General Structure Information
| PDB ID | 1jmo |
| HGNC Gene Label(s) | SERPIND1 |
| Structure Name | crystal structure of the heparin cofactor ii-s195a thrombin complex |
| Resolution | 2.2Å |
| Reference | AUTH T.P.BAGLIN,R.W.CARRELL,F.C.CHURCH,C.T.ESMON,J.A.HUNTINGTONTITL CRYSTAL STRUCTURES OF NATIVE AND THROMBIN-COMPLEXED HEPARINTITL 2 COFACTOR II REVEAL A MULTISTEP ALLOSTERIC MECHANISM.REF PROC.NATL.ACAD.SCI.USA V. 99 11079 2002REFN ISSN 0027-8424PMID 12169660DOI 10.1073/PNAS.162232399 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 425 |
| Number Of SNVs | 122 |
| Number Of Permutations | 67273 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.009 |
| p-value | 0.608 |
COSMIC
| Number Of Residues | 425 |
| Number Of SNVs | 6 |
| Number Of Permutations | 593 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.267 |
| p-value | 0.509 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 122 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.093 |
| p-value | 0.677 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 22:21133829 | rs537121106 | D>N | A:58 | (59.20, 47.03, 107.86) |
| 22:21133832 | rs567081979 COSM4102791 COSM4102792 |
D>N | A:59 | (60.01, 42.96, 106.12) |
| 22:21133841 | D>H | A:62 | (54.96, 34.26, 105.48) | |
| 22:21133845 | rs369438159 | L>P | A:63 | (55.21, 32.72, 110.02) |
| 22:21133854 | I>T | A:66 | (59.21, 30.90, 107.07) | |
| 22:21133860 | rs34324685 | S>N | A:68 | (57.12, 25.28, 105.04) |
| 22:21133871 | rs372976032 | D>N | A:72 | (58.76, 18.55, 110.16) |
| 22:21133877 | I>V | A:74 | (57.11, 15.93, 104.64) | |
| 22:21133880 | COSM1032330 COSM1032331 |
D>N | A:75 | (56.59, 14.11, 108.31) |
| 22:21133886 | rs181925405 | V>I | A:77 | (49.35, 13.29, 110.13) |
| 22:21133889 | D>N | A:78 | (46.64, 15.35, 107.63) | |
| 22:21133908 | P>L | A:84 | (29.56, 8.89, 107.30) | |
| 22:21133916 | S>T | A:87 | (26.30, 16.18, 113.74) | |
| 22:21133922 | V>M | A:89 | (24.32, 23.15, 116.64) | |
| 22:21133937 | I>V | A:94 | (17.77, 34.71, 121.35) | |
| 22:21133956 | G>D | A:100 | (18.10, 46.44, 130.81) | |
| 22:21133959 | K>R | A:101 | (19.10, 47.01, 127.51) | |
| 22:21133965 | R>Q | A:103 | (11.05, 51.89, 124.95) | |
| 22:21133973 | COSM1032333 COSM1032334 |
R>C | A:106 | (15.10, 46.87, 124.13) |
| 22:21133983 | I>T | A:109 | (20.62, 46.43, 119.74) | |
| 22:21133991 | rs576001943 | A>T | A:112 | (23.13, 47.09, 114.48) |
| 22:21133992 | A>G | A:112 | (23.13, 47.09, 114.48) | |
| 22:21134012 | Y>H | A:119 | (30.55, 46.02, 106.36) | |
| 22:21134022 | L>P | A:122 | (28.77, 47.24, 101.04) | |
| 22:21134037 | rs202123183 | N>I | A:127 | (38.21, 46.47, 96.23) |
| 22:21134038 | N>K | A:127 | (38.21, 46.47, 96.23) | |
| 22:21134042 | F>V | A:129 | (42.10, 47.67, 97.58) | |
| 22:21134045 | rs146203260 | D>N | A:130 | (38.69, 49.83, 98.98) |
| 22:21134067 | rs116401176 | V>A | A:137 | (21.48, 56.03, 111.82) |
| 22:21134072 | I>V | A:139 | (20.66, 53.29, 106.37) | |
| 22:21134078 | T>A | A:141 | (16.15, 56.50, 109.60) | |
| 22:21134085 | M>T | A:143 | (14.18, 52.08, 105.15) | |
| 22:21134086 | rs374297570 | M>I | A:143 | (14.18, 52.08, 105.15) |
| 22:21134094 | rs367748211 | I>T | A:146 | (10.11, 54.62, 102.86) |
| 22:21134097 | S>F | A:147 | (7.70, 52.46, 105.78) | |
| 22:21134100 | L>S | A:148 | (5.43, 55.90, 106.74) | |
| 22:21134117 | T>P | A:154 | (6.70, 46.06, 99.93) | |
| 22:21134126 | rs371947168 | Q>E | A:157 | (10.44, 42.65, 101.96) |
| 22:21134130 | V>A | A:158 | (11.42, 46.77, 105.03) | |
| 22:21134136 | rs186996599 | S>L | A:160 | (12.09, 41.81, 108.20) |
| 22:21134141 | L>V | A:162 | (15.48, 46.91, 108.72) | |
| 22:21134143 | L>F | A:162 | (15.48, 46.91, 108.72) | |
| 22:21134165 | A>T | A:170 | (9.89, 42.32, 122.23) | |
| 22:21134187 | rs371866990 | T>M | A:177 | (3.70, 53.71, 116.38) |
| 22:21134198 | N>H | A:181 | (7.28, 57.51, 118.22) | |
| 22:21134201 | L>F | A:182 | (11.71, 55.56, 119.25) | |
| 22:21134217 | rs375270208 | T>I | A:187 | (16.25, 62.47, 114.86) |
| 22:21134222 | R>C | A:189 | (19.88, 62.97, 121.92) | |
| 22:21134223 | rs5907 | R>H | A:189 | (19.88, 62.97, 121.92) |
| 22:21134240 | F>L | A:195 | (24.99, 66.90, 122.61) | |
| 22:21134249 | T>A | A:198 | (30.16, 68.38, 113.76) | |
| 22:21134258 | S>A | A:201 | (22.27, 65.47, 107.90) | |
| 22:21134270 | L>F | A:205 | (12.41, 61.26, 99.91) | |
| 22:21134295 | I>N | A:213 | (3.70, 63.66, 97.23) | |
| 22:21134301 | L>P | A:215 | (-1.36, 65.03, 102.59) | |
| 22:21134306 | rs551137262 | F>L | A:217 | (4.64, 59.98, 102.84) |
| 22:21134310 | rs1042435 | K>R | A:218 | (4.65, 65.72, 102.30) |
| 22:21134349 | rs139434064 | I>T | A:231 | (8.53, 68.37, 94.70) |
| 22:21134390 | N>H | A:245 | (23.29, 76.26, 96.42) | |
| 22:21134412 | K>R | A:252 | (26.34, 76.34, 108.23) | |
| 22:21134429 | A>T | A:258 | (23.67, 66.40, 96.82) | |
| 22:21134430 | rs115355953 | A>V | A:258 | (23.67, 66.40, 96.82) |
| 22:21134435 | E>K | A:260 | (25.63, 66.68, 91.31) | |
| 22:21134442 | rs145370736 | I>T | A:262 | (21.08, 62.18, 89.45) |
| 22:21134448 | rs375194591 | P>R | A:264 | (17.69, 62.68, 83.97) |
| 22:21134463 | M>T | A:269 | (16.25, 59.83, 95.24) | |
| 22:21138281 | P>L | A:285 | (49.74, 65.66, 121.13) | |
| 22:21138283 | V>M | A:286 | (50.67, 68.40, 117.45) | |
| 22:21138291 | M>I | A:288 | (53.57, 63.04, 119.53) | |
| 22:21138292 | T>A | A:289 | (52.20, 63.95, 114.58) | |
| 22:21138295 | H>Y | A:290 | (54.91, 60.06, 113.97) | |
| 22:21138310 | rs181138395 | R>W | A:295 | (52.30, 46.46, 107.65) |
| 22:21138341 | S>F | A:305 | (50.17, 60.86, 109.35) | |
| 22:21138343 | rs377527021 | M>V | A:306 | (50.74, 58.00, 113.19) |
| 22:21138344 | M>T | A:306 | (50.74, 58.00, 113.19) | |
| 22:21138365 | rs199641999 | F>C | A:313 | (43.01, 55.47, 126.58) |
| 22:21138370 | rs370736969 COSM1032354 COSM1032355 |
A>T | A:315 | (41.14, 47.96, 126.22) |
| 22:21138382 | Q>K | A:319 | (41.86, 35.33, 122.25) | |
| 22:21138397 | D>N | A:324 | (43.44, 44.00, 119.51) | |
| 22:21138418 | rs141555645 | V>M | A:331 | (33.21, 65.77, 123.33) |
| 22:21138419 | V>A | A:331 | (33.21, 65.77, 123.33) | |
| 22:21138424 | G>C | A:333 | (28.91, 60.85, 124.29) | |
| 22:21138428 | rs147046923 | I>N | A:334 | (30.42, 60.28, 121.05) |
| 22:21138432 | S>R | A:335 | (32.71, 56.43, 121.22) | |
| 22:21138440 | rs199499153 | I>T | A:338 | (39.64, 51.09, 117.25) |
| 22:21138453 | H>Q | A:342 | (45.61, 39.70, 116.64) | |
| 22:21138478 | E>K | A:351 | (34.44, 41.89, 108.06) | |
| 22:21138494 | COSM444730 COSM444731 |
P>R | A:356 | (25.32, 43.06, 118.35) |
| 22:21138496 | rs17853377 | R>W | A:357 | (25.61, 38.46, 121.64) |
| 22:21138497 | rs375640869 | R>Q | A:357 | (25.61, 38.46, 121.64) |
| 22:21138505 | rs376828409 | E>K | A:360 | (27.43, 43.75, 125.10) |
| 22:21138509 | rs371383837 | R>K | A:361 | (32.39, 39.40, 123.51) |
| 22:21138511 | W>R | A:362 | (34.51, 43.34, 121.14) | |
| 22:21138529 | N>D | A:368 | (41.02, 51.99, 132.23) | |
| 22:21140297 | rs368023291 COSM3992034 COSM3992035 |
R>Q | A:371 | (46.71, 51.99, 127.23) |
| 22:21140309 | L>P | A:375 | (45.19, 56.83, 115.39) | |
| 22:21140329 | K>E | A:382 | (33.07, 57.01, 100.56) | |
| 22:21140330 | K>R | A:382 | (33.07, 57.01, 100.56) | |
| 22:21140348 | E>V | A:388 | (21.86, 46.39, 93.97) | |
| 22:21140363 | M>T | A:393 | (19.75, 42.34, 102.66) | |
| 22:21140375 | rs138599284 | M>T | A:397 | (8.56, 44.21, 96.46) |
| 22:21140378 | L>Q | A:398 | (11.09, 49.19, 97.56) | |
| 22:21140393 | G>A | A:403 | (5.51, 47.66, 93.97) | |
| 22:21140401 | A>T | A:406 | (0.23, 53.47, 97.82) | |
| 22:21140410 | S>A | A:409 | (1.74, 57.89, 94.92) | |
| 22:21140415 | D>E | A:410 | (-2.14, 57.65, 93.67) | |
| 22:21140420 | COSM1535114 COSM1535115 |
R>K | A:412 | (3.10, 51.70, 90.00) |
| 22:21140431 | D>N | A:416 | (16.50, 52.84, 90.67) | |
| 22:21141174 | rs141717277 | Q>H | A:421 | (27.75, 61.28, 101.07) |
| 22:21141179 | rs5904 | T>M | A:423 | (32.17, 62.83, 105.42) |
| 22:21141187 | rs137958110 | V>L | A:426 | (40.26, 61.67, 112.03) |
| 22:21141188 | V>A | A:426 | (40.26, 61.67, 112.03) | |
| 22:21141197 | E>A | A:429 | (41.25, 68.74, 116.38) | |
| 22:21141200 | G>D | A:430 | (40.70, 68.35, 121.29) | |
| 22:21141214 | T>P | A:435 | (49.39, 64.58, 132.59) | |
| 22:21141218 | V>A | A:436 | (53.23, 65.25, 130.39) | |
| 22:21141224 | COSM1032360 COSM1032361 |
T>M | A:438 | (57.93, 61.48, 133.31) |
| 22:21141226 | V>M | A:439 | (59.06, 59.19, 136.60) | |
| 22:21141236 | M>K | A:442 | (62.12, 52.25, 132.71) | |
| 22:21141257 | rs201913067 COSM478752 COSM478753 |
R>H | A:449 | (53.35, 51.61, 123.03) |
| 22:21141263 | rs200605188 | T>I | A:451 | (49.84, 50.24, 117.26) |
| 22:21141265 | rs201814439 | V>I | A:452 | (46.41, 51.67, 114.66) |
| 22:21141268 | D>Y | A:453 | (50.13, 49.56, 112.26) | |
| 22:21141271 | rs552213670 | R>S | A:454 | (47.82, 46.46, 111.71) |
| 22:21141272 | R>H | A:454 | (47.82, 46.46, 111.71) | |
| 22:21141277 | F>L | A:456 | (41.42, 50.51, 111.20) | |
| 22:21141286 | L>F | A:459 | (32.39, 50.87, 115.58) | |
| 22:21141292 | Y>H | A:461 | (28.39, 52.51, 119.15) | |
| 22:21141298 | H>N | A:463 | (26.93, 55.54, 126.35) | |
| 22:21141301 | R>C | A:464 | (21.09, 58.62, 127.07) | |
| 22:21141302 | R>H | A:464 | (21.09, 58.62, 127.07) | |
| 22:21141305 | T>S | A:465 | (21.11, 55.59, 122.59) | |
| 22:21141310 | C>S | A:467 | (23.50, 54.68, 118.30) | |
| 22:21141322 | M>V | A:471 | (30.44, 51.06, 110.21) | |
| 22:21141324 | M>I | A:471 | (30.44, 51.06, 110.21) | |
| 22:21141344 | S>T | A:478 | (46.43, 57.53, 102.08) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 22:21134039 | COSM3713621 | T>P | A:128 | (40.04, 44.06, 100.06) |
| 22:21134445 | COSM3681384 | D>A | A:263 | (19.04, 59.63, 85.45) |
| 22:21138322 | COSM3708150 | R>G | A:299 | (52.64, 41.65, 100.03) |
| 22:21138334 | COSM3708153 | K>Q | A:303 | (55.50, 56.33, 105.69) |
| 22:21140434 | COSM1682126 | L>M | A:417 | (19.26, 56.38, 93.85) |
| 22:21141193 | COSM725531 | E>K | A:428 | (45.37, 66.00, 115.90) |
| 22:21141329 | COSM1032364 | R>T | A:473 | (37.31, 48.51, 105.36) |