General Structure Information
| PDB ID | 3l5h |
| HGNC Gene Label(s) | IL6ST |
| Structure Name | crystal structure of the full ectodomain of human gp130: new insights into the molecular assembly of receptor complexes |
| Resolution | 3.6Å |
| Reference | AUTH Y.XU,N.KERSHAW,C.S.LUO,P.SOO,M.POCOCK,P.E.CZABOTAR,AUTH 2 D.J.HILTON,N.A.NICOLA,T.P.J.GARRETT,J.G.ZHANGTITL CRYSTAL STRUCTURE OF THE ENTIRE ECTODOMAIN OF GP130:TITL 2 INSIGHTS INTO THE MOLECULAR ASSEMBLY OF THE TALL CYTOKINETITL 3 RECEPTOR COMPLEXESREF TO BE PUBLISHEDREFN |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 585 |
| Number Of SNVs | 157 |
| Number Of Permutations | 52916 |
| Optimal Distance Threshold | 11.0 |
| K Statistic | 0.031 |
| p-value | 0.62 |
COSMIC
| Number Of Residues | 585 |
| Number Of SNVs | 15 |
| Number Of Permutations | 8863 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.019 |
| p-value | 0.91 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 157 |
| Number Of COSMIC SNVs | 14 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | -0.018 |
| p-value | 0.815 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:55265662 | rs536592543 | G>V | A:7 | (10.32, -27.74, -0.65) |
| 5:55265626 | H>R | A:19 | (16.07, -4.61, 14.89) | |
| 5:55265623 | S>F | A:20 | (17.61, -7.74, 10.91) | |
| 5:55265611 | A>V | A:24 | (15.03, -16.37, 2.22) | |
| 5:55265584 | M>T | A:33 | (8.95, -28.39, -11.07) | |
| 5:55265581 | D>G | A:34 | (8.13, -31.62, -13.59) | |
| 5:55265563 | A>V | A:40 | (9.91, -20.08, -9.39) | |
| 5:55265557 | rs200651075 | Y>C | A:42 | (3.96, -20.24, -9.00) |
| 5:55265546 | K>E | A:46 | (2.56, -16.57, 2.14) | |
| 5:55265539 | N>S | A:48 | (-2.27, -15.97, 7.44) | |
| 5:55265536 | H>R | A:49 | (-3.47, -11.20, 6.30) | |
| 5:55265533 | F>S | A:50 | (-1.65, -11.18, 3.11) | |
| 5:55265525 | rs554002581 | P>T | A:53 | (4.27, -8.92, -2.00) |
| 5:55265522 | rs200081300 | K>E | A:54 | (5.13, -9.79, -6.12) |
| 5:55265516 | Q>E | A:56 | (9.29, -8.66, -3.39) | |
| 5:55265510 | T>A | A:58 | (14.41, -12.19, -5.95) | |
| 5:55265479 | T>I | A:68 | (14.55, -10.07, 2.17) | |
| 5:55265465 | rs142583572 | A>T | A:73 | (8.30, -7.02, 15.37) |
| 5:55265459 | rs368013040 | L>I | A:75 | (6.14, -12.72, 20.04) |
| 5:55265437 | rs370154111 | N>S | A:82 | (3.04, -21.69, 1.14) |
| 5:55265428 | T>R | A:85 | (-1.15, -24.62, -9.63) | |
| 5:55265423 | G>R | A:87 | (-4.05, -22.24, -12.88) | |
| 5:55265407 | N>S | A:92 | (1.54, -26.30, 1.56) | |
| 5:55265384 | S>T | A:100 | (11.95, -13.12, 18.68) | |
| 5:55264219 | rs148424276 | P>S | A:104 | (23.03, -10.97, 25.42) |
| 5:55264191 | I>N | A:113 | (27.98, -16.93, 50.59) | |
| 5:55264192 | rs200551540 | I>V | A:113 | (27.98, -16.93, 50.59) |
| 5:55264186 | N>H | A:115 | (26.86, -20.52, 54.21) | |
| 5:55264183 | COSM3828205 | E>K | A:116 | (29.55, -22.62, 58.47) |
| 5:55264156 | D>N | A:125 | (21.21, -9.79, 38.89) | |
| 5:55264153 | rs2228044 | G>R | A:126 | (20.17, -10.72, 34.51) |
| 5:55264149 | G>E | A:127 | (17.85, -8.41, 33.76) | |
| 5:55264128 | T>K | A:134 | (19.56, -17.87, 28.54) | |
| 5:55260139 | rs572435166 | A>T | A:143 | (46.57, -18.50, 39.51) |
| 5:55260131 | H>Q | A:145 | (43.87, -24.47, 39.71) | |
| 5:55260125 | F>L | A:147 | (38.79, -24.27, 40.36) | |
| 5:55260111 | A>G | A:152 | (22.84, -22.94, 36.39) | |
| 5:55260105 | COSM245026 | R>H | A:154 | (17.56, -25.84, 35.00) |
| 5:55260106 | rs146382783 | R>C | A:154 | (17.56, -25.84, 35.00) |
| 5:55260099 | T>I | A:156 | (17.62, -21.82, 40.03) | |
| 5:55260097 | P>S | A:157 | (18.29, -19.09, 36.92) | |
| 5:55260054 | N>S | A:171 | (43.10, -14.06, 46.50) | |
| 5:55260052 | I>V | A:172 | (39.31, -16.57, 44.15) | |
| 5:55260046 | V>I | A:174 | (34.37, -14.85, 40.26) | |
| 5:55260013 | V>F | A:185 | (29.07, -12.33, 27.38) | |
| 5:55259997 | I>T | A:190 | (34.99, -10.74, 41.39) | |
| 5:55259994 | N>S | A:191 | (39.70, -10.75, 43.51) | |
| 5:55259983 | rs183743555 | V>L | A:195 | (37.92, -15.63, 54.73) |
| 5:55259325 | rs199518876 COSM482911 |
N>S | A:201 | (26.58, -21.78, 61.70) |
| 5:55259322 | P>L | A:202 | (24.20, -20.06, 64.58) | |
| 5:55259297 | N>K | A:210 | (20.61, -16.37, 88.41) | |
| 5:55259290 | E>K | A:213 | (23.05, -14.19, 94.09) | |
| 5:55259283 | S>F | A:215 | (19.50, -9.19, 91.86) | |
| 5:55259278 | I>V | A:217 | (22.94, -9.89, 87.35) | |
| 5:55259272 | rs150242954 | K>E | A:219 | (25.91, -15.58, 83.50) |
| 5:55259267 | rs373310801 | L>F | A:220 | (24.86, -15.93, 79.41) |
| 5:55259257 | N>D | A:224 | (31.17, -20.06, 69.49) | |
| 5:55259250 | rs369812743 | S>T | A:226 | (32.19, -24.44, 63.66) |
| 5:55259239 | rs148108192 | V>I | A:230 | (39.22, -19.62, 60.87) |
| 5:55259235 | rs375553493 COSM1437952 |
I>T | A:231 | (36.74, -16.42, 62.06) |
| 5:55259233 | I>L | A:232 | (37.74, -13.21, 64.65) | |
| 5:55259226 | K>T | A:234 | (31.31, -9.15, 65.50) | |
| 5:55259224 | Y>H | A:235 | (29.51, -12.34, 69.31) | |
| 5:55259211 | Y>C | A:239 | (18.16, -7.64, 76.46) | |
| 5:55259205 | T>I | A:241 | (10.87, -8.41, 78.89) | |
| 5:55259197 | A>T | A:244 | (7.97, -7.56, 75.13) | |
| 5:55259190 | T>I | A:246 | (10.64, -4.34, 72.39) | |
| 5:55259181 | Q>R | A:249 | (20.89, -4.76, 70.81) | |
| 5:55256383 | rs369630533 | P>A | A:252 | (28.48, -3.37, 69.89) |
| 5:55256370 | A>G | A:256 | (34.15, -7.96, 69.84) | |
| 5:55256332 | P>T | A:269 | (14.33, -7.35, 90.17) | |
| 5:55256323 | E>Q | A:272 | (10.67, -14.23, 82.46) | |
| 5:55256316 | V>A | A:274 | (14.18, -13.76, 76.82) | |
| 5:55256305 | rs141500365 | R>C | A:278 | (23.62, -11.26, 64.88) |
| 5:55256293 | rs367560170 | E>K | A:282 | (36.73, -8.98, 63.78) |
| 5:55256250 | S>I | A:296 | (14.85, -17.62, 79.49) | |
| 5:55256251 | S>R | A:296 | (14.85, -17.62, 79.49) | |
| 5:55256238 | Y>C | A:300 | (16.87, -12.62, 91.82) | |
| 5:55256233 | D>N | A:302 | (16.08, -8.44, 96.14) | |
| 5:55256230 | R>G | A:303 | (15.79, -7.61, 101.12) | |
| 5:55253114 | S>P | A:305 | (11.60, -1.79, 97.97) | |
| 5:55253092 | Y>C | A:312 | (-5.44, 5.01, 112.26) | |
| 5:55253093 | COSM1328752 | Y>H | A:312 | (-5.44, 5.01, 112.26) |
| 5:55253086 | I>T | A:314 | (-11.02, 4.91, 115.13) | |
| 5:55253084 | rs577060675 | D>Y | A:315 | (-15.08, 2.20, 115.79) |
| 5:55253080 | P>L | A:316 | (-17.00, 4.60, 117.48) | |
| 5:55253069 | Q>K | A:320 | (-16.36, 0.96, 128.43) | |
| 5:55253056 | T>I | A:324 | (-11.28, -1.00, 118.21) | |
| 5:55253045 | rs199818715 | V>M | A:328 | (-5.51, -0.92, 106.71) |
| 5:55252062 | T>I | A:331 | (-0.32, -4.61, 97.80) | |
| 5:55252056 | rs145020363 | P>L | A:333 | (3.77, -3.11, 93.35) |
| 5:55252035 | K>R | A:340 | (6.56, -13.29, 96.46) | |
| 5:55252036 | K>E | A:340 | (6.56, -13.29, 96.46) | |
| 5:55252014 | T>S | A:347 | (5.04, -3.97, 115.53) | |
| 5:55252002 | W>S | A:351 | (3.67, 3.21, 126.99) | |
| 5:55251991 | rs370934743 | L>V | A:355 | (5.92, -4.29, 122.83) |
| 5:55251987 | rs149924543 | Q>R | A:356 | (2.57, -6.91, 121.92) |
| 5:55251972 | N>S | A:361 | (-1.22, -13.48, 105.49) | |
| 5:55251970 | rs554775919 | A>T | A:362 | (-3.70, -10.01, 105.60) |
| 5:55251967 | T>S | A:363 | (-4.31, -6.44, 104.87) | |
| 5:55251952 | N>D | A:368 | (-7.76, -4.28, 121.39) | |
| 5:55251945 | T>R | A:370 | (-5.54, 1.81, 124.82) | |
| 5:55251940 | D>H | A:372 | (-2.41, 4.99, 126.07) | |
| 5:55251936 | R>H | A:373 | (1.77, 8.45, 121.95) | |
| 5:55251937 | rs139103669 | R>C | A:373 | (1.77, 8.45, 121.95) |
| 5:55251933 | Y>S | A:374 | (-0.47, 2.60, 121.44) | |
| 5:55251931 | rs2228043 | L>V | A:375 | (4.03, 3.37, 117.57) |
| 5:55251925 | T>A | A:377 | (5.61, -1.37, 113.08) | |
| 5:55251907 | COSM3920223 | L>V | A:383 | (12.35, -15.26, 100.00) |
| 5:55251904 | V>F | A:384 | (15.04, -12.31, 100.75) | |
| 5:55251874 | rs61755737 | I>V | A:394 | (-2.49, 5.27, 117.41) |
| 5:55251861 | D>G | A:398 | (-6.53, 14.15, 123.62) | |
| 5:55251859 | F>I | A:399 | (-3.80, 14.69, 118.58) | |
| 5:55250817 | COSM123734 | T>I | A:402 | (-3.10, 20.60, 114.94) |
| 5:55250812 | rs199939306 | P>S | A:404 | (-3.97, 22.12, 108.56) |
| 5:55250794 | A>T | A:410 | (-9.48, 19.91, 93.00) | |
| 5:55250791 | rs376610689 | F>V | A:411 | (-7.42, 19.68, 89.32) |
| 5:55250787 | rs140433866 | P>R | A:412 | (-9.48, 18.17, 85.97) |
| 5:55250775 | M>K | A:416 | (-6.63, 11.81, 85.28) | |
| 5:55250757 | COSM3975588 | T>S | A:422 | (0.52, 24.46, 100.15) |
| 5:55250743 | S>P | A:427 | (7.45, 19.18, 107.94) | |
| 5:55250727 | rs2228046 | I>T | A:432 | (-3.26, 9.77, 104.07) |
| 5:55250722 | E>Q | A:434 | (-9.43, 9.87, 102.97) | |
| 5:55250713 | rs369431167 | V>M | A:437 | (-19.41, 9.39, 95.77) |
| 5:55250701 | rs562633426 | K>E | A:441 | (-28.18, 6.40, 97.12) |
| 5:55250698 | A>S | A:442 | (-24.70, 5.93, 98.38) | |
| 5:55250682 | D>G | A:447 | (-10.38, 5.09, 98.05) | |
| 5:55250676 | Q>P | A:449 | (-3.95, 7.64, 97.70) | |
| 5:55250667 | D>G | A:452 | (6.01, 10.22, 100.05) | |
| 5:55250662 | T>P | A:454 | (7.13, 15.52, 100.02) | |
| 5:55250659 | V>M | A:455 | (4.32, 15.41, 97.62) | |
| 5:55250655 | rs112901728 | H>R | A:456 | (2.88, 19.62, 96.27) |
| 5:55250653 | R>C | A:457 | (0.95, 18.63, 92.08) | |
| 5:55250649 | T>I | A:458 | (-1.67, 13.75, 93.67) | |
| 5:55250644 | L>I | A:460 | (-6.92, 10.50, 92.78) | |
| 5:55248161 | K>R | A:468 | (-21.21, 10.89, 90.13) | |
| 5:55248150 | I>V | A:472 | (-11.25, 14.83, 98.05) | |
| 5:55248140 | T>I | A:475 | (-4.93, 13.79, 106.19) | |
| 5:55248135 | rs34417936 | V>I | A:477 | (0.94, 12.63, 108.83) |
| 5:55248110 | COSM1486833 | P>L | A:485 | (-8.44, 17.37, 108.43) |
| 5:55248102 | rs148372700 | I>V | A:488 | (-12.31, 19.40, 97.98) |
| 5:55247894 | K>I | A:499 | (-33.62, 15.99, 85.29) | |
| 5:55247883 | V>I | A:503 | (-40.71, 26.97, 88.30) | |
| 5:55247879 | rs144353104 | R>Q | A:504 | (-43.40, 27.95, 92.79) |
| 5:55247856 | COSM1068982 | E>K | A:512 | (-43.81, 43.01, 89.31) |
| 5:55247842 | E>D | A:516 | (-39.73, 30.03, 94.54) | |
| 5:55247837 | rs368246591 | D>A | A:518 | (-35.86, 24.33, 94.46) |
| 5:55247826 | rs375131282 | V>I | A:522 | (-26.72, 16.11, 93.89) |
| 5:55247813 | N>S | A:526 | (-24.57, 15.32, 86.36) | |
| 5:55247795 | rs3730294 | Y>F | A:532 | (-30.21, 28.85, 87.83) |
| 5:55247787 | F>L | A:535 | (-35.99, 31.09, 79.09) | |
| 5:55247783 | Y>C | A:536 | (-39.93, 36.02, 80.32) | |
| 5:55247777 | T>I | A:538 | (-46.69, 35.66, 76.03) | |
| 5:55247772 | I>V | A:540 | (-47.79, 37.01, 71.27) | |
| 5:55247424 | V>L | A:548 | (-29.38, 33.78, 87.83) | |
| 5:55247421 | D>N | A:549 | (-25.91, 35.07, 89.72) | |
| 5:55247393 | S>F | A:558 | (-40.01, 42.75, 86.05) | |
| 5:55247391 | rs149607573 | S>A | A:559 | (-41.98, 45.14, 83.73) |
| 5:55247378 | COSM123733 | D>G | A:563 | (-54.79, 40.88, 82.12) |
| 5:55247348 | Y>C | A:573 | (-27.01, 26.47, 82.10) | |
| 5:55247340 | E>K | A:576 | (-20.45, 20.91, 79.78) | |
| 5:55247322 | P>A | A:582 | (-40.55, 22.38, 84.34) | |
| 5:55247298 | rs147049759 | K>E | A:590 | (-56.35, 43.47, 87.23) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:55265534 | COSM1437955 | F>V | A:50 | (-1.65, -11.18, 3.11) |
| 5:55264153 | COSM5019669 | G>R | A:126 | (20.17, -10.72, 34.51) |
| 5:55260105 | COSM245026 | R>H | A:154 | (17.56, -25.84, 35.00) |
| 5:55260018 | COSM1437954 | G>E | A:183 | (25.86, -14.15, 21.74) |
| 5:55260001 | COSM1437953 | H>Y | A:189 | (36.41, -10.58, 36.12) |
| 5:55259998 | COSM1620405 | I>V | A:190 | (34.99, -10.74, 41.39) |
| 5:55259235 | COSM1437952 | I>K | A:231 | (36.74, -16.42, 62.06) |
| 5:55256385 | COSM1671655 | P>L | A:251 | (26.67, -2.58, 73.77) |
| 5:55253108 | COSM3429537 | A>S | A:307 | (6.85, 0.48, 102.26) |
| 5:55252063 | COSM1437949 | T>A | A:331 | (-0.32, -4.61, 97.80) |
| 5:55252041 | COSM1186770 | N>S | A:338 | (11.51, -7.45, 94.29) |
| 5:55251931 | COSM5019621 | L>V | A:375 | (4.03, 3.37, 117.57) |
| 5:55250817 | COSM123734 | T>I | A:402 | (-3.10, 20.60, 114.94) |
| 5:55247807 | COSM1671654 | F>C | A:528 | (-19.83, 21.94, 90.67) |
| 5:55247378 | COSM123733 | D>V | A:563 | (-54.79, 40.88, 82.12) |