General Structure Information
| PDB ID | 4kng |
| HGNC Gene Label(s) | LGR5 |
| Structure Name | crystal structure of human lgr5-rspo1-rnf43 |
| Resolution | 2.5Å |
| Reference | AUTH P.H.CHEN,X.CHEN,Z.LIN,D.FANG,X.HETITL THE STRUCTURAL BASIS OF R-SPONDIN RECOGNITION BY LGR5 ANDTITL 2 RNF43.REF GENES DEV. V. 27 1345 2013REFN ISSN 0890-9369PMID 23756651DOI 10.1101/GAD.219915.113 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 461 |
| Number Of SNVs | 131 |
| Number Of Permutations | 67468 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.069 |
| p-value | 0.123 |
COSMIC
| Number Of Residues | 461 |
| Number Of SNVs | 5 |
| Number Of Permutations | 2985 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.1 |
| p-value | 0.91 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 131 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.083 |
| p-value | 0.739 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:71833958 | G>D | B:33 | (-22.43, 23.55, 4.47) | |
| 12:71833981 | rs150864769 | E>K | B:41 | (-15.30, 26.45, 11.34) |
| 12:71833985 | P>L | B:42 | (-16.57, 29.74, 9.51) | |
| 12:71833987 | rs139369662 | D>N | B:43 | (-12.60, 30.56, 6.15) |
| 12:71833988 | D>G | B:43 | (-12.60, 30.56, 6.15) | |
| 12:71833989 | D>E | B:43 | (-12.60, 30.56, 6.15) | |
| 12:71833991 | G>V | B:44 | (-14.86, 33.63, 6.36) | |
| 12:71834003 | L>P | B:48 | (-16.30, 25.91, 4.58) | |
| 12:71834008 | V>M | B:50 | (-14.45, 20.69, 6.17) | |
| 12:71834035 | rs375163459 | E>Q | B:59 | (-16.04, 8.48, -1.87) |
| 12:71834041 | P>T | B:61 | (-18.76, 13.07, -1.12) | |
| 12:71834045 | S>C | B:62 | (-22.09, 14.20, -2.25) | |
| 12:71898402 | COSM1513215 | S>N | B:74 | (-7.80, 12.12, 8.54) |
| 12:71898404 | M>V | B:75 | (-7.51, 8.53, 10.80) | |
| 12:71898406 | COSM1705930 | M>I | B:75 | (-7.51, 8.53, 10.80) |
| 12:71898410 | N>D | B:77 | (-11.23, 3.02, 6.07) | |
| 12:71898437 | rs370230855 | L>M | B:86 | (-14.49, 16.58, -5.43) |
| 12:71898443 | rs143081365 | S>C | B:88 | (-14.96, 21.44, -7.63) |
| 12:71898445 | S>R | B:88 | (-14.96, 21.44, -7.63) | |
| 12:71898446 | rs199760997 | L>I | B:89 | (-12.97, 21.85, -4.26) |
| 12:71898449 | R>C | B:90 | (-13.08, 26.98, -7.34) | |
| 12:71898450 | rs142158288 | R>H | B:90 | (-13.08, 26.98, -7.34) |
| 12:71918187 | rs200516824 | R>S | B:96 | (-5.21, 17.36, 6.96) |
| 12:71918188 | R>H | B:96 | (-5.21, 17.36, 6.96) | |
| 12:71918202 | rs531998322 | A>T | B:101 | (-5.76, 2.84, 2.68) |
| 12:71918211 | Y>H | B:104 | (-3.43, 4.39, -7.71) | |
| 12:71918214 | I>V | B:105 | (-2.82, 8.39, -6.18) | |
| 12:71918217 | P>T | B:106 | (-5.31, 8.62, -9.35) | |
| 12:71918218 | P>L | B:106 | (-5.31, 8.62, -9.35) | |
| 12:71918254 | V>A | B:118 | (-1.34, 21.67, 2.15) | |
| 12:71928897 | rs553085219 | M>T | B:120 | (-1.44, 15.92, 4.62) |
| 12:71928911 | rs375946555 | Q>E | B:125 | (-0.55, 1.70, 2.65) |
| 12:71928918 | rs577749360 | R>T | B:127 | (4.33, -0.20, -1.97) |
| 12:71928921 | H>L | B:128 | (4.55, 4.39, -6.34) | |
| 12:71928923 | COSM3772722 | V>I | B:129 | (5.89, 8.79, -5.63) |
| 12:71928945 | N>S | B:136 | (1.54, 20.25, -12.93) | |
| 12:71928951 | R>Q | B:138 | (1.77, 24.89, -11.50) | |
| 12:71946869 | H>D | B:149 | (4.84, 0.93, 2.42) | |
| 12:71946874 | I>M | B:150 | (7.71, 5.06, -0.76) | |
| 12:71946884 | rs373436137 COSM272886 |
P>S | B:154 | (8.80, 8.53, -10.02) |
| 12:71946890 | S>G | B:156 | (8.86, 13.18, -13.47) | |
| 12:71946892 | S>R | B:156 | (8.86, 13.18, -13.47) | |
| 12:71946915 | L>P | B:164 | (7.39, 22.23, -3.19) | |
| 12:71946950 | rs531377941 | E>Q | B:176 | (18.31, 5.23, -4.73) |
| 12:71946959 | rs565985845 COSM1364057 |
V>I | B:179 | (18.97, 12.62, -8.39) |
| 12:71946975 | S>N | B:184 | (12.36, 19.85, -10.18) | |
| 12:71946981 | rs144739516 | S>L | B:186 | (14.34, 25.13, -6.97) |
| 12:71946983 | A>T | B:187 | (12.01, 25.94, -4.04) | |
| 12:71946992 | A>T | B:190 | (12.29, 21.45, 3.58) | |
| 12:71946995 | M>L | B:191 | (14.13, 17.32, 2.46) | |
| 12:71947018 | I>M | B:198 | (19.58, 5.89, 2.03) | |
| 12:71947022 | H>Y | B:200 | (25.85, 6.40, -2.06) | |
| 12:71947025 | I>L | B:201 | (25.00, 10.40, -0.86) | |
| 12:71947027 | I>M | B:201 | (25.00, 10.40, -0.86) | |
| 12:71947038 | A>V | B:205 | (22.31, 14.64, -5.26) | |
| 12:71947044 | G>E | B:207 | (22.37, 20.45, -6.98) | |
| 12:71947060 | L>F | B:212 | (17.49, 23.21, 1.01) | |
| 12:71947064 | rs148122019 | V>I | B:214 | (16.35, 21.75, 6.38) |
| 12:71950400 | rs184379194 | H>Y | B:216 | (16.36, 16.23, 8.36) |
| 12:71950404 | L>R | B:217 | (19.68, 12.19, 5.69) | |
| 12:71950407 | rs117535164 | H>R | B:218 | (17.35, 11.04, 10.85) |
| 12:71950422 | H>R | B:223 | (28.01, 2.97, 3.22) | |
| 12:71950433 | K>Q | B:227 | (34.80, 13.76, -2.21) | |
| 12:71950438 | K>N | B:228 | (31.38, 17.03, -5.01) | |
| 12:71950440 | C>F | B:229 | (27.17, 15.15, -1.86) | |
| 12:71950446 | D>A | B:231 | (28.27, 20.44, -4.20) | |
| 12:71950463 | E>K | B:237 | (20.87, 27.16, 7.66) | |
| 12:71953379 | rs372106110 | N>D | B:244 | (23.80, 6.76, 9.49) |
| 12:71953416 | L>P | B:256 | (27.66, 23.55, 3.27) | |
| 12:71953418 | S>P | B:257 | (28.60, 28.51, 3.76) | |
| 12:71953421 | N>Y | B:258 | (25.06, 29.29, 4.99) | |
| 12:71953431 | E>V | B:261 | (22.13, 22.39, 13.15) | |
| 12:71955568 | H>N | B:265 | (24.59, 11.76, 16.60) | |
| 12:71955569 | rs368660988 | H>R | B:265 | (24.59, 11.76, 16.60) |
| 12:71955587 | COSM943235 | S>L | B:271 | (38.73, 11.02, 12.39) |
| 12:71955591 | I>M | B:272 | (37.75, 15.14, 13.28) | |
| 12:71955599 | K>R | B:275 | (41.62, 22.74, 7.70) | |
| 12:71955608 | rs80351734 | V>A | B:278 | (37.27, 25.77, 6.85) |
| 12:71955614 | rs145924075 | N>S | B:280 | (31.40, 25.45, 7.94) |
| 12:71955629 | rs538333891 | T>K | B:285 | (25.20, 23.22, 16.59) |
| 12:71960189 | F>S | B:288 | (31.12, 15.19, 17.55) | |
| 12:71960210 | F>Y | B:295 | (43.44, 12.98, 15.73) | |
| 12:71960213 | V>A | B:296 | (41.22, 15.98, 16.54) | |
| 12:71960237 | L>S | B:304 | (33.87, 28.13, 14.74) | |
| 12:71960249 | R>K | B:308 | (28.92, 30.24, 22.19) | |
| 12:71960416 | L>V | B:312 | (36.48, 16.33, 22.49) | |
| 12:71960425 | A>P | B:315 | (40.36, 11.50, 21.84) | |
| 12:71960440 | E>Q | B:320 | (49.21, 19.00, 20.87) | |
| 12:71960441 | rs370233161 | E>G | B:320 | (49.21, 19.00, 20.87) |
| 12:71960626 | L>S | B:335 | (39.85, 17.49, 26.00) | |
| 12:71960644 | rs181911196 | S>L | B:341 | (51.56, 17.05, 28.20) |
| 12:71960658 | rs116452232 | T>P | B:346 | (49.22, 31.70, 25.59) |
| 12:71960686 | rs150655850 | Q>R | B:355 | (31.92, 29.67, 31.94) |
| 12:71960689 | V>G | B:356 | (33.69, 25.06, 31.94) | |
| 12:71965302 | rs147617068 | S>F | B:360 | (39.85, 14.86, 32.60) |
| 12:71965309 | N>K | B:362 | (44.75, 14.16, 30.06) | |
| 12:71965326 | P>L | B:368 | (49.72, 27.12, 33.05) | |
| 12:71965328 | S>C | B:369 | (48.45, 30.97, 34.32) | |
| 12:71965329 | S>T | B:369 | (48.45, 30.97, 34.32) | |
| 12:71965337 | V>I | B:372 | (43.81, 35.40, 31.07) | |
| 12:71965343 | Q>E | B:374 | (39.48, 36.52, 34.58) | |
| 12:71965344 | Q>R | B:374 | (39.48, 36.52, 34.58) | |
| 12:71965349 | rs186409843 | L>F | B:376 | (37.12, 30.10, 34.55) |
| 12:71966638 | R>K | B:382 | (38.74, 14.46, 37.66) | |
| 12:71966641 | rs12303775 | H>R | B:383 | (42.45, 11.12, 36.88) |
| 12:71966649 | I>V | B:386 | (49.32, 17.69, 38.33) | |
| 12:71966655 | rs148289646 | E>K | B:388 | (54.20, 22.50, 41.92) |
| 12:71966664 | V>L | B:391 | (51.21, 31.70, 43.19) | |
| 12:71966670 | T>A | B:393 | (48.05, 28.43, 38.68) | |
| 12:71966671 | T>N | B:393 | (48.05, 28.43, 38.68) | |
| 12:71966675 | F>L | B:394 | (44.48, 27.89, 39.94) | |
| 12:71966685 | L>F | B:398 | (37.54, 36.69, 41.16) | |
| 12:71966686 | rs375599630 | L>R | B:398 | (37.54, 36.69, 41.16) |
| 12:71966689 | S>N | B:399 | (34.14, 33.67, 39.37) | |
| 12:71966692 | rs368637483 | L>R | B:400 | (36.80, 29.65, 40.65) |
| 12:71966695 | COSM549864 | R>Q | B:401 | (30.91, 28.92, 41.58) |
| 12:71966698 | rs146135159 | S>L | B:402 | (35.04, 24.35, 41.21) |
| 12:71971724 | I>V | B:410 | (49.52, 17.37, 44.02) | |
| 12:71971728 | rs147277449 | A>G | B:411 | (53.10, 17.59, 46.85) |
| 12:71971733 | I>L | B:413 | (49.94, 23.38, 47.52) | |
| 12:71971736 | rs541937377 COSM1213302 |
H>Y | B:414 | (52.56, 28.73, 47.28) |
| 12:71971738 | H>Q | B:414 | (52.56, 28.73, 47.28) | |
| 12:71971743 | rs140436677 | N>S | B:416 | (49.53, 32.66, 48.93) |
| 12:71971758 | L>S | B:421 | (40.30, 31.92, 44.77) | |
| 12:71971766 | rs138215571 | L>V | B:424 | (36.46, 28.49, 46.07) |
| 12:71971773 | rs377594428 | K>R | B:426 | (32.72, 23.00, 45.49) |
| 12:71971774 | rs149599979 | K>N | B:426 | (32.72, 23.00, 45.49) |
| 12:71972585 | rs146110108 | D>N | B:428 | (38.68, 17.40, 45.07) |
| 12:71972607 | rs73339868 | S>L | B:435 | (50.98, 16.42, 53.09) |
| 12:71972631 | H>R | B:443 | (37.88, 31.18, 53.74) | |
| 12:71972634 | rs569017913 | G>V | B:444 | (34.56, 29.36, 51.75) |
| 12:71972639 | rs201933235 | T>A | B:446 | (30.60, 24.20, 50.95) |
| 12:71972655 | T>I | B:451 | (40.18, 11.32, 50.77) | |
| 12:71972662 | N>K | B:453 | (45.74, 12.77, 50.98) | |
| 12:71972667 | rs536797990 | A>D | B:455 | (51.39, 12.37, 54.46) |
| 12:71972674 | rs146398590 | Q>H | B:457 | (49.94, 11.61, 59.28) |
| 12:71972676 | S>N | B:458 | (49.59, 16.11, 59.48) | |
| 12:71972677 | rs375595231 | S>R | B:458 | (49.59, 16.11, 59.48) |
| 12:71972681 | I>L | B:460 | (45.98, 19.84, 61.96) | |
| 12:71972684 | rs148594770 | S>P | B:461 | (41.71, 20.33, 60.55) |
| 12:71972703 | E>G | B:467 | (31.35, 28.68, 55.54) | |
| 12:71972708 | K>E | B:469 | (28.30, 22.97, 54.61) | |
| 12:71974065 | E>K | B:472 | (35.84, 13.47, 52.08) | |
| 12:71974077 | A>S | B:476 | (38.60, 8.85, 60.74) | |
| 12:71974083 | Q>K | B:478 | (39.77, 15.71, 62.17) | |
| 12:71974090 | C>Y | B:480 | (35.26, 13.27, 65.72) | |
| 12:71974095 | rs76115696 | F>L | B:482 | (34.25, 19.21, 64.61) |
| 12:71976296 | rs201703093 | S>L | B:538 | (25.01, 20.49, 58.79) |
| 12:71976301 | Q>K | B:540 | (27.45, 15.51, 56.38) | |
| 12:71976302 | rs147607370 | Q>R | B:540 | (27.45, 15.51, 56.38) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:71898411 | COSM3688548 | N>S | B:77 | (-11.23, 3.02, 6.07) |
| 12:71928954 | COSM1606604 | S>I | B:139 | (0.03, 26.23, -5.50) |
| 12:71955587 | COSM943235 | S>L | B:271 | (38.73, 11.02, 12.39) |
| 12:71960209 | COSM3734311 | F>L | B:295 | (43.44, 12.98, 15.73) |
| 12:71966646 | COSM1705932 | E>K | B:385 | (50.75, 12.97, 35.80) |