General Structure Information
| PDB ID | 3w1g |
| HGNC Gene Label(s) | LIG4 |
| Structure Name | crystal structure of human dna ligase iv-artemis complex (native) |
| Resolution | 2.55Å |
| Reference | AUTH T.OCHI,X.GU,T.L.BLUNDELLTITL STRUCTURE OF THE CATALYTIC REGION OF DNA LIGASE IV INTITL 2 COMPLEX WITH AN ARTEMIS FRAGMENT SHEDS LIGHT ONTITL 3 DOUBLE-STRAND BREAK REPAIRREF STRUCTURE V. 21 672 2013REFN ISSN 0969-2126PMID 23523427DOI 10.1016/J.STR.2013.02.014 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 583 |
| Number Of SNVs | 152 |
| Number Of Permutations | 73604 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.046 |
| p-value | 0.413 |
COSMIC
| Number Of Residues | 583 |
| Number Of SNVs | 10 |
| Number Of Permutations | 5467 |
| Optimal Distance Threshold | 20.0 |
| K Statistic | 0.067 |
| p-value | 0.102 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 152 |
| Number Of COSMIC SNVs | 9 |
| Optimal Distance Threshold | 44.0 |
| K Statistic | -0.192 |
| p-value | 0.104 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 13:108863591 | rs1805388 | T>I | A:9 | (4.38, 15.40, 183.45) |
| 13:108863585 | A>G | A:11 | (5.85, 20.20, 182.57) | |
| 13:108863583 | rs554949695 | S>T | A:12 | (2.95, 19.65, 185.09) |
| 13:108863573 | COSM3968527 | P>L | A:15 | (6.76, 27.18, 186.31) |
| 13:108863567 | A>V | A:17 | (8.57, 31.41, 184.68) | |
| 13:108863565 | D>N | A:18 | (10.91, 28.85, 186.31) | |
| 13:108863560 | L>F | A:19 | (11.74, 28.45, 180.79) | |
| 13:108863561 | L>W | A:19 | (11.74, 28.45, 180.79) | |
| 13:108863543 | R>Q | A:25 | (19.38, 33.96, 184.90) | |
| 13:108863526 | G>R | A:31 | (29.16, 34.43, 177.98) | |
| 13:108863523 | R>C | A:32 | (29.88, 29.09, 175.08) | |
| 13:108863520 | A>T | A:33 | (30.05, 30.00, 180.14) | |
| 13:108863514 | K>E | A:35 | (25.00, 32.24, 177.86) | |
| 13:108863486 | D>V | A:44 | (20.69, 19.41, 186.40) | |
| 13:108863484 | S>T | A:45 | (16.60, 20.74, 188.22) | |
| 13:108863479 | rs2232636 CM068005 |
W>C | A:46 | (12.84, 19.14, 183.57) |
| 13:108863481 | W>R | A:46 | (12.84, 19.14, 183.57) | |
| 13:108863474 | K>T | A:48 | (18.16, 16.20, 190.25) | |
| 13:108863475 | rs368782869 COSM333915 |
K>Q | A:48 | (18.16, 16.20, 190.25) |
| 13:108863472 | F>L | A:49 | (10.99, 17.01, 189.65) | |
| 13:108863456 | H>R | A:54 | (8.88, 9.58, 187.11) | |
| 13:108863449 | N>K | A:56 | (7.86, 4.38, 191.25) | |
| 13:108863438 | V>A | A:60 | (8.49, 6.89, 181.66) | |
| 13:108863409 | rs193107403 | L>V | A:70 | (9.71, 26.23, 174.05) |
| 13:108863403 | L>V | A:72 | (15.42, 24.56, 170.17) | |
| 13:108863387 | rs199707115 | R>K | A:77 | (9.72, 19.88, 162.81) |
| 13:108863381 | rs370907523 | R>T | A:79 | (3.76, 22.65, 167.76) |
| 13:108863348 | A>V | A:90 | (-0.37, 44.39, 167.58) | |
| 13:108863337 | I>V | A:94 | (-3.52, 47.81, 170.47) | |
| 13:108863324 | rs143897303 | N>S | A:98 | (-7.26, 50.10, 176.06) |
| 13:108863320 | L>F | A:99 | (-3.07, 51.07, 173.83) | |
| 13:108863318 | rs562040248 | P>L | A:100 | (-3.71, 54.98, 172.85) |
| 13:108863310 | G>R | A:103 | (-0.22, 56.37, 169.60) | |
| 13:108863307 | K>E | A:104 | (3.30, 55.77, 170.01) | |
| 13:108863276 | T>I | A:114 | (13.44, 44.40, 161.37) | |
| 13:108863236 | rs61752350 | M>I | A:127 | (12.38, 43.69, 173.42) |
| 13:108863223 | rs370586288 | V>L | A:132 | (4.35, 48.41, 175.80) |
| 13:108863208 | C>R | A:137 | (1.66, 43.67, 182.50) | |
| 13:108863201 | Q>R | A:139 | (0.20, 39.95, 185.05) | |
| 13:108863180 | Q>R | A:146 | (1.76, 20.81, 180.20) | |
| 13:108863169 | D>N | A:150 | (-1.65, 22.68, 175.85) | |
| 13:108863147 | S>I | A:157 | (-4.96, 23.31, 165.23) | |
| 13:108863138 | rs142013741 | S>Y | A:160 | (-4.62, 24.31, 160.14) |
| 13:108863128 | rs541777192 | R>S | A:163 | (-10.99, 26.37, 163.26) |
| 13:108863117 | rs138021217 | I>R | A:167 | (-6.19, 31.52, 166.80) |
| 13:108863093 | rs373262036 | I>T | A:175 | (-1.40, 37.35, 176.68) |
| 13:108863087 | COSM1188745 | Q>L | A:177 | (-3.05, 33.82, 182.41) |
| 13:108863088 | COSM3772768 | Q>E | A:177 | (-3.05, 33.82, 182.41) |
| 13:108863054 | R>Q | A:188 | (12.17, 36.24, 171.46) | |
| 13:108863050 | M>I | A:189 | (8.77, 30.72, 171.90) | |
| 13:108863027 | G>A | A:197 | (23.68, 33.52, 171.96) | |
| 13:108863025 | rs151152559 | V>I | A:198 | (23.61, 29.95, 172.25) |
| 13:108863010 | I>V | A:203 | (21.67, 23.83, 173.20) | |
| 13:108863007 | F>L | A:204 | (21.31, 19.57, 170.66) | |
| 13:108862970 | N>S | A:216 | (21.66, 14.68, 162.35) | |
| 13:108862964 | T>I | A:218 | (16.22, 11.83, 164.41) | |
| 13:108862950 | K>E | A:223 | (13.72, 11.29, 170.54) | |
| 13:108862943 | C>F | A:225 | (14.87, 14.14, 174.86) | |
| 13:108862931 | rs142957638 | H>R | A:229 | (16.35, 11.76, 180.56) |
| 13:108862926 | rs3093765 | P>S | A:231 | (23.41, 12.25, 180.89) |
| 13:108862904 | rs201289944 | I>T | A:238 | (23.86, 7.00, 166.14) |
| 13:108862899 | I>V | A:240 | (19.85, 6.25, 158.79) | |
| 13:108862896 | rs202178095 | T>A | A:241 | (16.31, 4.81, 161.16) |
| 13:108862884 | A>T | A:245 | (14.21, 12.14, 159.49) | |
| 13:108862860 | I>V | A:253 | (31.23, 25.57, 146.91) | |
| 13:108862857 | A>T | A:254 | (34.18, 23.86, 144.04) | |
| 13:108862851 | I>V | A:256 | (37.16, 23.86, 138.05) | |
| 13:108862844 | H>R | A:258 | (41.63, 23.84, 143.23) | |
| 13:108862814 | F>S | A:268 | (36.31, 12.04, 139.88) | |
| 13:108862790 | rs202208029 | G>D | A:276 | (14.91, 20.71, 143.43) |
| 13:108862785 | rs574912936 | R>C | A:278 | (17.60, 16.76, 149.13) |
| 13:108862779 | Q>K | A:280 | (14.03, 11.40, 152.87) | |
| 13:108862772 | H>L | A:282 | (11.65, 6.58, 154.44) | |
| 13:108862763 | G>V | A:285 | (5.90, -1.98, 151.24) | |
| 13:108862748 | Y>F | A:290 | (7.73, 10.45, 150.48) | |
| 13:108862739 | R>Q | A:293 | (16.94, 20.31, 152.89) | |
| 13:108862734 | rs371739985 | G>R | A:295 | (11.86, 17.26, 158.24) |
| 13:108862719 | rs143810759 | D>N | A:300 | (-0.21, 14.04, 152.62) |
| 13:108862715 | Q>R | A:301 | (2.66, 15.86, 147.68) | |
| 13:108862706 | A>V | A:304 | (1.42, 6.47, 151.78) | |
| 13:108862658 | K>R | A:320 | (13.91, -4.75, 141.31) | |
| 13:108862656 | A>T | A:321 | (11.21, -8.41, 143.91) | |
| 13:108862652 | D>V | A:322 | (13.71, -8.25, 146.65) | |
| 13:108862649 | rs376108062 | I>T | A:323 | (13.00, -4.52, 147.31) |
| 13:108862650 | I>L | A:323 | (13.00, -4.52, 147.31) | |
| 13:108862617 | A>T | A:334 | (8.97, 18.78, 137.18) | |
| 13:108862613 | Y>C | A:335 | (8.84, 14.73, 132.89) | |
| 13:108862601 | rs549389506 | T>I | A:339 | (9.18, 18.11, 126.23) |
| 13:108862592 | F>S | A:342 | (13.45, 17.25, 134.41) | |
| 13:108862569 | D>H | A:350 | (2.01, 27.61, 139.10) | |
| 13:108862556 | M>T | A:354 | (1.23, 22.99, 135.63) | |
| 13:108862548 | rs566324623 | D>Y | A:357 | (-3.80, 20.80, 136.31) |
| 13:108862523 | rs144322912 | C>F | A:365 | (15.68, 12.00, 140.88) |
| 13:108862504 | M>I | A:371 | (17.94, 0.92, 154.57) | |
| 13:108862506 | M>V | A:371 | (17.94, 0.92, 154.57) | |
| 13:108862481 | rs558534036 | H>P | A:379 | (28.78, 3.79, 157.81) |
| 13:108862460 | Y>C | A:386 | (26.08, 5.14, 143.15) | |
| 13:108862448 | rs35469724 | S>N | A:390 | (20.90, -0.55, 140.32) |
| 13:108862437 | T>A | A:394 | (13.26, -0.71, 137.34) | |
| 13:108862434 | P>S | A:395 | (14.23, 2.81, 135.87) | |
| 13:108862431 | I>V | A:396 | (9.79, 4.85, 135.30) | |
| 13:108862424 | rs538646268 | G>D | A:398 | (9.43, 10.61, 134.71) |
| 13:108862413 | rs374180232 | I>V | A:402 | (19.20, 6.29, 138.59) |
| 13:108862409 | V>A | A:403 | (21.02, 10.58, 138.77) | |
| 13:108862386 | K>E | A:411 | (40.57, 20.42, 135.28) | |
| 13:108862381 | N>K | A:412 | (39.02, 18.35, 131.66) | |
| 13:108862382 | N>S | A:412 | (39.02, 18.35, 131.66) | |
| 13:108862371 | rs148273759 | D>Y | A:416 | (33.95, 18.62, 129.21) |
| 13:108862356 | A>T | A:421 | (25.38, 21.34, 131.88) | |
| 13:108862352 | I>T | A:422 | (25.45, 25.18, 131.54) | |
| 13:108862349 | D>G | A:423 | (24.37, 23.53, 126.63) | |
| 13:108862329 | rs143618179 | M>L | A:430 | (27.52, 17.07, 141.82) |
| 13:108862302 | K>E | A:439 | (29.14, 11.95, 156.60) | |
| 13:108862299 | P>A | A:440 | (24.30, 12.98, 158.07) | |
| 13:108862296 | D>N | A:441 | (23.94, 18.16, 158.35) | |
| 13:108862292 | K>R | A:442 | (28.20, 17.00, 157.95) | |
| 13:108862280 | rs199934893 | G>A | A:446 | (32.56, 14.01, 149.40) |
| 13:108862276 | W>C | A:447 | (27.96, 14.29, 148.44) | |
| 13:108862272 | rs138156481 | K>Q | A:449 | (28.28, 22.58, 144.80) |
| 13:108862263 | P>S | A:452 | (29.38, 28.79, 136.83) | |
| 13:108862254 | V>I | A:455 | (30.38, 38.38, 136.72) | |
| 13:108862242 | M>V | A:459 | (28.15, 40.12, 132.03) | |
| 13:108862235 | rs2232640 | E>G | A:461 | (22.37, 41.96, 130.80) |
| 13:108862227 | I>V | A:464 | (21.47, 38.87, 122.49) | |
| 13:108862221 | COSM325682 | I>V | A:466 | (17.28, 34.79, 118.26) |
| 13:108862180 | rs529839175 | M>I | A:479 | (10.97, 21.53, 120.04) |
| 13:108862152 | E>K | A:489 | (26.49, 46.47, 111.89) | |
| 13:108862145 | rs548324829 | P>L | A:491 | (22.88, 51.54, 112.21) |
| 13:108862121 | rs201683262 | V>A | A:499 | (24.19, 43.66, 109.72) |
| 13:108862122 | V>M | A:499 | (24.19, 43.66, 109.72) | |
| 13:108862118 | F>S | A:500 | (22.48, 41.48, 113.19) | |
| 13:108862115 | rs370368065 | H>R | A:501 | (28.24, 40.56, 113.42) |
| 13:108862116 | H>Y | A:501 | (28.24, 40.56, 113.42) | |
| 13:108862110 | L>F | A:503 | (28.35, 36.15, 120.31) | |
| 13:108862104 | rs375284799 | R>C | A:505 | (25.47, 26.85, 119.93) |
| 13:108862097 | G>E | A:507 | (20.48, 26.86, 125.17) | |
| 13:108862079 | rs538857114 | K>R | A:513 | (5.68, 27.30, 128.81) |
| 13:108862061 | G>A | A:519 | (9.04, 28.53, 119.51) | |
| 13:108862049 | A>G | A:523 | (8.11, 28.49, 113.74) | |
| 13:108862034 | P>L | A:528 | (16.39, 27.39, 105.18) | |
| 13:108862013 | rs374074342 | P>L | A:535 | (22.11, 35.26, 105.00) |
| 13:108862010 | rs552242241 | S>N | A:536 | (22.83, 39.64, 104.34) |
| 13:108862000 | rs3742212 | L>F | A:539 | (27.46, 38.06, 109.23) |
| 13:108861978 | V>I | A:547 | (17.60, 27.49, 110.79) | |
| 13:108861969 | E>K | A:550 | (15.01, 37.72, 108.65) | |
| 13:108861944 | Q>R | A:558 | (18.60, 38.65, 129.67) | |
| 13:108861923 | V>A | A:565 | (36.17, 33.98, 125.18) | |
| 13:108861924 | rs140584260 | V>I | A:565 | (36.17, 33.98, 125.18) |
| 13:108861921 | rs151324221 | P>S | A:566 | (38.76, 34.21, 122.49) |
| 13:108861914 | rs202041497 | D>G | A:568 | (37.03, 30.86, 114.99) |
| 13:108861911 | M>T | A:569 | (32.86, 29.26, 116.32) | |
| 13:108861912 | M>V | A:569 | (32.86, 29.26, 116.32) | |
| 13:108861897 | rs201308256 | C>R | A:574 | (33.85, 36.40, 120.50) |
| 13:108861887 | COSM1677789 | R>H | A:577 | (33.26, 29.86, 129.71) |
| 13:108861888 | rs141337521 | R>C | A:577 | (33.26, 29.86, 129.71) |
| 13:108861882 | P>S | A:579 | (26.00, 30.47, 128.00) | |
| 13:108861878 | rs146616552 | R>Q | A:580 | (21.00, 30.06, 131.77) |
| 13:108861869 | K>T | A:583 | (14.65, 37.37, 131.55) | |
| 13:108861858 | rs377478239 | D>N | A:587 | (10.31, 43.84, 126.91) |
| 13:108861845 | H>R | A:591 | (14.89, 47.99, 117.09) | |
| 13:108861828 | COSM119978 | D>N | A:597 | (30.03, 48.85, 120.37) |
| 13:108861825 | rs372708277 | D>N | A:598 | (27.59, 47.86, 123.07) |
| 13:108861819 | rs61731910 | E>K | A:600 | (34.63, 46.08, 121.82) |
| 13:108861810 | R>W | A:603 | (35.79, 42.02, 124.80) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 13:108863591 | COSM3753570 | T>I | A:9 | (4.38, 15.40, 183.45) |
| 13:108863123 | COSM2262568 | D>G | A:165 | (-12.15, 33.04, 167.33) |
| 13:108863098 | COSM1606832 | Q>H | A:173 | (-5.97, 31.45, 177.30) |
| 13:108862991 | COSM3710998 | N>S | A:209 | (27.70, 13.73, 174.66) |
| 13:108862644 | COSM3704508 | I>V | A:325 | (12.83, -2.30, 153.50) |
| 13:108862331 | COSM1677790 | I>S | A:429 | (28.58, 19.61, 137.97) |
| 13:108862179 | COSM3704507 | M>V | A:480 | (14.97, 24.46, 118.48) |
| 13:108862011 | COSM1606831 | S>G | A:536 | (22.83, 39.64, 104.34) |
| 13:108861887 | COSM1677789 | R>H | A:577 | (33.26, 29.86, 129.71) |
| 13:108861849 | COSM1677788 | W>R | A:590 | (14.40, 44.38, 115.11) |