General Structure Information
| PDB ID | 1nwt |
| HGNC Gene Label(s) | CHI3L1 |
| Structure Name | crystal structure of human cartilage gp39 (hc-gp39) in complex with chitopentaose |
| Resolution | 2.5Å |
| Reference | AUTH F.FUSETTI,T.PIJNING,K.H.KALK,E.BOS,B.W.DIJKSTRATITL CRYSTAL STRUCTURE AND CARBOHYDRATE-BINDING PROPERTIES OF THETITL 2 HUMAN CARTILAGE GLYCOPROTEIN-39REF J.BIOL.CHEM. V. 278 37753 2003REFN ISSN 0021-9258PMID 12851408DOI 10.1074/JBC.M303137200 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 362 |
| Number Of SNVs | 105 |
| Number Of Permutations | 36595 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.023 |
| p-value | 0.876 |
COSMIC
| Number Of Residues | 362 |
| Number Of SNVs | 8 |
| Number Of Permutations | 1473 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.179 |
| p-value | 0.796 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 105 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | -0.172 |
| p-value | 0.325 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:203154465 | rs146010120 | R>Q | A:35 | (35.82, 7.12, 29.22) |
| 1:203154466 | rs143744874 | R>W | A:35 | (35.82, 7.12, 29.22) |
| 1:203154447 | rs150798384 | C>S | A:41 | (31.57, 7.67, 34.56) |
| 1:203154439 | D>N | A:44 | (27.70, 10.18, 41.00) | |
| 1:203154435 | A>D | A:45 | (25.95, 8.27, 37.75) | |
| 1:203154436 | A>T | A:45 | (25.95, 8.27, 37.75) | |
| 1:203154426 | rs540860117 | R>H | A:48 | (20.67, 4.69, 44.51) |
| 1:203154427 | rs143563909 | R>C | A:48 | (20.67, 4.69, 44.51) |
| 1:203154405 | I>T | A:55 | (31.48, -5.23, 41.17) | |
| 1:203154400 | S>G | A:57 | (36.71, -2.51, 38.56) | |
| 1:203154384 | S>N | A:62 | (51.02, -4.01, 46.61) | |
| 1:203154379 | rs114478844 | D>N | A:64 | (51.63, -9.62, 49.06) |
| 1:203154373 | I>V | A:66 | (44.08, -5.31, 48.75) | |
| 1:203154369 | D>G | A:67 | (46.10, -1.11, 47.25) | |
| 1:203154370 | rs199705137 COSM1644492 |
D>N | A:67 | (46.10, -1.11, 47.25) |
| 1:203154366 | T>I | A:68 | (44.46, 1.57, 45.82) | |
| 1:203154362 | rs527687380 | W>C | A:69 | (45.08, 0.14, 39.51) |
| 1:203154363 | W>S | A:69 | (45.08, 0.14, 39.51) | |
| 1:203154349 | V>M | A:74 | (39.21, 6.45, 48.58) | |
| 1:203154345 | T>M | A:75 | (36.77, 9.44, 46.52) | |
| 1:203154340 | Y>H | A:77 | (36.68, 2.72, 46.80) | |
| 1:203154337 | rs149615845 | G>S | A:78 | (32.20, 6.35, 48.43) |
| 1:203153757 | rs574537613 | N>K | A:87 | (19.28, 0.80, 48.17) |
| 1:203153759 | N>D | A:87 | (19.28, 0.80, 48.17) | |
| 1:203153729 | rs377634812 | G>R | A:97 | (42.26, -7.77, 38.49) |
| 1:203153717 | F>L | A:101 | (46.67, -7.79, 37.52) | |
| 1:203153713 | G>V | A:102 | (48.06, -10.48, 35.06) | |
| 1:203152911 | rs111396343 | K>T | A:108 | (54.63, -14.57, 42.44) |
| 1:203152908 | I>R | A:109 | (50.19, -13.73, 45.33) | |
| 1:203152887 | R>H | A:116 | (48.13, -18.26, 50.08) | |
| 1:203152888 | rs199779694 COSM3671592 |
R>C | A:116 | (48.13, -18.26, 50.08) |
| 1:203152884 | R>Q | A:117 | (47.35, -15.20, 56.00) | |
| 1:203152885 | rs142590705 | R>W | A:117 | (47.35, -15.20, 56.00) |
| 1:203152882 | T>P | A:118 | (49.63, -11.37, 53.38) | |
| 1:203152876 | I>F | A:120 | (43.76, -13.80, 52.68) | |
| 1:203152867 | rs200519289 | V>L | A:123 | (40.86, -8.41, 52.12) |
| 1:203152863 | rs372451627 COSM678079 |
P>L | A:124 | (39.12, -8.25, 55.39) |
| 1:203152864 | rs115095389 | P>A | A:124 | (39.12, -8.25, 55.39) |
| 1:203152860 | rs140857184 | P>L | A:125 | (40.60, -5.11, 56.68) |
| 1:203152854 | L>R | A:127 | (36.59, -4.68, 52.17) | |
| 1:203152851 | rs147131854 | R>H | A:128 | (34.25, -4.53, 56.79) |
| 1:203152852 | rs367636349 | R>C | A:128 | (34.25, -4.53, 56.79) |
| 1:203152846 | H>N | A:130 | (37.65, 1.54, 51.96) | |
| 1:203152842 | G>V | A:131 | (32.42, -0.27, 52.35) | |
| 1:203152804 | rs374975768 | R>W | A:144 | (47.49, -25.56, 34.49) |
| 1:203152801 | rs880633 | R>G | A:145 | (49.92, -24.39, 36.97) |
| 1:203152788 | rs199534052 | H>P | A:149 | (47.97, -22.91, 43.52) |
| 1:203152769 | K>N | A:155 | (39.49, -23.43, 50.93) | |
| 1:203152771 | K>E | A:155 | (39.49, -23.43, 50.93) | |
| 1:203151970 | A>D | A:159 | (37.85, -18.83, 55.79) | |
| 1:203151966 | E>D | A:160 | (39.87, -14.89, 56.95) | |
| 1:203151968 | COSM902454 | E>K | A:160 | (39.87, -14.89, 56.95) |
| 1:203151932 | rs371142487 | L>F | A:172 | (32.67, -10.30, 53.76) |
| 1:203151928 | rs376843376 | L>P | A:173 | (30.05, -11.48, 49.74) |
| 1:203151920 | rs200963493 | A>T | A:176 | (34.18, -15.21, 40.61) |
| 1:203151907 | A>V | A:180 | (33.60, -18.86, 28.85) | |
| 1:203151892 | I>T | A:185 | (36.94, -23.67, 31.79) | |
| 1:203151873 | I>M | A:191 | (33.91, -25.63, 38.57) | |
| 1:203151875 | I>V | A:191 | (33.91, -25.63, 38.57) | |
| 1:203151872 | A>T | A:192 | (33.21, -28.39, 41.92) | |
| 1:203151868 | K>R | A:193 | (36.54, -28.47, 44.54) | |
| 1:203150412 | rs376460075 | H>Y | A:197 | (34.47, -22.68, 49.04) |
| 1:203150391 | rs149440066 | M>V | A:204 | (33.40, -13.67, 31.47) |
| 1:203150384 | Y>C | A:206 | (32.02, -11.44, 27.90) | |
| 1:203150385 | rs139024042 | Y>H | A:206 | (32.02, -11.44, 27.90) |
| 1:203150382 | rs141218577 | D>H | A:207 | (35.21, -11.70, 24.65) |
| 1:203150375 | H>R | A:209 | (34.94, -13.94, 17.05) | |
| 1:203150369 | A>D | A:211 | (40.20, -10.29, 14.94) | |
| 1:203150370 | A>S | A:211 | (40.20, -10.29, 14.94) | |
| 1:203150365 | rs193291700 | W>C | A:212 | (41.99, -15.09, 16.56) |
| 1:203150363 | rs368942218 | R>H | A:213 | (39.09, -16.76, 14.74) |
| 1:203150364 | rs147953761 | R>C | A:213 | (39.09, -16.76, 14.74) |
| 1:203150352 | G>S | A:217 | (31.83, -12.17, 14.73) | |
| 1:203150330 | rs114837679 | R>Q | A:224 | (27.22, -23.62, 16.71) |
| 1:203150322 | COSM3481836 | E>K | A:227 | (27.07, -26.56, 11.99) |
| 1:203150310 | rs371464402 | P>S | A:231 | (34.46, -21.40, 14.01) |
| 1:203150301 | F>L | A:234 | (33.13, -25.61, 22.32) | |
| 1:203149776 | Y>C | A:239 | (29.46, -25.47, 25.72) | |
| 1:203149762 | M>L | A:244 | (30.23, -24.02, 34.26) | |
| 1:203149722 | rs562001678 | G>D | A:257 | (27.00, -12.63, 31.07) |
| 1:203149719 | I>T | A:258 | (24.96, -9.68, 29.54) | |
| 1:203149708 | rs200949867 | G>R | A:262 | (31.29, -4.30, 21.24) |
| 1:203149665 | A>V | A:276 | (33.37, -11.91, 6.57) | |
| 1:203149666 | A>P | A:276 | (33.37, -11.91, 6.57) | |
| 1:203149647 | G>E | A:282 | (37.94, -1.52, 14.51) | |
| 1:203149636 | rs138989209 | R>W | A:286 | (33.82, 10.98, 20.43) |
| 1:203149629 | T>S | A:288 | (36.25, 3.91, 24.12) | |
| 1:203149602 | rs376330429 | Y>C | A:297 | (28.31, 5.30, 24.73) |
| 1:203148994 | rs372170408 COSM2213572 |
F>L | A:302 | (27.80, 2.36, 13.67) |
| 1:203148990 | rs563596931 COSM1201048 |
R>C | A:304 | (23.56, 8.18, 13.07) |
| 1:203148987 | COSM1337974 | G>R | A:305 | (23.07, 4.49, 8.75) |
| 1:203148980 | T>I | A:307 | (22.23, -2.21, 8.37) | |
| 1:203148969 | I>F | A:311 | (22.47, -13.49, 13.94) | |
| 1:203148963 | rs148946875 | G>S | A:313 | (20.36, -18.76, 16.24) |
| 1:203148950 | P>R | A:317 | (22.52, -8.10, 17.09) | |
| 1:203148938 | K>R | A:321 | (28.07, 2.21, 8.72) | |
| 1:203148925 | W>C | A:325 | (30.41, -6.91, 11.62) | |
| 1:203148927 | W>R | A:325 | (30.41, -6.91, 11.62) | |
| 1:203148921 | G>R | A:327 | (28.85, -6.93, 17.75) | |
| 1:203148918 | rs201739718 | Y>H | A:328 | (24.94, -4.88, 18.79) |
| 1:203148915 | rs142178236 | D>N | A:329 | (23.79, -7.22, 23.03) |
| 1:203148905 | rs377177381 | E>G | A:332 | (15.32, -8.01, 20.76) |
| 1:203148902 | rs145322357 | S>I | A:333 | (19.28, -9.48, 22.92) |
| 1:203148900 | rs572161451 | V>I | A:334 | (19.23, -8.57, 26.61) |
| 1:203148896 | rs367962164 | K>R | A:335 | (13.92, -9.57, 26.50) |
| 1:203148893 | S>T | A:336 | (16.43, -13.36, 24.91) | |
| 1:203148700 | rs370477111 | K>R | A:342 | (14.28, -16.77, 33.90) |
| 1:203148698 | rs114984905 | D>N | A:343 | (14.29, -20.97, 30.98) |
| 1:203148685 | rs527531482 COSM902451 |
A>V | A:347 | (21.19, -16.44, 39.74) |
| 1:203148682 | rs376352545 | G>D | A:348 | (21.50, -14.39, 36.94) |
| 1:203148676 | M>T | A:350 | (27.34, -10.11, 34.53) | |
| 1:203148677 | M>V | A:350 | (27.34, -10.11, 34.53) | |
| 1:203148674 | rs148314652 | V>I | A:351 | (26.49, -6.19, 33.40) |
| 1:203148668 | A>S | A:353 | (29.62, -2.17, 31.88) | |
| 1:203148655 | rs530402801 | D>V | A:357 | (24.87, 1.27, 29.11) |
| 1:203148649 | F>S | A:359 | (26.25, 6.91, 31.36) | |
| 1:203148643 | rs370960745 | G>D | A:361 | (20.55, 8.73, 27.71) |
| 1:203148632 | COSM3369507 | G>S | A:365 | (17.31, 7.91, 23.21) |
| 1:203148619 | R>H | A:369 | (19.84, 8.08, 32.53) | |
| 1:203148613 | P>L | A:371 | (19.25, 1.17, 28.20) | |
| 1:203148610 | L>P | A:372 | (21.09, -2.54, 27.60) | |
| 1:203148592 | D>V | A:378 | (12.62, -4.76, 33.18) | |
| 1:203148590 | A>T | A:379 | (13.22, -9.29, 32.32) | |
| 1:203148581 | rs145648214 | A>S | A:382 | (8.96, -10.69, 34.30) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:203154457 | COSM1337976 | D>N | A:38 | (29.23, 13.07, 27.60) |
| 1:203154356 | COSM83962 | W>C | A:71 | (43.60, 10.30, 41.74) |
| 1:203152855 | COSM425048 | L>V | A:127 | (36.59, -4.68, 52.17) |
| 1:203151968 | COSM902454 | E>K | A:160 | (39.87, -14.89, 56.95) |
| 1:203151867 | COSM176588 | K>N | A:193 | (36.54, -28.47, 44.54) |
| 1:203148912 | COSM1689638 | D>N | A:330 | (19.76, -5.19, 21.56) |
| 1:203148646 | COSM1601539 | Q>L | A:360 | (24.63, 10.29, 29.96) |
| 1:203148634 | COSM1601538 | C>Y | A:364 | (20.01, 5.79, 22.36) |