General Structure Information
| PDB ID | 1psi |
| HGNC Gene Label(s) | SERPINA1 |
| Structure Name | intact recombined alpha1-antitrypsin mutant phe 51 to leu |
| Resolution | 2.92Å |
| Reference | AUTH P.R.ELLIOTT,D.A.LOMAS,R.W.CARRELL,J.P.ABRAHAMSTITL INHIBITORY CONFORMATION OF THE REACTIVE LOOP OFTITL 2 ALPHA 1-ANTITRYPSIN.REF NAT.STRUCT.BIOL. V. 3 676 1996REFN ISSN 1072-8368PMID 8756325DOI 10.1038/NSB0896-676 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 371 |
| Number Of SNVs | 115 |
| Number Of Permutations | 27820 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | 0.15 |
| p-value | 0.105 |
ClinVar
| Number Of Residues | 371 |
| Number Of SNVs | 17 |
| Number Of Permutations | 3936 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.022 |
| p-value | 0.943 |
COSMIC
| Number Of Residues | 371 |
| Number Of SNVs | 11 |
| Number Of Permutations | 8993 |
| Optimal Distance Threshold | 11.0 |
| K Statistic | 0.018 |
| p-value | 0.9 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 115 |
| Number Of ClinVar SNVs | 16 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | -0.013 |
| p-value | 0.78 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 115 |
| Number Of COSMIC SNVs | 8 |
| Optimal Distance Threshold | 21.0 |
| K Statistic | -0.146 |
| p-value | 0.549 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:94849412 | A>P | A:31 | (8.31, 2.31, 13.18) | |
| 14:94849397 | S>G | A:36 | (9.31, -6.00, 12.01) | |
| 14:94849387 | R>H | A:39 | (4.90, -7.51, 14.05) | |
| 14:94849388 | rs28931570 | R>C | A:39 | (4.90, -7.51, 14.05) |
| 14:94849384 | Q>R | A:40 | (10.65, -11.67, 14.19) | |
| 14:94849381 | rs28931569 | L>P | A:41 | (10.97, -11.16, 18.75) |
| 14:94849378 | A>V | A:42 | (6.28, -12.33, 19.09) | |
| 14:94849374 | rs140744031 | H>Q | A:43 | (4.86, -14.76, 15.92) |
| 14:94849369 | rs199687431 COSM3769530 |
S>F | A:45 | (9.21, -15.84, 21.38) |
| 14:94849364 | rs11575873 | S>R | A:47 | (6.09, -16.92, 27.12) |
| 14:94849336 | S>N | A:56 | (19.86, 1.35, 19.51) | |
| 14:94849331 | rs113817720 | A>T | A:58 | (19.39, 1.42, 13.85) |
| 14:94849325 | rs111850950 | A>T | A:60 | (24.07, 0.98, 14.73) |
| 14:94849306 | rs564267551 | L>R | A:66 | (28.87, 4.63, 7.02) |
| 14:94849289 | rs376616935 | T>A | A:72 | (26.59, -5.38, 2.20) |
| 14:94849262 | N>D | A:81 | (12.17, -0.64, 7.30) | |
| 14:94849249 | rs199422213 COSM3982997 CM971177 |
T>M | A:85 | (14.25, 3.86, -4.38) |
| 14:94849240 | P>L | A:88 | (17.88, 10.24, 0.05) | |
| 14:94849227 | I>M | A:92 | (19.03, 7.69, 5.99) | |
| 14:94849201 | rs709932 | R>H | A:101 | (20.95, 17.85, 18.46) |
| 14:94849202 | R>C | A:101 | (20.95, 17.85, 18.46) | |
| 14:94849183 | D>A | A:107 | (13.57, 19.21, 25.36) | |
| 14:94849174 | L>P | A:110 | (15.91, 11.10, 29.62) | |
| 14:94849165 | T>S | A:113 | (22.51, 4.37, 29.62) | |
| 14:94849159 | G>A | A:115 | (25.52, 2.36, 23.29) | |
| 14:94849160 | rs11558261 | G>S | A:115 | (25.52, 2.36, 23.29) |
| 14:94849146 | F>L | A:119 | (34.66, -4.31, 20.20) | |
| 14:94849145 | rs374198121 | L>F | A:120 | (37.79, -3.77, 15.18) |
| 14:94849139 | rs537285845 | E>K | A:122 | (45.08, -5.45, 17.93) |
| 14:94849118 | rs369060615 | K>E | A:129 | (35.84, 8.93, 7.04) |
| 14:94849115 | rs576575224 | F>L | A:130 | (34.03, 3.66, 10.00) |
| 14:94849109 | E>K | A:132 | (36.25, 10.35, 10.79) | |
| 14:94849105 | D>G | A:133 | (31.93, 8.61, 10.32) | |
| 14:94849103 | V>F | A:134 | (31.98, 6.08, 14.53) | |
| 14:94849073 | T>A | A:144 | (41.33, -2.23, 18.67) | |
| 14:94849065 | N>K | A:146 | (43.79, -9.96, 20.83) | |
| 14:94849052 | rs149770048 | E>K | A:151 | (37.75, -15.64, 27.64) |
| 14:94849028 | D>N | A:159 | (34.55, -4.66, 31.02) | |
| 14:94849022 | rs147247134 | V>M | A:161 | (28.72, -2.68, 28.67) |
| 14:94849015 | K>T | A:163 | (32.75, 1.50, 31.90) | |
| 14:94849013 | G>S | A:164 | (28.35, 2.14, 30.94) | |
| 14:94848988 | rs368433503 | L>S | A:172 | (26.30, -9.04, 27.00) |
| 14:94848983 | K>E | A:174 | (27.64, -15.47, 27.80) | |
| 14:94848978 | E>D | A:175 | (30.01, -17.94, 23.50) | |
| 14:94848970 | R>K | A:178 | (34.83, -20.31, 16.30) | |
| 14:94848962 | V>I | A:181 | (37.66, -10.13, 13.41) | |
| 14:94848950 | V>L | A:185 | (28.10, -4.28, 21.78) | |
| 14:94848941 | I>V | A:188 | (19.25, 0.78, 26.00) | |
| 14:94848929 | G>C | A:192 | (12.43, 7.01, 34.52) | |
| 14:94847463 | rs368117781 | P>H | A:197 | (4.63, 10.73, 40.57) |
| 14:94847443 | rs199422208 COSM4053234 CM012639 |
E>K | A:204 | (-0.58, -2.64, 47.56) |
| 14:94847432 | rs145410420 | D>E | A:207 | (-3.19, -10.65, 41.43) |
| 14:94847428 | H>N | A:209 | (-4.42, -12.92, 35.19) | |
| 14:94847424 | V>E | A:210 | (0.06, -15.39, 33.54) | |
| 14:94847425 | rs374168370 | V>M | A:210 | (0.06, -15.39, 33.54) |
| 14:94847420 | D>E | A:211 | (-2.90, -17.74, 32.37) | |
| 14:94847418 | Q>R | A:212 | (-7.81, -16.32, 30.77) | |
| 14:94847419 | Q>K | A:212 | (-7.81, -16.32, 30.77) | |
| 14:94847415 | rs6647 | V>A | A:213 | (-6.86, -19.58, 34.85) |
| 14:94847412 | T>I | A:214 | (-3.07, -18.43, 36.11) | |
| 14:94847407 | rs72552401 | V>M | A:216 | (1.56, -13.96, 39.56) |
| 14:94847391 | M>T | A:221 | (2.49, 0.88, 40.65) | |
| 14:94847385 | rs544632177 COSM1371797 |
R>H | A:223 | (-2.15, 8.20, 39.93) |
| 14:94847386 | rs28929470 | R>C | A:223 | (-2.15, 8.20, 39.93) |
| 14:94847379 | rs577164283 | G>A | A:225 | (-6.36, 10.30, 38.14) |
| 14:94847380 | G>R | A:225 | (-6.36, 10.30, 38.14) | |
| 14:94847377 | M>V | A:226 | (-6.73, 13.24, 35.53) | |
| 14:94847373 | COSM3936678 | F>C | A:227 | (-4.19, 8.86, 34.52) |
| 14:94847371 | N>Y | A:228 | (-3.54, 10.27, 28.29) | |
| 14:94847368 | rs575123943 | I>L | A:229 | (-6.57, 6.52, 29.76) |
| 14:94847354 | rs376294932 | K>N | A:233 | (-13.10, -0.43, 20.67) |
| 14:94847343 | S>I | A:237 | (-6.99, -1.78, 23.80) | |
| 14:94847328 | M>T | A:242 | (2.74, 7.50, 31.53) | |
| 14:94847314 | N>D | A:247 | (12.60, 13.68, 26.36) | |
| 14:94847290 | P>T | A:255 | (-4.88, -6.27, 25.86) | |
| 14:94847286 | rs121912714 | D>V | A:256 | (-9.51, -6.27, 25.41) |
| 14:94847284 | E>K | A:257 | (-11.42, -11.16, 27.35) | |
| 14:94847281 | rs370923940 | G>R | A:258 | (-8.06, -11.89, 23.79) |
| 14:94847269 | rs149537225 | H>Y | A:262 | (-6.38, -7.02, 17.18) |
| 14:94847262 | rs17580 | E>V | A:264 | (0.70, -7.81, 18.71) |
| 14:94847260 | N>H | A:265 | (-1.45, -7.70, 14.35) | |
| 14:94847250 | T>I | A:268 | (-0.34, 1.79, 13.13) | |
| 14:94847251 | T>A | A:268 | (-0.34, 1.79, 13.13) | |
| 14:94847246 | rs141095970 | H>Q | A:269 | (3.61, 5.94, 12.76) |
| 14:94847245 | D>N | A:270 | (-1.44, 6.66, 11.99) | |
| 14:94847235 | T>N | A:273 | (0.91, 9.68, 15.76) | |
| 14:94847230 | F>L | A:275 | (-2.94, 7.09, 20.59) | |
| 14:94847220 | rs377668175 | N>I | A:278 | (-4.21, 12.66, 22.87) |
| 14:94845944 | rs141620200 | A>S | A:284 | (-8.45, 6.88, 36.57) |
| 14:94845940 | S>N | A:285 | (-7.96, 3.88, 38.86) | |
| 14:94845935 | H>Y | A:287 | (-4.02, -0.52, 39.32) | |
| 14:94845930 | L>F | A:288 | (1.58, 0.38, 36.40) | |
| 14:94845929 | P>S | A:289 | (3.21, -2.87, 37.01) | |
| 14:94845920 | S>T | A:292 | (13.12, -4.72, 36.03) | |
| 14:94845908 | T>A | A:296 | (19.15, -10.22, 25.60) | |
| 14:94845890 | rs139964603 | V>I | A:302 | (17.05, -10.76, 14.83) |
| 14:94845851 | COSM315081 COSM1707816 |
G>W | A:315 | (30.82, -11.36, 2.02) |
| 14:94845835 | G>V | A:320 | (35.33, 1.11, 5.16) | |
| 14:94845836 | rs367797069 COSM1477872 |
G>R | A:320 | (35.33, 1.11, 5.16) |
| 14:94845833 | V>F | A:321 | (36.03, -0.86, 8.03) | |
| 14:94845817 | P>L | A:326 | (39.27, -10.07, 5.01) | |
| 14:94845818 | rs377739083 | P>S | A:326 | (39.27, -10.07, 5.01) |
| 14:94845805 | rs201788603 COSM136983 |
S>F | A:330 | (31.12, -12.09, 14.08) |
| 14:94844974 | rs373630097 COSM4053232 CM109803 |
V>M | A:333 | (24.76, -8.27, 21.04) |
| 14:94844968 | rs200945035 COSM1740068 CM083102 |
K>E | A:335 | (21.00, -6.21, 27.25) |
| 14:94844965 | rs1802959 | A>P | A:336 | (17.49, -3.94, 26.92) |
| 14:94844961 | rs1131139 COSM4053231 |
V>G | A:337 | (17.46, -2.49, 30.65) |
| 14:94844953 | rs201318727 | I>V | A:340 | (9.03, 0.94, 35.50) |
| 14:94844947 | rs28929474 | E>K | A:342 | (7.02, 4.38, 42.37) |
| 14:94844943 | K>T | A:343 | (9.55, 9.82, 40.28) | |
| 14:94844940 | rs551595739 | G>E | A:344 | (12.97, 7.06, 40.19) |
| 14:94844926 | rs12077 | G>R | A:349 | (9.10, 16.16, 43.17) |
| 14:94844923 | A>T | A:350 | (7.21, 18.28, 42.09) | |
| 14:94844920 | M>L | A:351 | (4.40, 18.50, 44.34) | |
| 14:94844908 | A>T | A:355 | (-9.21, 17.84, 38.79) | |
| 14:94844897 | rs372140596 | M>I | A:358 | (-18.01, 13.79, 41.89) |
| 14:94844896 | S>A | A:359 | (-16.79, 9.96, 39.12) | |
| 14:94844866 | rs61761869 | P>S | A:369 | (-0.48, -9.78, 29.25) |
| 14:94844847 | I>T | A:375 | (7.90, 7.73, 22.18) | |
| 14:94844843 | rs1303 | E>D | A:376 | (11.78, 11.78, 21.91) |
| 14:94844835 | T>S | A:379 | (11.94, 12.53, 17.42) | |
| 14:94844832 | K>R | A:380 | (7.39, 11.43, 17.43) | |
| 14:94844827 | P>T | A:382 | (11.01, 4.22, 18.44) | |
| 14:94844818 | rs149800596 | M>V | A:385 | (8.55, -2.17, 21.36) |
| 14:94844793 | rs200467663 | Q>L | A:393 | (10.86, -12.90, 32.61) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:94849388 | rs28931570 | R>C | A:39 | (4.90, -7.51, 14.05) |
| 14:94849381 | rs28931569 | L>P | A:41 | (10.97, -11.16, 18.75) |
| 14:94849345 | rs55819880 | S>F | A:53 | (16.05, -0.16, 20.97) |
| 14:94849303 | rs28931568 | G>E | A:67 | (31.42, 0.60, 5.86) |
| 14:94849249 | rs199422213 | T>M | A:85 | (14.25, 3.86, -4.38) |
| 14:94849228 | rs28931572 | I>N | A:92 | (19.03, 7.69, 5.99) |
| 14:94849160 | rs11558261 | G>S | A:115 | (25.52, 2.36, 23.29) |
| 14:94847443 | rs199422208 | E>K | A:204 | (-0.58, -2.64, 47.56) |
| 14:94847380 | rs764220898 | G>R | A:225 | (-6.36, 10.30, 38.14) |
| 14:94847286 | rs121912714 | D>V | A:256 | (-9.51, -6.27, 25.41) |
| 14:94847262 | rs17580 | E>V | A:264 | (0.70, -7.81, 18.71) |
| 14:94844965 | rs1802959 | A>T | A:336 | (17.49, -3.94, 26.92) |
| 14:94844947 | rs28929474 | E>K | A:342 | (7.02, 4.38, 42.37) |
| 14:94844912 | rs28929473 | L>F | A:353 | (-2.91, 19.58, 42.47) |
| 14:94844898 | rs121912713 | M>R | A:358 | (-18.01, 13.79, 41.89) |
| 14:94844884 | rs121912712 | E>K | A:363 | (-10.13, -0.26, 38.55) |
| 14:94844865 | rs199422209 | P>L | A:369 | (-0.48, -9.78, 29.25) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:94849388 | COSM959169 | R>C | A:39 | (4.90, -7.51, 14.05) |
| 14:94849369 | COSM3769530 | S>Y | A:45 | (9.21, -15.84, 21.38) |
| 14:94849309 | COSM1707818 | S>F | A:65 | (26.33, 1.62, 6.61) |
| 14:94849201 | COSM3736121 | R>H | A:101 | (20.95, 17.85, 18.46) |
| 14:94849066 | COSM3711635 | N>T | A:146 | (43.79, -9.96, 20.83) |
| 14:94849012 | COSM144436 | G>D | A:164 | (28.35, 2.14, 30.94) |
| 14:94847385 | COSM1371797 | R>H | A:223 | (-2.15, 8.20, 39.93) |
| 14:94847386 | COSM1749042 | R>C | A:223 | (-2.15, 8.20, 39.93) |
| 14:94847271 | COSM1678218 | Q>P | A:261 | (-2.13, -11.50, 17.88) |
| 14:94844962 | COSM1608098 | V>M | A:337 | (17.46, -2.49, 30.65) |
| 14:94844843 | COSM147838 | E>D | A:376 | (11.78, 11.78, 21.91) |
| 14:94844815 | COSM3499313 | G>R | A:386 | (7.26, -4.29, 24.31) |