65, 28.81, 18.90) | |
| 19:48631271 | L>F | A:610 | (72.67, 33.51, 21.60) | |
| 19:48631258 | rs3731003 | T>I | A:614 | (74.84, 29.91, 30.04) |
| 19:48631235 | A>T | A:622 | (51.71, 34.42, 28.71) | |
| 19:48631232 | V>M | A:623 | (49.69, 35.38, 25.47) | |
| 19:48631225 | W>S | A:625 | (49.19, 33.99, 18.85) | |
| 19:48631219 | rs546799751 COSM4079801 |
R>Q | A:627 | (48.52, 30.23, 14.77) |
| 19:48631220 | R>W | A:627 | (48.52, 30.23, 14.77) | |
| 19:48631214 | K>Q | A:629 | (43.07, 33.88, 13.14) | |
| 19:48631210 | K>R | A:630 | (49.02, 35.10, 12.60) | |
| 19:48631206 | Q>H | A:631 | (45.36, 38.03, 16.45) | |
| 19:48631184 | rs201804541 | T>A | A:639 | (41.93, 30.20, 31.34) |
| 19:48631180 | T>I | A:640 | (41.49, 26.53, 28.56) | |
| 19:48631177 | rs34087182 | R>L | A:641 | (46.89, 25.83, 28.56) |
| 19:48631178 | COSM567192 | R>C | A:641 | (46.89, 25.83, 28.56) |
| 19:48631172 | R>C | A:643 | (47.61, 22.68, 34.61) | |
| 19:48630599 | rs56105837 | D>N | A:647 | (49.64, 16.86, 27.56) |
| 19:48630595 | rs151010868 | A>V | A:648 | (52.35, 18.69, 24.28) |
| 19:48630589 | E>A | A:650 | (47.08, 16.80, 24.22) | |
| 19:48630582 | Q>H | A:652 | (43.57, 22.24, 21.79) | |
| 19:48630563 | A>T | A:659 | (59.38, 39.94, 26.78) | |
| 19:48630541 | rs528501965 | N>S | A:666 | (75.34, 34.18, 31.46) |
| 19:48626565 | rs200049505 | R>H | A:672 | (71.44, 45.68, 43.15) |
| 19:48626566 | rs55950593 | R>C | A:672 | (71.44, 45.68, 43.15) |
| 19:48626559 | P>L | A:674 | (69.86, 49.73, 35.00) | |
| 19:48626557 | L>V | A:675 | (65.25, 48.84, 32.52) | |
| 19:48626553 | S>Y | A:676 | (68.58, 50.40, 30.39) | |
| 19:48626550 | rs3731008 | R>L | A:677 | (73.16, 46.87, 30.40) |
| 19:48626551 | R>W | A:677 | (73.16, 46.87, 30.40) | |
| 19:48626547 | R>H | A:678 | (67.40, 45.26, 33.19) | |
| 19:48626544 | R>Q | A:679 | (65.22, 47.59, 27.15) | |
| 19:48626545 | rs531348489 | R>W | A:679 | (65.22, 47.59, 27.15) |
| 19:48626540 | rs568934454 | Q>H | A:680 | (71.27, 46.69, 26.06) |
| 19:48626533 | R>W | A:683 | (66.31, 44.78, 23.10) | |
| 19:48626525 | rs549131231 | N>K | A:685 | (71.68, 38.07, 24.26) |
| 19:48626527 | N>D | A:685 | (71.68, 38.07, 24.26) | |
| 19:48626522 | F>L | A:686 | (67.38, 36.55, 24.33) | |
| 19:48626508 | G>D | A:691 | (54.08, 33.80, 18.23) | |
| 19:48626506 | E>K | A:692 | (57.17, 31.40, 18.80) | |
| 19:48626494 | rs373324917 | A>T | A:696 | (57.63, 44.22, 24.19) |
| 19:48626482 | D>N | A:700 | (61.28, 55.49, 24.32) | |
| 19:48626475 | K>R | A:702 | (58.87, 63.69, 27.62) | |
| 19:48626470 | rs377540560 | I>F | A:704 | (51.47, 64.26, 26.10) |
| 19:48626458 | rs140087554 | A>T | A:708 | (47.81, 58.58, 23.86) |
| 19:48626455 | E>Q | A:709 | (48.62, 57.02, 20.84) | |
| 19:48626448 | L>R | A:711 | (46.84, 53.94, 25.50) | |
| 19:48626265 | E>K | A:720 | (45.07, 45.57, 30.40) | |
| 19:48626261 | G>V | A:721 | (47.83, 48.89, 27.94) | |
| 19:48626240 | rs369986976 | D>V | A:728 | (68.56, 55.67, 34.35) |
| 19:48626238 | V>I | A:729 | (66.05, 56.99, 37.57) | |
| 19:48626217 | A>T | A:736 | (62.71, 46.44, 48.78) | |
| 19:48626207 | S>L | A:739 | (57.16, 46.84, 44.50) | |
| 19:48626201 | N>S | A:741 | (58.88, 50.88, 40.57) | |
| 19:48624561 | D>H | A:751 | (38.98, 56.14, 28.13) | |
| 19:48624555 | rs146309259 | V>M | A:753 | (34.57, 56.84, 32.04) |
| 19:48624522 | rs368406296 COSM191456 |
A>T | A:764 | (22.82, 40.07, 50.62) |
| 19:48624510 | rs371393033 | R>W | A:768 | (33.63, 36.67, 56.02) |
| 19:48624501 | rs121434561 | R>W | A:771 | (33.17, 44.20, 55.00) |
| 19:48624495 | G>S | A:773 | (28.00, 42.41, 60.95) | |
| 19:48624491 | rs201362120 | R>Q | A:774 | (29.02, 45.23, 59.10) |
| 19:48624492 | rs201073563 | R>W | A:774 | (29.02, 45.23, 59.10) |
| 19:48624468 | rs571123414 | S>A | A:782 | (19.98, 43.00, 34.70) |
| 19:48624464 | Y>C | A:783 | (14.60, 44.85, 32.75) | |
| 19:48624462 | D>N | A:784 | (15.30, 40.77, 30.38) | |
| 19:48624459 | COSM1213359 | E>K | A:785 | (13.16, 43.91, 28.38) |
| 19:48624434 | I>K | A:793 | (25.22, 40.46, 36.28) | |
| 19:48622395 | rs142509098 | K>R | A:813 | (18.04, 45.72, 57.81) |
| 19:48621032 | COSM3422970 | V>L | A:816 | (14.90, 41.52, 54.10) |
| 19:48621016 | rs542028224 | R>H | A:821 | (9.80, 39.54, 44.57) |
| 19:48621008 | V>M | A:824 | (14.45, 37.13, 40.46) | |
| 19:48621005 | R>W | A:825 | (17.05, 33.95, 35.55) | |
| 19:48620993 | A>T | A:829 | (24.08, 31.84, 41.68) | |
| 19:48620960 | COSM325681 | A>T | A:840 | (18.47, 49.19, 44.58) |
| 19:48620957 | rs370645196 | V>L | A:841 | (19.84, 51.21, 41.39) |
| 19:48620943 | rs145821638 | K>N | A:845 | (33.54, 51.08, 36.38) |
| 19:48620923 | S>F | A:852 | (28.93, 33.38, 32.65) | |
| 19:48620905 | A>V | A:858 | (22.32, 37.98, 28.37) | |
| 19:48620906 | rs546126921 | A>S | A:858 | (22.32, 37.98, 28.37) |
| 19:48620903 | COSM1734850 | R>W | A:859 | (21.21, 34.66, 27.90) |
| 19:48620900 | G>C | A:860 | (21.34, 34.18, 24.12) | |
| 19:48619194 | R>H | A:871 | (37.69, 41.46, 34.12) | |
| 19:48619189 | P>A | A:873 | (33.43, 44.33, 39.77) | |
| 19:48619185 | R>Q | A:874 | (35.18, 48.84, 39.74) | |
| 19:48619180 | I>F | A:876 | (30.75, 53.95, 41.73) | |
| 19:48619176 | R>P | A:877 | (26.54, 57.05, 41.53) | |
| 19:48619170 | COSM3536441 | R>H | A:879 | (21.63, 56.44, 39.36) |
| 19:48619161 | K>R | A:882 | (17.57, 54.63, 37.84) | |
| 19:48619155 | rs201176712 COSM998857 |
P>L | A:884 | (14.49, 48.46, 38.95) |
| 19:48619153 | E>K | A:885 | (12.04, 49.26, 35.93) | |
| 19:48619144 | T>A | A:888 | (21.16, 48.21, 32.72) | |
| 19:48619140 | T>S | A:889 | (19.35, 46.20, 29.48) | |
| 19:48619141 | T>A | A:889 | (19.35, 46.20, 29.48) | |
| 19:48618985 | A>V | A:894 | (24.69, 42.56, 24.92) | |
| 19:48618973 | R>Q | A:898 | (26.80, 43.05, 20.91) | |
| 19:48618974 | rs201890024 | R>W | A:898 | (26.80, 43.05, 20.91) |
| 19:48618965 | S>R | A:901 | (35.30, 42.40, 19.83) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:48643270 | COSM712113 | V>L | A:349 | (40.37, 22.49, 54.56) |
| 19:48631264 | COSM32368 | S>L | A:612 | (76.25, 32.62, 24.56) |
| 19:48630577 | COSM1196262 | Q>L | A:654 | (49.39, 27.56, 20.64) |
| 19:48630569 | COSM1681168 | L>V | A:657 | (56.11, 34.07, 25.72) |
| 19:48626217 | COSM4535593 | A>T | A:736 | (62.71, 46.44, 48.78) |
| 19:48619206 | COSM1751024 | G>D | A:867 | (26.05, 34.65, 29.91) |
| 19:48619186 | COSM712117 | R>W | A:874 | (35.18, 48.84, 39.74) |