General Structure Information
| PDB ID | 3wef |
| HGNC Gene Label(s) | FDFT1 |
| Structure Name | crystal structure of the human squalene synthase in complex with farnesyl thiopyrophosphate |
| Resolution | 2.35Å |
| Reference | AUTH C.I.LIU,W.Y.JENG,W.J.CHANG,M.F.SHIH,T.P.KO,A.H.J.WANGTITL STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF HUMANTITL 2 SQUALENE SYNTHASEREF ACTA CRYSTALLOGR.,SECT.D V. 70 231 2014REFN ISSN 0907-4449DOI 10.1107/S1399004713026230 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 333 |
| Number Of SNVs | 130 |
| Number Of Permutations | 20720 |
| Optimal Distance Threshold | 20.0 |
| K Statistic | 0.271 |
| p-value | 0.332 |
COSMIC
| Number Of Residues | 333 |
| Number Of SNVs | 5 |
| Number Of Permutations | 1194 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.1 |
| p-value | 0.718 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 130 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 11.0 |
| K Statistic | -0.072 |
| p-value | 0.869 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 8:11666309 | L>F | C:36 | (-4.16, 37.57, 38.43) | |
| 8:11666313 | rs558707651 | S>N | C:37 | (-5.19, 33.09, 38.71) |
| 8:11666327 | T>A | C:42 | (-2.71, 28.41, 45.29) | |
| 8:11666328 | T>S | C:42 | (-2.71, 28.41, 45.29) | |
| 8:11666336 | K>E | C:45 | (0.29, 29.03, 48.97) | |
| 8:11666337 | rs11549147 | K>R | C:45 | (0.29, 29.03, 48.97) |
| 8:11666366 | A>S | C:55 | (11.13, 30.01, 45.28) | |
| 8:11666379 | Q>R | C:59 | (9.10, 33.52, 42.22) | |
| 8:11666387 | D>H | C:62 | (12.62, 35.55, 32.46) | |
| 8:11666391 | rs542597307 | G>E | C:63 | (8.37, 34.38, 31.72) |
| 8:11667177 | N>Y | C:67 | (4.21, 29.76, 35.51) | |
| 8:11667180 | A>S | C:68 | (6.77, 26.01, 34.08) | |
| 8:11667181 | A>V | C:68 | (6.77, 26.01, 34.08) | |
| 8:11667201 | V>I | C:75 | (4.24, 17.84, 39.66) | |
| 8:11667222 | rs561714716 | L>V | C:82 | (3.09, 9.44, 46.30) |
| 8:11667238 | rs200217031 | T>S | C:87 | (1.55, 4.77, 54.86) |
| 8:11667240 | rs201072068 | I>V | C:88 | (1.62, 4.09, 50.52) |
| 8:11667246 | V>M | C:90 | (4.75, -1.48, 47.28) | |
| 8:11667253 | K>R | C:92 | (-1.86, 1.59, 47.27) | |
| 8:11667258 | V>F | C:94 | (3.53, 0.80, 41.73) | |
| 8:11667261 | P>S | C:95 | (0.05, 1.76, 40.55) | |
| 8:11667262 | P>L | C:95 | (0.05, 1.76, 40.55) | |
| 8:11667270 | H>N | C:98 | (3.77, 2.98, 36.87) | |
| 8:11667273 | N>H | C:99 | (-0.66, 5.98, 36.18) | |
| 8:11667279 | rs145118363 | H>D | C:101 | (1.79, 10.08, 33.11) |
| 8:11667288 | rs61732866 | L>V | C:104 | (-1.20, 15.69, 34.95) |
| 8:11667300 | D>H | C:108 | (-11.63, 15.52, 39.32) | |
| 8:11667302 | D>E | C:108 | (-11.63, 15.52, 39.32) | |
| 8:11667306 | rs371554178 COSM1195669 |
R>W | C:110 | (-8.47, 15.19, 45.05) |
| 8:11667307 | R>Q | C:110 | (-8.47, 15.19, 45.05) | |
| 8:11667313 | M>R | C:112 | (-7.25, 12.63, 50.56) | |
| 8:11667318 | rs11549152 | S>G | C:114 | (-0.92, 11.36, 52.83) |
| 8:11667340 | V>A | C:121 | (0.38, 18.95, 46.83) | |
| 8:11667342 | L>V | C:122 | (-1.33, 14.90, 46.82) | |
| 8:11667354 | P>A | C:126 | (-6.93, 19.45, 41.41) | |
| 8:11667358 | rs556051417 | T>M | C:127 | (-5.26, 23.51, 41.70) |
| 8:11679265 | L>V | C:130 | (-6.10, 23.77, 36.20) | |
| 8:11679280 | L>V | C:135 | (1.37, 25.26, 30.88) | |
| 8:11679299 | rs150867299 | T>I | C:141 | (5.23, 17.29, 26.31) |
| 8:11679302 | rs200465082 | V>E | C:142 | (8.54, 18.20, 28.98) |
| 8:11679308 | A>V | C:144 | (4.79, 14.21, 31.28) | |
| 8:11679311 | D>G | C:145 | (8.40, 12.49, 29.33) | |
| 8:11679314 | I>S | C:146 | (10.20, 13.77, 33.04) | |
| 8:11679319 | rs138781417 | R>W | C:148 | (6.80, 8.08, 31.22) |
| 8:11679320 | rs201022112 | R>Q | C:148 | (6.80, 8.08, 31.22) |
| 8:11679323 | COSM168244 | R>T | C:149 | (11.55, 9.18, 31.49) |
| 8:11679329 | G>D | C:151 | (8.06, 6.37, 37.96) | |
| 8:11679331 | I>V | C:152 | (9.21, 3.71, 35.38) | |
| 8:11679335 | G>E | C:153 | (12.03, 4.21, 38.62) | |
| 8:11679350 | L>S | C:158 | (9.65, 0.97, 46.03) | |
| 8:11679358 | H>Y | C:161 | (18.03, -0.96, 49.14) | |
| 8:11679365 | rs200916527 | T>I | C:163 | (23.97, -1.99, 44.72) |
| 8:11679378 | rs545547539 | E>D | C:167 | (22.19, 0.72, 40.24) |
| 8:11679384 | D>E | C:169 | (24.67, 6.94, 38.62) | |
| 8:11683543 | rs139230476 | Y>C | C:174 | (15.26, 6.55, 37.21) |
| 8:11683548 | rs141644705 | A>S | C:176 | (17.53, 14.17, 39.50) |
| 8:11683560 | G>R | C:180 | (17.46, 18.43, 34.43) | |
| 8:11683563 | I>V | C:181 | (16.80, 16.20, 31.38) | |
| 8:11683572 | S>T | C:184 | (16.99, 21.75, 29.99) | |
| 8:11683576 | COSM603664 | R>H | C:185 | (13.06, 18.72, 27.46) |
| 8:11683578 | L>I | C:186 | (11.34, 23.62, 30.03) | |
| 8:11683583 | F>L | C:187 | (15.60, 26.17, 30.46) | |
| 8:11683585 | S>L | C:188 | (15.17, 25.03, 24.82) | |
| 8:11683595 | E>D | C:191 | (12.82, 30.33, 22.09) | |
| 8:11683605 | P>T | C:195 | (18.77, 24.60, 21.16) | |
| 8:11683611 | V>I | C:197 | (20.51, 23.28, 26.84) | |
| 8:11683612 | V>A | C:197 | (20.51, 23.28, 26.84) | |
| 8:11683620 | D>N | C:200 | (23.65, 17.72, 26.35) | |
| 8:11683630 | rs140001524 | R>H | C:203 | (27.19, 17.75, 29.46) |
| 8:11683635 | rs200601839 | N>H | C:205 | (22.15, 13.58, 34.28) |
| 8:11683637 | N>K | C:205 | (22.15, 13.58, 34.28) | |
| 8:11683641 | rs376734953 | M>V | C:207 | (23.49, 19.72, 36.94) |
| 8:11683643 | M>I | C:207 | (23.49, 19.72, 36.94) | |
| 8:11683645 | G>D | C:208 | (21.55, 16.21, 39.33) | |
| 8:11683652 | F>L | C:210 | (27.00, 17.66, 42.27) | |
| 8:11683679 | D>E | C:219 | (20.99, 13.77, 54.35) | |
| 8:11683681 | rs139729511 | Y>F | C:220 | (24.20, 8.21, 57.35) |
| 8:11683692 | Q>E | C:224 | (19.92, 5.43, 59.33) | |
| 8:11683694 | Q>H | C:224 | (19.92, 5.43, 59.33) | |
| 8:11683696 | Q>L | C:225 | (17.31, 8.95, 62.60) | |
| 8:11683704 | rs376692522 | R>G | C:228 | (15.20, 7.44, 54.81) |
| 8:11683705 | R>K | C:228 | (15.20, 7.44, 54.81) | |
| 8:11683707 | E>K | C:229 | (19.49, 2.22, 53.45) | |
| 8:11683724 | E>D | C:234 | (29.03, -2.65, 45.55) | |
| 8:11687753 | V>F | C:235 | (30.93, 1.55, 48.67) | |
| 8:11687758 | COSM1193197 | W>C | C:236 | (27.44, -0.34, 52.86) |
| 8:11687771 | K>E | C:241 | (29.12, -6.45, 58.93) | |
| 8:11687779 | L>F | C:243 | (24.84, 1.82, 56.18) | |
| 8:11687787 | F>S | C:246 | (29.07, 4.21, 58.81) | |
| 8:11687789 | A>T | C:247 | (26.18, 5.75, 63.80) | |
| 8:11687790 | A>V | C:247 | (26.18, 5.75, 63.80) | |
| 8:11687798 | E>Q | C:250 | (32.41, 1.78, 67.46) | |
| 8:11687805 | rs140063318 | I>T | C:252 | (34.06, 7.74, 63.17) |
| 8:11687816 | rs570109609 | V>M | C:256 | (35.18, 9.49, 57.31) |
| 8:11687820 | rs151238023 | Q>L | C:257 | (37.68, 5.93, 55.31) |
| 8:11687834 | L>V | C:262 | (30.75, 8.60, 48.27) | |
| 8:11687837 | I>V | C:263 | (32.80, 13.33, 48.48) | |
| 8:11687838 | I>T | C:263 | (32.80, 13.33, 48.48) | |
| 8:11687844 | rs140885465 | N>S | C:265 | (31.58, 9.63, 42.91) |
| 8:11687846 | A>T | C:266 | (30.65, 13.64, 43.07) | |
| 8:11687860 | I>M | C:270 | (32.33, 19.54, 38.94) | |
| 8:11687861 | P>S | C:271 | (33.40, 18.90, 34.93) | |
| 8:11687862 | P>R | C:271 | (33.40, 18.90, 34.93) | |
| 8:11687864 | D>N | C:272 | (29.54, 18.04, 32.99) | |
| 8:11687865 | D>A | C:272 | (29.54, 18.04, 32.99) | |
| 8:11687867 | V>I | C:273 | (28.40, 21.65, 36.27) | |
| 8:11687868 | rs368325351 | V>G | C:273 | (28.40, 21.65, 36.27) |
| 8:11687879 | L>V | C:277 | (26.67, 26.69, 34.19) | |
| 8:11687882 | S>P | C:278 | (29.13, 27.60, 29.91) | |
| 8:11687894 | N>D | C:282 | (18.86, 33.87, 30.76) | |
| 8:11687897 | Q>E | C:283 | (21.31, 36.33, 34.50) | |
| 8:11687898 | Q>R | C:283 | (21.31, 36.33, 34.50) | |
| 8:11687903 | V>L | C:285 | (18.39, 30.51, 33.77) | |
| 8:11689051 | A>S | C:302 | (32.02, 20.79, 54.68) | |
| 8:11689058 | Y>C | C:304 | (36.93, 15.75, 52.61) | |
| 8:11689060 | N>H | C:305 | (37.82, 14.46, 56.63) | |
| 8:11689061 | N>S | C:305 | (37.82, 14.46, 56.63) | |
| 8:11689068 | rs138035023 | Q>H | C:307 | (34.18, 12.93, 62.54) |
| 8:11689073 | rs544192341 | V>A | C:309 | (28.34, 13.84, 58.74) |
| 8:11689077 | rs556178209 | F>L | C:310 | (28.69, 10.33, 60.61) |
| 8:11689081 | COSM3896314 | G>W | C:312 | (24.77, 16.15, 62.62) |
| 8:11689084 | A>P | C:313 | (24.02, 18.90, 60.76) | |
| 8:11689097 | rs200992419 | R>Q | C:317 | (32.44, 27.02, 56.39) |
| 8:11689109 | A>V | C:321 | (36.92, 37.32, 51.13) | |
| 8:11689128 | D>E | C:327 | (27.60, 36.68, 43.39) | |
| 8:11689133 | T>I | C:329 | (25.77, 36.08, 38.95) | |
| 8:11689136 | rs148180939 | N>S | C:330 | (29.56, 35.75, 36.83) |
| 8:11689137 | N>K | C:330 | (29.56, 35.75, 36.83) | |
| 8:11689140 | M>I | C:331 | (30.77, 31.19, 34.56) | |
| 8:11689141 | COSM1496746 | P>S | C:332 | (33.74, 33.92, 35.75) |
| 8:11689142 | P>L | C:332 | (33.74, 33.92, 35.75) | |
| 8:11689144 | rs111415615 | A>S | C:333 | (32.55, 33.74, 39.60) |
| 8:11689148 | V>A | C:334 | (30.88, 30.21, 39.48) | |
| 8:11689151 | K>I | C:335 | (34.93, 29.08, 36.66) | |
| 8:11689161 | I>M | C:338 | (33.95, 25.87, 41.78) | |
| 8:11689162 | rs370878820 | Y>H | C:339 | (38.30, 26.60, 40.29) |
| 8:11689175 | E>G | C:343 | (42.53, 24.13, 47.65) | |
| 8:11695900 | Y>D | C:346 | (44.48, 19.19, 47.12) | |
| 8:11695904 | H>R | C:347 | (45.49, 21.94, 52.63) | |
| 8:11695913 | P>R | C:350 | (44.05, 12.69, 54.35) | |
| 8:11695915 | rs572243364 | D>N | C:351 | (48.41, 10.64, 52.96) |
| 8:11695918 | S>P | C:352 | (45.45, 7.83, 55.75) | |
| 8:11695921 | D>Y | C:353 | (42.00, 8.43, 52.79) | |
| 8:11695931 | rs79708434 | S>C | C:356 | (43.99, 10.20, 48.61) |
| 8:11695935 | S>R | C:357 | (45.05, 9.36, 44.62) | |
| 8:11695937 | rs202175915 | K>R | C:358 | (40.85, 8.04, 43.40) |
| 8:11695939 | T>A | C:359 | (40.50, 13.02, 45.59) | |
| 8:11695940 | rs150943942 | T>R | C:359 | (40.50, 13.02, 45.59) |
| 8:11695957 | T>A | C:365 | (40.72, 16.91, 36.06) | |
| 8:11695960 | rs565608299 | I>F | C:366 | (38.23, 20.08, 38.01) |
| 8:11695963 | R>W | C:367 | (42.91, 22.28, 39.90) | |
| 8:11695964 | rs373360995 | R>Q | C:367 | (42.91, 22.28, 39.90) |
| 8:11695967 | COSM272691 | T>M | C:368 | (42.43, 21.19, 33.30) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 8:11666348 | COSM3715935 | Q>E | C:49 | (3.94, 25.85, 51.78) |
| 8:11679263 | COSM3718699 | S>Y | C:129 | (-3.68, 19.98, 37.18) |
| 8:11679307 | COSM1157774 | A>T | C:144 | (4.79, 14.21, 31.28) |
| 8:11683599 | COSM3715876 | E>K | C:193 | (18.72, 29.26, 26.97) |
| 8:11695899 | COSM3164744 | I>M | C:345 | (38.51, 19.44, 49.41) |