General Structure Information
| PDB ID | 1wuu |
| HGNC Gene Label(s) | GALK1 |
| Structure Name | crystal structure of human galactokinase complexed with mgamppnp and galactose |
| Resolution | 2.5Å |
| Reference | AUTH J.B.THODEN,D.J.TIMSON,R.J.REECE,H.M.HOLDENTITL MOLECULAR STRUCTURE OF HUMAN GALACTOKINASE:TITL 2 IMPLICATIONS FOR TYPE II GALACTOSEMIAREF J.BIOL.CHEM. V. 280 9662 2005REFN ISSN 0021-9258PMID 15590630DOI 10.1074/JBC.M412916200 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 381 |
| Number Of SNVs | 117 |
| Number Of Permutations | 50748 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.045 |
| p-value | 0.089 |
ClinVar
| Number Of Residues | 381 |
| Number Of SNVs | 3 |
| Number Of Permutations | 235 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.333 |
| p-value | 0.55 |
Ripley’s K Analysis Plots
ExACClinVar
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 117 |
| Number Of ClinVar SNVs | 3 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.256 |
| p-value | 0.458 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 17:73761210 | A>G | C:3 | (95.91, 125.43, 10.41) | |
| 17:73761169 | R>G | C:17 | (90.00, 106.13, -5.87) | |
| 17:73761162 | A>D | C:19 | (97.24, 103.55, -4.76) | |
| 17:73761156 | R>Q | C:21 | (93.22, 102.41, -10.67) | |
| 17:73761144 | G>E | C:25 | (95.62, 97.79, -10.99) | |
| 17:73761145 | G>R | C:25 | (95.62, 97.79, -10.99) | |
| 17:73761141 | A>V | C:26 | (92.85, 97.76, -9.49) | |
| 17:73761136 | rs104894572 | P>T | C:28 | (89.19, 99.54, -5.22) |
| 17:73761123 | V>A | C:32 | (86.72, 101.40, 5.75) | |
| 17:73761102 | rs536209426 | N>S | C:39 | (91.58, 113.04, 26.04) |
| 17:73761094 | rs370714053 | G>R | C:42 | (91.76, 111.54, 31.20) |
| 17:73761084 | rs376599506 | T>M | C:45 | (92.37, 106.91, 33.68) |
| 17:73761075 | N>S | C:48 | (93.58, 102.82, 36.48) | |
| 17:73761072 | Q>R | C:49 | (88.70, 100.55, 36.41) | |
| 17:73761057 | rs146045315 | P>R | C:54 | (87.24, 111.44, 24.36) |
| 17:73760151 | rs376959270 | T>M | C:61 | (92.57, 105.62, 8.84) |
| 17:73760143 | V>M | C:64 | (90.86, 100.89, -0.03) | |
| 17:73760130 | R>L | C:68 | (93.73, 88.02, -2.54) | |
| 17:73760121 | G>A | C:71 | (94.54, 83.91, 0.26) | |
| 17:73760103 | T>I | C:77 | (101.20, 101.97, 4.21) | |
| 17:73760085 | D>G | C:83 | (108.41, 100.77, 10.03) | |
| 17:73760083 | E>K | C:84 | (111.67, 100.91, 6.51) | |
| 17:73760079 | P>H | C:85 | (108.88, 98.11, 4.98) | |
| 17:73760080 | P>S | C:85 | (108.88, 98.11, 4.98) | |
| 17:73760073 | rs572575400 | R>Q | C:87 | (105.02, 98.14, -0.10) |
| 17:73760066 | rs144915547 | Q>H | C:89 | (103.40, 90.59, 0.72) |
| 17:73760049 | A>V | C:95 | (95.92, 76.19, 13.44) | |
| 17:73760043 | R>H | C:97 | (100.57, 80.64, 9.96) | |
| 17:73760040 | S>L | C:98 | (99.81, 81.40, 14.57) | |
| 17:73760037 | L>P | C:99 | (99.58, 85.36, 12.76) | |
| 17:73760032 | P>S | C:101 | (104.83, 89.25, 16.26) | |
| 17:73760019 | R>Q | C:105 | (108.12, 98.06, 14.20) | |
| 17:73760020 | R>W | C:105 | (108.12, 98.06, 14.20) | |
| 17:73760007 | Y>C | C:109 | (99.36, 98.07, 15.34) | |
| 17:73760002 | K>E | C:111 | (99.67, 90.77, 11.89) | |
| 17:73759996 | V>M | C:113 | (92.85, 92.68, 13.95) | |
| 17:73759981 | P>T | C:118 | (85.75, 87.29, 15.66) | |
| 17:73759517 | A>D | C:120 | (84.33, 83.22, 9.89) | |
| 17:73759514 | P>L | C:121 | (85.17, 82.32, 6.82) | |
| 17:73759512 | L>F | C:122 | (88.69, 85.97, 6.96) | |
| 17:73759505 | G>D | C:124 | (91.81, 87.84, 1.39) | |
| 17:73759494 | V>M | C:128 | (95.50, 101.09, 0.59) | |
| 17:73759491 | V>M | C:129 | (96.79, 102.30, 4.67) | |
| 17:73759484 | S>T | C:131 | (96.41, 108.54, 7.62) | |
| 17:73759460 | L>P | C:139 | (95.96, 111.99, 17.94) | |
| 17:73759451 | S>L | C:142 | (96.68, 103.23, 17.06) | |
| 17:73759436 | V>G | C:147 | (89.15, 100.23, 14.05) | |
| 17:73759430 | T>M | C:149 | (91.41, 97.00, 10.14) | |
| 17:73759227 | rs575077063 | S>L | C:160 | (77.91, 88.85, 15.62) |
| 17:73759224 | G>V | C:161 | (78.88, 91.29, 17.88) | |
| 17:73759221 | rs555279924 | T>R | C:162 | (79.57, 93.61, 20.85) |
| 17:73759209 | rs145732791 | R>H | C:166 | (83.12, 95.43, 17.05) |
| 17:73759210 | rs367550108 | R>C | C:166 | (83.12, 95.43, 17.05) |
| 17:73759207 | rs372078515 | A>T | C:167 | (87.26, 97.02, 21.07) |
| 17:73759192 | Q>E | C:172 | (94.38, 91.17, 22.67) | |
| 17:73759154 | COSM1303357 | I>M | C:184 | (89.16, 100.58, 27.18) |
| 17:73759125 | Q>R | C:194 | (78.50, 110.22, 16.79) | |
| 17:73759120 | G>S | C:196 | (79.43, 116.70, 18.03) | |
| 17:73759114 | A>T | C:198 | (81.87, 113.86, 23.53) | |
| 17:73759098 | C>Y | C:203 | (86.61, 102.50, 31.92) | |
| 17:73758964 | S>C | C:205 | (81.07, 100.49, 33.10) | |
| 17:73758961 | L>W | C:206 | (82.39, 100.09, 29.19) | |
| 17:73758953 | rs371785693 | S>R | C:209 | (77.94, 109.41, 27.87) |
| 17:73758943 | P>R | C:212 | (76.79, 117.80, 23.77) | |
| 17:73758937 | rs369906636 | S>L | C:214 | (78.14, 122.30, 19.60) |
| 17:73758938 | S>P | C:214 | (78.14, 122.30, 19.60) | |
| 17:73758920 | V>M | C:220 | (89.38, 122.42, 19.88) | |
| 17:73758917 | L>F | C:221 | (94.03, 124.32, 19.36) | |
| 17:73758908 | N>D | C:224 | (102.20, 118.58, 16.76) | |
| 17:73758895 | rs374114654 | R>H | C:228 | (107.75, 109.80, 18.46) |
| 17:73758896 | rs544282036 | R>C | C:228 | (107.75, 109.80, 18.46) |
| 17:73758875 | E>K | C:235 | (108.30, 104.26, 30.96) | |
| 17:73758862 | rs575139300 CM040744 |
R>Q | C:239 | (104.32, 105.12, 34.68) |
| 17:73758859 | rs145837971 | R>Q | C:240 | (98.77, 99.09, 33.23) |
| 17:73758860 | rs376343759 | R>W | C:240 | (98.77, 99.09, 33.23) |
| 17:73758856 | rs373103005 COSM984456 |
R>H | C:241 | (104.52, 97.73, 35.59) |
| 17:73758857 | R>C | C:241 | (104.52, 97.73, 35.59) | |
| 17:73758843 | rs561544412 | E>D | C:245 | (102.27, 98.03, 42.27) |
| 17:73758841 | V>G | C:246 | (99.01, 101.05, 44.64) | |
| 17:73758835 | rs368904895 | R>Q | C:248 | (98.79, 95.07, 44.11) |
| 17:73758836 | rs541580127 | R>W | C:248 | (98.79, 95.07, 44.11) |
| 17:73758832 | rs149825190 | A>V | C:249 | (98.35, 97.93, 48.64) |
| 17:73758833 | A>T | C:249 | (98.35, 97.93, 48.64) | |
| 17:73758811 | rs372321234 | R>Q | C:256 | (86.67, 104.26, 39.49) |
| 17:73758812 | rs376790302 CM993834 |
R>W | C:256 | (86.67, 104.26, 39.49) |
| 17:73758809 | E>K | C:257 | (87.50, 101.13, 43.67) | |
| 17:73758787 | E>V | C:264 | (97.96, 109.69, 53.34) | |
| 17:73754672 | COSM1522292 | D>Y | C:268 | (103.47, 104.33, 55.12) |
| 17:73754666 | V>M | C:270 | (103.46, 102.78, 48.77) | |
| 17:73754660 | rs558638718 | K>E | C:272 | (108.42, 107.75, 47.73) |
| 17:73754656 | E>G | C:273 | (107.73, 106.92, 41.62) | |
| 17:73754648 | R>W | C:276 | (104.87, 110.79, 42.65) | |
| 17:73754644 | rs370029131 CM071782 |
R>Q | C:277 | (103.31, 107.79, 39.21) |
| 17:73754639 | rs567589849 | R>W | C:279 | (99.11, 112.44, 44.05) |
| 17:73754633 | COSM4069685 CM071783 |
V>M | C:281 | (94.96, 108.24, 38.82) |
| 17:73754617 | rs145641205 | R>Q | C:286 | (87.66, 113.88, 42.53) |
| 17:73754615 | R>C | C:287 | (91.23, 116.03, 37.54) | |
| 17:73754608 | A>V | C:289 | (83.73, 114.04, 36.53) | |
| 17:73754594 | A>T | C:294 | (81.19, 121.69, 33.20) | |
| 17:73754584 | R>H | C:297 | (78.04, 123.45, 34.33) | |
| 17:73754585 | R>C | C:297 | (78.04, 123.45, 34.33) | |
| 17:73754569 | A>V | C:302 | (86.05, 125.04, 34.89) | |
| 17:73754560 | R>H | C:305 | (89.44, 126.30, 36.16) | |
| 17:73754561 | R>C | C:305 | (89.44, 126.30, 36.16) | |
| 17:73754546 | rs201681295 | S>G | C:310 | (95.61, 117.56, 34.22) |
| 17:73754539 | rs181526665 | R>H | C:312 | (99.75, 120.66, 38.21) |
| 17:73754540 | rs201972845 | R>C | C:312 | (99.75, 120.66, 38.21) |
| 17:73754449 | D>N | C:317 | (102.51, 113.56, 40.29) | |
| 17:73754418 | Q>P | C:327 | (107.76, 124.78, 26.11) | |
| 17:73754377 | S>G | C:341 | (96.07, 123.53, 28.03) | |
| 17:73754367 | rs371517491 CM993835 |
T>M | C:344 | (96.96, 114.63, 24.62) |
| 17:73754364 | G>V | C:345 | (97.84, 111.26, 25.78) | |
| 17:73754362 | rs375690568 CM001698 |
G>S | C:346 | (100.70, 109.54, 26.89) |
| 17:73754359 | G>C | C:347 | (103.30, 111.28, 26.14) | |
| 17:73754349 | G>D | C:350 | (103.19, 115.32, 20.96) | |
| 17:73754343 | rs370412722 | T>M | C:352 | (98.59, 120.16, 23.02) |
| 17:73754341 | V>M | C:353 | (94.26, 119.77, 24.10) | |
| 17:73754338 | T>A | C:354 | (93.75, 124.03, 23.67) | |
| 17:73754320 | A>T | C:360 | (91.60, 133.22, 19.72) | |
| 17:73754308 | rs374566360 | A>T | C:364 | (96.99, 131.39, 19.90) |
| 17:73754301 | rs538714933 | R>Q | C:366 | (99.84, 134.97, 15.98) |
| 17:73754296 | I>V | C:368 | (101.71, 128.95, 20.85) | |
| 17:73754199 | G>S | C:373 | (111.29, 125.81, 19.97) | |
| 17:73754196 | rs201811960 | G>R | C:374 | (109.93, 124.92, 17.19) |
| 17:73754190 | A>T | C:376 | (104.27, 123.65, 15.52) | |
| 17:73754177 | rs371917340 | L>P | C:380 | (91.28, 124.21, 14.51) |
| 17:73754163 | COSM2156859 | D>N | C:385 | (81.47, 110.59, 13.01) |
| 17:73754157 | rs549837719 | A>T | C:387 | (83.52, 104.07, 12.26) |
| 17:73754153 | K>R | C:388 | (82.16, 105.82, 8.15) | |
| 17:73754144 | C>Y | C:391 | (80.38, 103.52, -0.51) | |
| 17:73754141 | rs371755069 | L>S | C:392 | (83.73, 102.59, -3.68) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 17:73761136 | rs104894572 | P>T | C:28 | (89.19, 99.54, -5.22) |
| 17:73761124 | rs104894576 | V>M | C:32 | (86.72, 101.40, 5.75) |
| 17:73759113 | rs80084721 | A>V | C:198 | (81.87, 113.86, 23.53) |