General Structure Information
| PDB ID | 2a2d |
| HGNC Gene Label(s) | GALK2 |
| Structure Name | x-ray structure of human n-acetyl galactosamine kinase complexed with mn-amppnp and n-acetyl glactosamine |
| Resolution | 2.2Å |
| Reference | AUTH J.B.THODEN,H.M.HOLDENTITL THE MOLECULAR ARCHITECTURE OF HUMANTITL 2 N-ACETYLGALACTOSAMINE KINASE.REF J.BIOL.CHEM. V. 280 32784 2005REFN ISSN 0021-9258PMID 16006554DOI 10.1074/JBC.M505730200 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 448 |
| Number Of SNVs | 136 |
| Number Of Permutations | 56852 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.02 |
| p-value | 0.659 |
COSMIC
| Number Of Residues | 448 |
| Number Of SNVs | 8 |
| Number Of Permutations | 2307 |
| Optimal Distance Threshold | 15.0 |
| K Statistic | 0.179 |
| p-value | 0.686 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 136 |
| Number Of COSMIC SNVs | 8 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | -0.074 |
| p-value | 0.682 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 15:49462532 | S>G | A:5 | (35.07, 61.77, 4.53) | |
| 15:49462538 | A>T | A:7 | (30.08, 58.53, 6.85) | |
| 15:49462547 | R>W | A:10 | (28.91, 48.91, 9.04) | |
| 15:49462550 | V>F | A:11 | (22.41, 49.14, 8.18) | |
| 15:49462554 | Q>R | A:12 | (21.16, 46.07, 10.01) | |
| 15:49462556 | V>L | A:13 | (17.29, 47.50, 6.34) | |
| 15:49493362 | L>F | A:19 | (15.84, 51.97, 4.58) | |
| 15:49493378 | rs139521545 | M>V | A:25 | (9.79, 50.81, -3.41) |
| 15:49493379 | M>T | A:25 | (9.79, 50.81, -3.41) | |
| 15:49493394 | F>S | A:30 | (14.94, 49.03, -10.45) | |
| 15:49493421 | rs558491610 | R>Q | A:39 | (21.47, 61.60, 4.89) |
| 15:49493423 | A>T | A:40 | (21.20, 64.53, 2.40) | |
| 15:49493441 | I>V | A:46 | (19.54, 80.52, 11.87) | |
| 15:49493442 | I>T | A:46 | (19.54, 80.52, 11.87) | |
| 15:49509390 | E>G | A:49 | (19.60, 84.89, 4.08) | |
| 15:49509393 | H>R | A:50 | (20.31, 86.32, -0.14) | |
| 15:49509395 | rs35720727 | I>V | A:51 | (25.64, 86.75, 2.68) |
| 15:49509399 | D>A | A:52 | (26.32, 82.72, 0.13) | |
| 15:49509414 | S>C | A:57 | (29.85, 83.98, 6.77) | |
| 15:49509417 | V>A | A:58 | (26.48, 81.56, 6.95) | |
| 15:49509419 | L>V | A:59 | (24.50, 80.33, 11.45) | |
| 15:49509425 | M>V | A:61 | (20.51, 74.05, 11.51) | |
| 15:49509431 | V>I | A:63 | (17.21, 69.61, 8.80) | |
| 15:49509449 | I>V | A:69 | (19.29, 57.86, -3.04) | |
| 15:49509453 | A>V | A:70 | (18.61, 53.77, -3.53) | |
| 15:49509469 | rs141088521 | K>N | A:75 | (28.82, 46.59, -15.60) |
| 15:49509474 | COSM4055402 COSM4055401 |
Y>C | A:77 | (28.08, 52.85, -20.54) |
| 15:49509476 | rs370698577 | A>T | A:78 | (22.51, 53.09, -17.65) |
| 15:49509477 | A>D | A:78 | (22.51, 53.09, -17.65) | |
| 15:49509485 | L>V | A:81 | (16.51, 58.27, -12.10) | |
| 15:49509492 | rs117291857 | N>S | A:83 | (10.77, 59.52, -6.88) |
| 15:49509500 | rs371025596 | P>T | A:86 | (4.10, 60.27, -7.69) |
| 15:49509503 | L>M | A:87 | (4.63, 64.47, -8.21) | |
| 15:49528059 | T>N | A:93 | (20.35, 58.59, -19.52) | |
| 15:49528070 | rs150063259 | N>D | A:97 | (26.51, 65.04, -23.37) |
| 15:49528079 | rs370436045 | I>V | A:100 | (21.45, 70.10, -17.60) |
| 15:49528082 | D>Y | A:101 | (17.15, 70.93, -19.01) | |
| 15:49528095 | P>L | A:105 | (13.63, 72.71, -13.83) | |
| 15:49528098 | L>W | A:106 | (12.72, 68.39, -14.86) | |
| 15:49528108 | N>K | A:109 | (18.14, 68.07, -14.21) | |
| 15:49528109 | Y>N | A:110 | (17.91, 69.86, -9.33) | |
| 15:49528110 | rs374849566 COSM217079 |
Y>C | A:110 | (17.91, 69.86, -9.33) |
| 15:49528117 | rs546498438 | L>F | A:112 | (22.20, 65.10, -13.88) |
| 15:49528133 | I>F | A:118 | (31.70, 63.84, -9.13) | |
| 15:49528137 | Q>R | A:119 | (31.42, 62.15, -13.92) | |
| 15:49531427 | rs148234101 | G>S | A:123 | (37.55, 63.33, -15.93) |
| 15:49531482 | S>N | A:141 | (10.06, 74.75, -3.12) | |
| 15:49531510 | rs573578687 | L>F | A:150 | (18.85, 65.94, -5.04) |
| 15:49531518 | C>F | A:153 | (22.80, 62.67, -2.55) | |
| 15:49531526 | rs374871677 | L>M | A:156 | (27.90, 60.79, -1.96) |
| 15:49531532 | T>A | A:158 | (28.40, 59.35, -8.09) | |
| 15:49531533 | T>M | A:158 | (28.40, 59.35, -8.09) | |
| 15:49531542 | V>G | A:161 | (29.45, 54.01, -7.73) | |
| 15:49531553 | N>D | A:165 | (37.93, 59.68, -1.55) | |
| 15:49531560 | COSM3501876 COSM3501875 |
S>C | A:167 | (36.42, 65.78, 1.29) |
| 15:49574194 | A>G | A:172 | (30.75, 71.04, -0.97) | |
| 15:49574208 | K>Q | A:177 | (31.36, 74.95, -8.69) | |
| 15:49574215 | E>G | A:179 | (23.03, 73.41, -7.58) | |
| 15:49574217 | rs201505722 COSM3782886 COSM3782885 |
R>C | A:180 | (26.46, 77.38, -9.54) |
| 15:49574218 | rs371610941 | R>H | A:180 | (26.46, 77.38, -9.54) |
| 15:49574223 | rs35507772 | I>V | A:182 | (19.89, 74.32, -12.56) |
| 15:49574224 | rs138250523 | I>T | A:182 | (19.89, 74.32, -12.56) |
| 15:49574232 | E>K | A:185 | (24.63, 81.92, -10.29) | |
| 15:49574244 | M>V | A:189 | (24.61, 77.79, 2.75) | |
| 15:49574251 | Q>R | A:191 | (25.77, 72.85, -0.91) | |
| 15:49574265 | rs142740588 | L>I | A:196 | (30.11, 70.13, 6.83) |
| 15:49575763 | A>T | A:202 | (25.53, 74.86, 14.57) | |
| 15:49575768 | K>N | A:203 | (28.28, 74.38, 11.94) | |
| 15:49575782 | S>N | A:208 | (37.50, 81.69, 0.87) | |
| 15:49575797 | T>I | A:213 | (32.37, 76.83, 13.39) | |
| 15:49575802 | rs373914978 | V>I | A:215 | (27.35, 77.48, 16.89) |
| 15:49575830 | V>A | A:224 | (9.90, 76.69, 14.89) | |
| 15:49575833 | I>T | A:225 | (10.33, 75.36, 10.60) | |
| 15:49575838 | rs539882250 | N>D | A:227 | (5.59, 76.67, 5.18) |
| 15:49575841 | S>R | A:228 | (4.18, 80.08, 3.80) | |
| 15:49575845 | C>Y | A:229 | (2.44, 77.56, 1.98) | |
| 15:49575854 | M>T | A:232 | (10.59, 80.02, -4.74) | |
| 15:49575856 | N>D | A:233 | (11.51, 76.85, -8.06) | |
| 15:49575866 | A>V | A:236 | (11.74, 79.04, -12.24) | |
| 15:49575868 | T>A | A:237 | (12.27, 82.29, -10.60) | |
| 15:49575886 | R>G | A:243 | (18.15, 90.44, -5.99) | |
| 15:49575901 | rs370443921 | R>W | A:248 | (28.58, 90.19, -10.04) |
| 15:49575902 | rs201091452 COSM189925 |
R>Q | A:248 | (28.58, 90.19, -10.04) |
| 15:49575910 | rs149420693 | A>S | A:251 | (31.09, 95.64, -6.07) |
| 15:49584543 | S>T | A:259 | (40.47, 103.10, -6.72) | |
| 15:49584591 | L>P | A:275 | (39.25, 98.68, 1.51) | |
| 15:49584603 | rs375576432 | L>P | A:279 | (31.10, 95.17, 7.92) |
| 15:49584612 | M>T | A:282 | (32.05, 98.88, 3.52) | |
| 15:49584620 | V>F | A:285 | (31.69, 103.19, 1.54) | |
| 15:49584626 | rs367574130 | E>K | A:287 | (25.60, 105.91, 2.14) |
| 15:49584630 | D>V | A:288 | (29.67, 107.68, 0.28) | |
| 15:49584639 | H>R | A:291 | (22.67, 106.15, -6.94) | |
| 15:49584642 | P>R | A:292 | (19.65, 105.68, -3.74) | |
| 15:49584651 | rs371808630 | Y>C | A:295 | (22.87, 102.82, -10.23) |
| 15:49584666 | I>S | A:300 | (26.13, 100.71, -15.00) | |
| 15:49584683 | rs529513884 | I>V | A:306 | (31.89, 99.47, -19.88) |
| 15:49584690 | L>P | A:308 | (25.50, 98.28, -22.91) | |
| 15:49584692 | E>K | A:309 | (27.47, 95.32, -26.40) | |
| 15:49584702 | R>Q | A:312 | (23.62, 92.65, -23.09) | |
| 15:49584705 | T>I | A:313 | (28.88, 89.97, -22.86) | |
| 15:49584711 | I>S | A:315 | (29.05, 91.41, -16.53) | |
| 15:49584713 | rs144789254 | L>M | A:316 | (24.90, 90.58, -17.40) |
| 15:49584719 | P>T | A:318 | (21.33, 84.88, -19.01) | |
| 15:49584722 | N>D | A:319 | (17.96, 85.36, -16.07) | |
| 15:49584723 | N>S | A:319 | (17.96, 85.36, -16.07) | |
| 15:49584726 | T>S | A:320 | (19.67, 89.70, -15.96) | |
| 15:49611813 | K>R | A:327 | (17.49, 98.13, -6.18) | |
| 15:49611822 | Q>R | A:330 | (19.15, 99.29, -1.95) | |
| 15:49611824 | R>W | A:331 | (19.64, 94.91, -3.11) | |
| 15:49611845 | rs148552843 | E>K | A:338 | (22.67, 89.92, 7.39) |
| 15:49611852 | rs146874010 | A>V | A:340 | (27.22, 91.75, 10.94) |
| 15:49611855 | rs376875144 | R>Q | A:341 | (22.66, 91.35, 10.99) |
| 15:49611857 | V>M | A:342 | (26.23, 86.52, 11.36) | |
| 15:49611858 | V>A | A:342 | (26.23, 86.52, 11.36) | |
| 15:49611878 | rs147794087 | C>G | A:349 | (26.23, 82.31, 21.18) |
| 15:49611885 | E>A | A:351 | (29.30, 86.31, 25.26) | |
| 15:49611890 | rs577880125 | P>S | A:353 | (24.21, 86.71, 27.55) |
| 15:49611938 | M>V | A:369 | (12.96, 94.43, 8.63) | |
| 15:49611947 | rs375693032 | R>W | A:372 | (10.14, 93.74, 4.53) |
| 15:49611948 | R>Q | A:372 | (10.14, 93.74, 4.53) | |
| 15:49611950 | D>Y | A:373 | (12.27, 96.48, 3.47) | |
| 15:49611956 | Y>H | A:375 | (18.34, 91.44, -1.15) | |
| 15:49611961 | E>D | A:376 | (12.86, 94.02, -2.15) | |
| 15:49611967 | S>R | A:378 | (9.69, 88.65, 1.24) | |
| 15:49611974 | E>Q | A:381 | (2.32, 85.36, 2.13) | |
| 15:49611980 | D>N | A:383 | (5.66, 89.51, 5.80) | |
| 15:49611999 | C>Y | A:389 | (4.95, 84.10, 14.93) | |
| 15:49612002 | COSM401550 COSM401549 |
R>Q | A:390 | (7.16, 88.47, 15.48) |
| 15:49620157 | G>E | A:393 | (6.49, 84.04, 21.33) | |
| 15:49620160 | A>V | A:394 | (8.22, 85.05, 18.91) | |
| 15:49620178 | rs139485976 | T>S | A:400 | (14.53, 80.64, 5.71) |
| 15:49620181 | G>E | A:401 | (16.31, 81.34, 2.57) | |
| 15:49620187 | G>V | A:403 | (12.37, 83.41, -0.49) | |
| 15:49620193 | G>V | A:405 | (8.53, 82.13, 0.21) | |
| 15:49620199 | C>Y | A:407 | (9.97, 78.86, 5.30) | |
| 15:49620210 | rs377181822 | M>V | A:411 | (14.07, 81.87, 18.84) |
| 15:49620211 | M>T | A:411 | (14.07, 81.87, 18.84) | |
| 15:49620216 | P>T | A:413 | (10.34, 80.54, 23.96) | |
| 15:49620220 | rs373620147 | A>V | A:414 | (10.04, 76.71, 25.83) |
| 15:49620228 | L>V | A:417 | (6.18, 75.54, 21.56) | |
| 15:49620229 | rs376206527 | L>P | A:417 | (6.18, 75.54, 21.56) |
| 15:49620249 | V>M | A:424 | (0.48, 79.61, 14.52) | |
| 15:49620252 | H>Y | A:425 | (-1.35, 75.02, 13.89) | |
| 15:49620253 | H>P | A:425 | (-1.35, 75.02, 13.89) | |
| 15:49620258 | A>T | A:427 | (-3.90, 81.55, 12.40) | |
| 15:49620307 | L>W | A:443 | (4.13, 74.15, 12.05) | |
| 15:49620312 | rs200728035 | A>T | A:445 | (10.45, 71.73, 15.50) |
| 15:49620319 | K>R | A:447 | (17.98, 70.05, 17.31) | |
| 15:49620345 | rs199516811 | L>F | A:456 | (26.42, 49.44, 3.78) |
| 15:49620352 | A>V | A:458 | (25.47, 44.66, 7.25) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 15:49509510 | COSM1207838 | P>L | A:89 | (8.76, 61.69, -13.26) |
| 15:49528110 | COSM217079 | Y>C | A:110 | (17.91, 69.86, -9.33) |
| 15:49531550 | COSM1158063 | R>W | A:164 | (37.45, 57.70, -7.92) |
| 15:49575788 | COSM2216236 | L>R | A:210 | (34.87, 75.75, 3.16) |
| 15:49575800 | COSM1608458 | D>V | A:214 | (30.89, 74.18, 16.19) |
| 15:49611824 | COSM4578310 | R>W | A:331 | (19.64, 94.91, -3.11) |
| 15:49611846 | COSM2216250 | E>G | A:338 | (22.67, 89.92, 7.39) |
| 15:49620186 | COSM1159387 | G>R | A:403 | (12.37, 83.41, -0.49) |