General Structure Information
| PDB ID | 1f5n |
| HGNC Gene Label(s) | GBP1 |
| Structure Name | human guanylate binding protein-1 in complex with the gtp analogue, gmppnp. |
| Resolution | 1.7Å |
| Reference | AUTH B.PRAKASH,L.RENAULT,G.J.PRAEFCKE,C.HERRMANN,AUTH 2 A.WITTINGHOFERTITL TRIPHOSPHATE STRUCTURE OF GUANYLATE-BINDINGTITL 2 PROTEIN 1 AND IMPLICATIONS FOR NUCLEOTIDE BINDINGTITL 3 AND GTPASE MECHANISM.REF EMBO J. V. 19 4555 2000REFN ISSN 0261-4189PMID 10970849DOI 10.1093/EMBOJ/19.17.4555 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 570 |
| Number Of SNVs | 148 |
| Number Of Permutations | 65227 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.069 |
| p-value | 0.01 |
COSMIC
| Number Of Residues | 570 |
| Number Of SNVs | 9 |
| Number Of Permutations | 14239 |
| Optimal Distance Threshold | 52.0 |
| K Statistic | 0.472 |
| p-value | 0.428 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 148 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 55.0 |
| K Statistic | -0.333 |
| p-value | 0.12 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:89528898 | rs148954716 | M>T | A:7 | (73.46, -16.02, 10.48) |
| 1:89528899 | M>V | A:7 | (73.46, -16.02, 10.48) | |
| 1:89528893 | G>R | A:9 | (76.42, -16.42, 13.52) | |
| 1:89528890 | rs369195107 | P>T | A:10 | (76.62, -14.01, 15.87) |
| 1:89528887 | rs149801739 | M>V | A:11 | (77.13, -9.93, 12.58) |
| 1:89528881 | L>F | A:13 | (73.63, -4.39, 13.77) | |
| 1:89528877 | rs375266486 | I>T | A:14 | (74.76, -1.17, 16.24) |
| 1:89528859 | COSM275265 | R>Q | A:20 | (81.57, 8.15, 18.12) |
| 1:89528850 | rs149277121 | A>V | A:23 | (75.99, 0.75, 11.14) |
| 1:89528847 | rs139551612 | N>I | A:24 | (77.89, -3.43, 10.26) |
| 1:89528844 | P>L | A:25 | (78.11, -2.39, 6.74) | |
| 1:89528827 | rs556340222 | L>F | A:31 | (69.18, -7.42, 7.25) |
| 1:89528818 | I>V | A:34 | (66.29, -11.59, 5.48) | |
| 1:89528809 | rs142645233 | P>T | A:37 | (58.56, -12.49, 8.37) |
| 1:89528805 | M>T | A:38 | (61.75, -10.34, 11.20) | |
| 1:89528806 | M>V | A:38 | (61.75, -10.34, 11.20) | |
| 1:89528791 | COSM1344748 | I>V | A:43 | (68.55, -8.83, 26.22) |
| 1:89528787 | V>A | A:44 | (68.43, -5.15, 28.22) | |
| 1:89528782 | rs567509135 | L>F | A:46 | (73.91, -4.79, 34.76) |
| 1:89528776 | rs370809506 | R>C | A:48 | (77.82, -8.32, 36.18) |
| 1:89528769 | G>D | A:50 | (73.42, -13.38, 31.50) | |
| 1:89528760 | Y>C | A:53 | (73.61, -18.81, 29.38) | |
| 1:89528746 | L>V | A:58 | (66.13, -17.98, 22.62) | |
| 1:89526001 | S>F | A:66 | (80.22, -13.85, 23.33) | |
| 1:89525989 | rs138624937 | T>M | A:70 | (81.02, -13.02, 36.95) |
| 1:89525968 | rs372508569 COSM1688005 |
G>E | A:77 | (76.85, -3.04, 21.40) |
| 1:89525966 | rs1048401 | I>V | A:78 | (73.58, -3.90, 19.20) |
| 1:89525961 | rs369238719 | W>C | A:79 | (77.22, -8.62, 18.32) |
| 1:89525959 | M>R | A:80 | (72.48, -9.61, 14.25) | |
| 1:89525950 | V>A | A:83 | (67.48, -17.80, 13.67) | |
| 1:89525947 | COSM1237789 | P>H | A:84 | (65.31, -20.38, 12.17) |
| 1:89525917 | V>G | A:94 | (65.88, -11.36, 15.16) | |
| 1:89525900 | rs146259663 | G>S | A:100 | (76.00, -3.53, 29.26) |
| 1:89525896 | L>P | A:101 | (73.36, -1.34, 31.21) | |
| 1:89525887 | rs138685353 | V>A | A:104 | (74.12, 5.84, 36.42) |
| 1:89525885 | rs536896435 | E>K | A:105 | (74.60, 5.39, 41.13) |
| 1:89525108 | G>D | A:107 | (78.92, 6.92, 35.08) | |
| 1:89525094 | D>N | A:112 | (74.18, 2.87, 28.41) | |
| 1:89525069 | V>A | A:120 | (62.63, -0.23, 22.58) | |
| 1:89525070 | rs368835338 | V>I | A:120 | (62.63, -0.23, 22.58) |
| 1:89525054 | rs374870319 | T>I | A:125 | (60.04, -8.85, 22.82) |
| 1:89525049 | rs147930913 | V>M | A:127 | (64.20, -8.92, 27.74) |
| 1:89525045 | Y>C | A:128 | (65.59, -5.30, 32.73) | |
| 1:89525026 | rs563821916 | I>M | A:134 | (61.76, -6.13, 42.10) |
| 1:89525013 | COSM465061 | M>V | A:139 | (63.27, 0.16, 40.37) |
| 1:89525003 | L>P | A:142 | (64.26, 0.87, 35.67) | |
| 1:89525000 | Y>S | A:143 | (66.52, 7.48, 34.69) | |
| 1:89524724 | Y>C | A:144 | (69.00, 3.52, 31.77) | |
| 1:89524718 | T>R | A:146 | (62.09, 7.07, 33.02) | |
| 1:89524707 | rs375149299 | H>D | A:150 | (64.03, 12.52, 28.10) |
| 1:89524657 | rs17130717 | E>D | A:166 | (51.78, 15.07, 25.11) |
| 1:89524637 | rs368456875 | S>N | A:173 | (51.20, 2.23, 20.18) |
| 1:89524617 | W>R | A:180 | (62.02, -7.36, 35.45) | |
| 1:89524614 | rs150289724 | T>A | A:181 | (64.53, -11.71, 33.36) |
| 1:89524603 | D>E | A:184 | (70.59, -15.57, 40.88) | |
| 1:89524598 | S>Y | A:186 | (66.06, -14.99, 46.67) | |
| 1:89524583 | A>V | A:191 | (51.61, -16.70, 50.59) | |
| 1:89524577 | rs201322839 | G>A | A:193 | (47.69, -20.27, 50.82) |
| 1:89524572 | P>S | A:195 | (52.39, -19.43, 46.26) | |
| 1:89524545 | Y>H | A:204 | (54.08, -6.87, 45.78) | |
| 1:89524530 | K>Q | A:209 | (54.58, 4.65, 47.84) | |
| 1:89523911 | rs75161612 | S>N | A:213 | (57.15, 12.94, 48.35) |
| 1:89523888 | L>M | A:221 | (58.57, 7.70, 37.63) | |
| 1:89523884 | P>H | A:222 | (59.79, 3.84, 37.64) | |
| 1:89523885 | P>S | A:222 | (59.79, 3.84, 37.64) | |
| 1:89523879 | COSM536415 | L>F | A:224 | (53.88, 4.93, 36.46) |
| 1:89523869 | R>Q | A:227 | (51.74, 0.21, 35.69) | |
| 1:89523870 | COSM912960 | R>W | A:227 | (51.74, 0.21, 35.69) |
| 1:89523839 | V>A | A:237 | (61.94, -16.49, 38.10) | |
| 1:89523830 | rs576498400 | R>Q | A:240 | (72.64, -18.90, 42.11) |
| 1:89523831 | R>W | A:240 | (72.64, -18.90, 42.11) | |
| 1:89523825 | rs143822672 | V>I | A:242 | (75.46, -23.58, 39.31) |
| 1:89523818 | R>P | A:244 | (81.22, -20.14, 44.64) | |
| 1:89523819 | rs372549555 | R>C | A:244 | (81.22, -20.14, 44.64) |
| 1:89523802 | rs144022371 | Q>H | A:249 | (82.71, -24.03, 34.27) |
| 1:89523803 | Q>R | A:249 | (82.71, -24.03, 34.27) | |
| 1:89523796 | rs149731935 | E>D | A:251 | (79.15, -21.90, 27.62) |
| 1:89523798 | E>K | A:251 | (79.15, -21.90, 27.62) | |
| 1:89523783 | E>K | A:256 | (72.58, -33.13, 32.95) | |
| 1:89523777 | rs566164121 | L>V | A:258 | (72.51, -27.26, 35.45) |
| 1:89523764 | rs371741027 COSM1134951 |
F>S | A:262 | (68.23, -22.48, 35.26) |
| 1:89523755 | Q>P | A:265 | (63.12, -21.58, 35.43) | |
| 1:89523756 | rs148526074 | Q>K | A:265 | (63.12, -21.58, 35.43) |
| 1:89523749 | A>V | A:267 | (62.18, -23.69, 28.98) | |
| 1:89523735 | Y>H | A:272 | (56.03, -15.99, 26.69) | |
| 1:89523731 | I>T | A:273 | (59.60, -15.88, 23.50) | |
| 1:89523725 | rs374475528 | S>T | A:275 | (54.34, -18.86, 21.62) |
| 1:89523719 | rs370963741 | S>Y | A:277 | (56.68, -13.21, 20.38) |
| 1:89523710 | rs375798125 | K>I | A:280 | (58.39, -5.42, 14.63) |
| 1:89523705 | L>V | A:282 | (55.71, -0.60, 11.53) | |
| 1:89523691 | rs538365990 | I>M | A:286 | (53.91, -2.37, 8.05) |
| 1:89523693 | rs139841530 | I>V | A:286 | (53.91, -2.37, 8.05) |
| 1:89523677 | rs571054459 | P>L | A:291 | (64.58, -5.03, 4.09) |
| 1:89523678 | P>S | A:291 | (64.58, -5.03, 4.09) | |
| 1:89523675 | rs534820766 | R>C | A:292 | (59.99, -3.43, 5.74) |
| 1:89522810 | E>D | A:294 | (68.41, -2.15, 6.21) | |
| 1:89522806 | L>M | A:296 | (64.06, 0.96, 11.15) | |
| 1:89522793 | rs144332469 | Y>C | A:300 | (65.46, 4.74, 14.53) |
| 1:89522791 | rs150474721 | V>I | A:301 | (71.85, 5.22, 13.92) |
| 1:89522788 | rs369692456 | N>D | A:302 | (71.61, 8.23, 10.79) |
| 1:89522784 | A>G | A:303 | (69.58, 10.39, 14.39) | |
| 1:89522749 | COSM175784 | A>P | A:315 | (60.94, 5.85, 10.12) |
| 1:89522739 | A>V | A:318 | (61.61, 6.70, 5.36) | |
| 1:89522740 | A>T | A:318 | (61.61, 6.70, 5.36) | |
| 1:89522726 | I>M | A:322 | (62.46, 3.34, 0.06) | |
| 1:89522715 | A>D | A:326 | (59.48, 0.91, -5.91) | |
| 1:89522698 | I>V | A:332 | (55.51, 1.69, -14.90) | |
| 1:89522691 | H>R | A:334 | (52.15, -4.95, -14.56) | |
| 1:89522675 | rs137876978 | M>I | A:339 | (50.25, -2.72, -23.24) |
| 1:89522661 | rs140288607 | Q>R | A:344 | (48.21, -6.62, -33.16) |
| 1:89522646 | rs1048425 | T>S | A:349 | (40.36, 0.52, -33.05) |
| 1:89522640 | Q>R | A:351 | (37.80, 1.74, -28.06) | |
| 1:89522636 | E>D | A:352 | (41.92, -2.41, -29.90) | |
| 1:89522627 | D>E | A:355 | (39.79, -0.85, -24.15) | |
| 1:89522626 | L>V | A:356 | (44.35, -2.84, -24.20) | |
| 1:89522619 | rs149073593 | R>T | A:358 | (40.12, 1.37, -18.58) |
| 1:89522603 | E>D | A:363 | (46.49, -4.71, -13.92) | |
| 1:89522585 | I>M | A:369 | (47.53, 0.80, -4.11) | |
| 1:89522580 | S>I | A:371 | (53.19, -1.81, -2.90) | |
| 1:89522571 | K>T | A:374 | (52.18, 6.59, 5.07) | |
| 1:89522560 | H>D | A:378 | (47.83, 11.61, -2.74) | |
| 1:89522546 | K>N | A:382 | (50.10, 13.03, -8.21) | |
| 1:89522538 | rs147875713 | A>V | A:385 | (50.03, 9.25, -13.60) |
| 1:89521910 | A>V | A:386 | (52.55, 10.94, -15.37) | |
| 1:89521907 | COSM1344742 | Q>P | A:387 | (55.52, 7.67, -15.34) |
| 1:89521902 | E>Q | A:389 | (49.74, 10.86, -19.53) | |
| 1:89521895 | rs142226400 | K>R | A:391 | (54.50, 4.99, -21.13) |
| 1:89521892 | rs139042305 | R>Q | A:392 | (48.32, 7.97, -23.39) |
| 1:89521893 | R>W | A:392 | (48.32, 7.97, -23.39) | |
| 1:89521860 | rs376697189 | S>P | A:403 | (48.05, 3.25, -39.72) |
| 1:89521850 | rs140785577 | R>H | A:406 | (48.31, -1.58, -43.59) |
| 1:89521841 | rs1048443 | A>G | A:409 | (50.62, 1.13, -48.91) |
| 1:89521814 | rs144519018 | L>P | A:418 | (43.75, 3.06, -61.64) |
| 1:89521810 | E>D | A:419 | (47.26, 6.62, -60.70) | |
| 1:89521808 | E>V | A:420 | (50.10, 4.48, -64.09) | |
| 1:89521796 | COSM912955 | A>G | A:424 | (47.95, 5.00, -70.49) |
| 1:89521773 | G>R | A:432 | (35.48, 4.31, -70.04) | |
| 1:89521766 | rs186728753 | R>H | A:434 | (29.32, 2.98, -68.12) |
| 1:89521767 | COSM465058 | R>C | A:434 | (29.32, 2.98, -68.12) |
| 1:89521759 | F>L | A:436 | (37.51, 5.14, -63.74) | |
| 1:89521761 | rs544489770 | F>L | A:436 | (37.51, 5.14, -63.74) |
| 1:89521740 | COSM912954 | L>M | A:443 | (40.04, -0.51, -56.11) |
| 1:89521724 | Y>F | A:448 | (36.88, 1.00, -47.07) | |
| 1:89521725 | Y>H | A:448 | (36.88, 1.00, -47.07) | |
| 1:89521715 | rs142020556 | P>L | A:451 | (42.97, -6.37, -42.78) |
| 1:89520552 | R>H | A:493 | (27.93, 10.28, -58.75) | |
| 1:89520553 | rs149483149 | R>C | A:493 | (27.93, 10.28, -58.75) |
| 1:89520544 | A>T | A:496 | (28.25, 13.65, -53.38) | |
| 1:89520528 | A>G | A:501 | (34.37, 11.26, -47.94) | |
| 1:89520507 | rs146959522 | E>G | A:508 | (38.38, 9.15, -38.58) |
| 1:89520503 | rs146081537 | M>I | A:509 | (39.16, 14.04, -36.92) |
| 1:89520497 | rs377677294 COSM197989 |
R>S | A:511 | (34.50, 8.82, -31.39) |
| 1:89520483 | M>T | A:516 | (41.66, 10.41, -26.25) | |
| 1:89520433 | E>K | A:533 | (39.58, 0.92, -2.06) | |
| 1:89520427 | rs530577122 | M>V | A:535 | (42.01, 6.68, 1.61) |
| 1:89520405 | rs1803630 | L>S | A:542 | (44.48, 4.12, 12.42) |
| 1:89520394 | Q>E | A:546 | (43.35, 4.52, 17.30) | |
| 1:89520391 | E>Q | A:547 | (39.78, 0.42, 18.79) | |
| 1:89520384 | T>N | A:549 | (45.71, 2.20, 22.50) | |
| 1:89520372 | K>R | A:553 | (45.58, 4.03, 27.77) | |
| 1:89520370 | L>F | A:554 | (40.45, 2.00, 29.49) | |
| 1:89519127 | G>R | A:564 | (43.85, 4.02, 44.83) | |
| 1:89519087 | Q>L | A:577 | (39.84, 12.96, 26.81) | |
| 1:89519083 | D>E | A:578 | (44.04, 13.58, 24.09) | |
| 1:89519071 | rs181237841 | K>N | A:582 | (44.28, 11.19, 17.69) |
| 1:89519073 | K>E | A:582 | (44.28, 11.19, 17.69) | |
| 1:89519069 | rs141247522 | M>T | A:583 | (39.67, 8.11, 17.20) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:89525903 | COSM3667592 | E>K | A:99 | (76.98, -2.58, 25.70) |
| 1:89522749 | COSM175784 | A>T | A:315 | (60.94, 5.85, 10.12) |
| 1:89522646 | COSM1344744 | T>S | A:349 | (40.36, 0.52, -33.05) |
| 1:89521850 | COSM2150288 | R>H | A:406 | (48.31, -1.58, -43.59) |
| 1:89521841 | COSM3751435 | A>G | A:409 | (50.62, 1.13, -48.91) |
| 1:89521784 | COSM197990 | S>L | A:428 | (40.63, 7.47, -73.07) |
| 1:89521767 | COSM465058 | R>C | A:434 | (29.32, 2.98, -68.12) |
| 1:89519089 | COSM197988 | I>M | A:576 | (41.70, 8.18, 27.11) |
| 1:89519075 | COSM912951 | T>M | A:581 | (40.86, 13.78, 19.50) |