General Structure Information
| PDB ID | 1imv |
| HGNC Gene Label(s) | SERPINF1 |
| Structure Name | 2.85 a crystal structure of pedf |
| Resolution | 2.85Å |
| Reference | AUTH M.SIMONOVIC,P.G.GETTINS,K.VOLZTITL CRYSTAL STRUCTURE OF HUMAN PEDF, A POTENT ANTI-ANGIOGENICTITL 2 AND NEURITE GROWTH-PROMOTING FACTOR.REF PROC.NATL.ACAD.SCI.USA V. 98 11131 2001REFN ISSN 0027-8424PMID 11562499DOI 10.1073/PNAS.211268598 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 375 |
| Number Of SNVs | 127 |
| Number Of Permutations | 30192 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.017 |
| p-value | 0.957 |
COSMIC
| Number Of Residues | 375 |
| Number Of SNVs | 3 |
| Number Of Permutations | 27 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.333 |
| p-value | 0.159 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 127 |
| Number Of COSMIC SNVs | 3 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.309 |
| p-value | 0.137 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 17:1673173 | A>P | A:18 | (31.87, 14.19, -2.99) | |
| 17:1673179 | rs149451759 | V>L | A:20 | (29.37, 16.99, -7.13) |
| 17:1673203 | K>Q | A:28 | (25.19, 26.81, -10.00) | |
| 17:1673212 | rs150899084 | V>M | A:31 | (30.50, 34.34, -4.98) |
| 17:1673224 | A>T | A:35 | (30.50, 31.98, 0.95) | |
| 17:1673240 | N>S | A:40 | (30.41, 26.26, 6.67) | |
| 17:1673245 | G>S | A:42 | (32.33, 29.87, 11.10) | |
| 17:1673254 | L>M | A:45 | (35.00, 29.28, 15.14) | |
| 17:1673255 | L>P | A:45 | (35.00, 29.28, 15.14) | |
| 17:1673260 | COSM3988799 | R>W | A:47 | (29.67, 24.76, 15.83) |
| 17:1673261 | COSM252806 | R>Q | A:47 | (29.67, 24.76, 15.83) |
| 17:1673263 | rs143827025 | V>L | A:48 | (34.66, 25.57, 19.07) |
| 17:1673276 | rs1136287 | T>M | A:52 | (35.34, 27.49, 24.70) |
| 17:1673285 | rs149768643 | T>M | A:55 | (28.31, 31.11, 30.96) |
| 17:1673293 | COSM4064257 | V>M | A:58 | (29.52, 34.36, 21.56) |
| 17:1673306 | P>L | A:62 | (33.91, 34.69, 11.23) | |
| 17:1673308 | L>F | A:63 | (34.80, 37.08, 6.90) | |
| 17:1673311 | S>C | A:64 | (38.00, 38.40, 9.64) | |
| 17:1673321 | T>M | A:67 | (40.36, 36.50, 5.08) | |
| 17:1673330 | rs144853088 | S>L | A:70 | (43.15, 32.52, 2.61) |
| 17:1673333 | A>G | A:71 | (46.00, 34.90, 2.74) | |
| 17:1673339 | rs369973630 | S>L | A:73 | (47.35, 30.17, 1.84) |
| 17:1674326 | COSM76384 | A>V | A:76 | (52.03, 27.94, 1.29) |
| 17:1674335 | COSM3818937 | R>Q | A:79 | (50.82, 20.30, 2.97) |
| 17:1674340 | E>Q | A:81 | (47.90, 25.13, 0.41) | |
| 17:1674350 | I>T | A:84 | (44.63, 26.16, 5.29) | |
| 17:1674355 | R>W | A:86 | (39.86, 19.59, 5.22) | |
| 17:1674370 | D>N | A:91 | (38.08, 20.38, -0.28) | |
| 17:1674375 | L>F | A:92 | (34.11, 20.61, -1.28) | |
| 17:1674379 | S>G | A:94 | (35.17, 22.59, -8.71) | |
| 17:1674383 | S>T | A:95 | (36.91, 26.49, -8.98) | |
| 17:1674398 | G>V | A:100 | (39.49, 36.05, -7.17) | |
| 17:1674404 | Y>C | A:102 | (38.00, 35.77, -0.44) | |
| 17:1674422 | T>M | A:108 | (30.01, 42.38, -2.27) | |
| 17:1674425 | V>A | A:109 | (30.37, 42.12, 1.96) | |
| 17:1674430 | A>T | A:111 | (29.92, 47.84, 0.58) | |
| 17:1674431 | rs148005190 | A>D | A:111 | (29.92, 47.84, 0.58) |
| 17:1674434 | rs1804145 | P>R | A:112 | (29.09, 51.22, 1.23) |
| 17:1674445 | rs562308050 | L>F | A:116 | (30.44, 45.00, 7.41) |
| 17:1674448 | rs142705862 | K>E | A:117 | (33.57, 48.44, 8.35) |
| 17:1674452 | S>N | A:118 | (36.13, 43.56, 7.51) | |
| 17:1674466 | rs548418598 | V>I | A:123 | (51.77, 40.23, 11.82) |
| 17:1674467 | rs376997671 | V>A | A:123 | (51.77, 40.23, 11.82) |
| 17:1674478 | rs527724800 | K>Q | A:127 | (63.68, 41.23, 10.74) |
| 17:1675172 | rs555882903 | R>H | A:129 | (63.77, 38.97, 2.92) |
| 17:1675174 | rs62640873 | I>V | A:130 | (58.73, 39.08, 3.05) |
| 17:1675180 | rs542035380 COSM3983282 |
S>P | A:132 | (57.86, 39.67, -3.68) |
| 17:1675181 | COSM3983283 | S>C | A:132 | (57.86, 39.67, -3.68) |
| 17:1675190 | V>G | A:135 | (53.49, 40.71, -1.31) | |
| 17:1675208 | S>L | A:141 | (43.50, 39.15, -4.00) | |
| 17:1675213 | G>R | A:143 | (44.34, 44.16, -0.01) | |
| 17:1675223 | rs368560431 | P>L | A:146 | (52.55, 42.43, 4.92) |
| 17:1675235 | T>M | A:150 | (59.78, 47.06, 15.45) | |
| 17:1675241 | N>S | A:152 | (59.41, 48.73, 20.53) | |
| 17:1675246 | R>C | A:154 | (56.16, 51.43, 24.49) | |
| 17:1675247 | R>H | A:154 | (56.16, 51.43, 24.49) | |
| 17:1675252 | rs77671583 | D>N | A:156 | (54.98, 47.12, 17.64) |
| 17:1675265 | I>N | A:160 | (48.33, 47.07, 15.72) | |
| 17:1675283 | A>V | A:166 | (41.70, 53.37, 10.02) | |
| 17:1675294 | rs146337776 | G>R | A:170 | (36.79, 54.29, 15.15) |
| 17:1675303 | rs144219428 | A>T | A:173 | (38.56, 49.56, 21.27) |
| 17:1675306 | R>G | A:174 | (41.93, 50.65, 21.71) | |
| 17:1675313 | rs1804148 | T>R | A:176 | (45.66, 47.35, 26.31) |
| 17:1675322 | I>N | A:179 | (52.62, 42.48, 21.59) | |
| 17:1675324 | P>A | A:180 | (52.85, 38.61, 22.28) | |
| 17:1675325 | P>R | A:180 | (52.85, 38.61, 22.28) | |
| 17:1675332 | rs200661635 | E>D | A:182 | (56.39, 35.20, 21.24) |
| 17:1675351 | G>S | A:189 | (40.43, 40.24, 12.93) | |
| 17:1675358 | A>V | A:191 | (34.86, 43.77, 12.80) | |
| 17:1675368 | K>N | A:194 | (25.28, 50.67, 13.52) | |
| 17:1678371 | F>L | A:201 | (11.91, 49.36, 16.11) | |
| 17:1678375 | S>A | A:203 | (11.70, 55.63, 20.65) | |
| 17:1678379 | R>T | A:204 | (7.33, 57.29, 21.21) | |
| 17:1678388 | S>F | A:207 | (10.43, 49.41, 27.72) | |
| 17:1678393 | rs531766837 | E>K | A:209 | (10.44, 44.89, 29.87) |
| 17:1678406 | L>W | A:213 | (19.27, 35.39, 32.44) | |
| 17:1678421 | T>I | A:218 | (15.06, 37.89, 36.07) | |
| 17:1678424 | rs375842984 | V>G | A:219 | (17.05, 40.85, 34.22) |
| 17:1678427 | R>T | A:220 | (13.59, 45.20, 34.06) | |
| 17:1678436 | rs371366860 | M>K | A:223 | (12.91, 45.19, 25.25) |
| 17:1678442 | rs374677194 | S>L | A:225 | (8.29, 47.40, 20.36) |
| 17:1678444 | D>H | A:226 | (6.49, 46.32, 16.36) | |
| 17:1678456 | V>L | A:230 | (6.45, 42.51, 8.81) | |
| 17:1678462 | R>C | A:232 | (10.58, 35.37, 6.15) | |
| 17:1678463 | R>H | A:232 | (10.58, 35.37, 6.15) | |
| 17:1678465 | Y>H | A:233 | (7.35, 32.17, 12.44) | |
| 17:1678468 | G>S | A:234 | (9.20, 29.57, 11.88) | |
| 17:1678480 | D>Y | A:238 | (12.97, 18.93, 14.96) | |
| 17:1678486 | S>G | A:240 | (12.60, 23.27, 19.89) | |
| 17:1678490 | C>S | A:241 | (12.97, 26.71, 17.52) | |
| 17:1679847 | rs369314029 | G>R | A:250 | (21.66, 46.39, 2.07) |
| 17:1679851 | S>T | A:251 | (20.76, 43.26, 1.07) | |
| 17:1679865 | rs145833645 | F>I | A:256 | (16.36, 36.65, 15.36) |
| 17:1679874 | P>S | A:259 | (14.43, 28.85, 22.32) | |
| 17:1679904 | I>L | A:269 | (20.00, 25.12, 17.57) | |
| 17:1679925 | E>K | A:276 | (24.20, 24.37, 3.38) | |
| 17:1679931 | I>V | A:278 | (20.73, 29.07, 6.80) | |
| 17:1679941 | rs112099952 | I>T | A:281 | (15.42, 28.05, 7.10) |
| 17:1679952 | rs146939364 | L>V | A:285 | (10.80, 31.35, 6.34) |
| 17:1679962 | V>A | A:288 | (3.71, 36.64, 9.51) | |
| 17:1679968 | rs190292375 | A>V | A:290 | (4.11, 40.12, 14.89) |
| 17:1680003 | E>K | A:302 | (39.61, 42.39, 22.64) | |
| 17:1680009 | E>K | A:304 | (43.78, 34.60, 21.33) | |
| 17:1680020 | K>N | A:307 | (43.11, 28.12, 22.79) | |
| 17:1680024 | L>V | A:309 | (41.82, 27.68, 15.15) | |
| 17:1680030 | E>K | A:311 | (39.87, 22.30, 19.20) | |
| 17:1680033 | M>V | A:312 | (39.20, 23.76, 13.90) | |
| 17:1680034 | rs150696039 | M>T | A:312 | (39.20, 23.76, 13.90) |
| 17:1680035 | rs373039314 | M>I | A:312 | (39.20, 23.76, 13.90) |
| 17:1680487 | rs138875154 | Q>R | A:315 | (47.66, 22.11, 16.03) |
| 17:1680490 | rs142170837 | S>F | A:316 | (50.02, 21.87, 11.55) |
| 17:1680494 | L>F | A:317 | (49.39, 25.82, 11.14) | |
| 17:1680498 | D>N | A:319 | (54.26, 22.28, 14.73) | |
| 17:1680500 | D>E | A:319 | (54.26, 22.28, 14.73) | |
| 17:1680504 | P>T | A:321 | (54.63, 25.04, 9.43) | |
| 17:1680507 | D>H | A:322 | (56.12, 24.88, 4.48) | |
| 17:1680523 | rs146326833 | T>K | A:327 | (60.43, 33.04, 4.46) |
| 17:1680540 | L>M | A:333 | (50.31, 30.16, 13.35) | |
| 17:1680547 | Q>R | A:335 | (49.55, 34.50, 18.05) | |
| 17:1680549 | V>M | A:336 | (44.63, 34.21, 15.87) | |
| 17:1680558 | rs371206627 | R>W | A:339 | (40.25, 43.68, 17.76) |
| 17:1680559 | rs144198046 | R>Q | A:339 | (40.25, 43.68, 17.76) |
| 17:1680562 | rs146075681 | A>V | A:340 | (34.34, 42.70, 17.44) |
| 17:1680568 | F>S | A:342 | (26.55, 43.69, 16.52) | |
| 17:1680571 | E>A | A:343 | (25.25, 48.81, 17.66) | |
| 17:1680589 | rs368630571 | A>V | A:349 | (14.24, 53.61, 6.98) |
| 17:1680636 | P>S | A:365 | (-2.10, 34.63, 15.79) | |
| 17:1680637 | P>L | A:365 | (-2.10, 34.63, 15.79) | |
| 17:1680654 | rs201113182 | N>Y | A:371 | (12.22, 37.23, 26.69) |
| 17:1680660 | rs563254260 | P>A | A:373 | (18.32, 32.89, 26.00) |
| 17:1680672 | rs9809 | V>I | A:377 | (22.63, 34.96, 11.93) |
| 17:1680693 | G>R | A:384 | (25.11, 34.45, 2.14) | |
| 17:1680696 | COSM1381155 | A>T | A:385 | (27.44, 35.64, 3.92) |
| 17:1680702 | L>F | A:387 | (28.38, 39.11, 7.90) | |
| 17:1680709 | rs369156271 | I>T | A:389 | (27.39, 34.61, 15.01) |
| 17:1680710 | I>M | A:389 | (27.39, 34.61, 15.01) | |
| 17:1680712 | G>D | A:390 | (25.32, 35.21, 18.29) | |
| 17:1680721 | rs375149633 | L>P | A:393 | (23.44, 34.12, 27.48) |
| 17:1680723 | D>N | A:394 | (23.21, 39.21, 29.27) | |
| 17:1680727 | P>L | A:395 | (21.22, 41.47, 27.04) | |
| 17:1680733 | rs369948749 | G>D | A:397 | (26.60, 42.36, 28.38) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 17:1673176 | COSM3712257 | L>M | A:19 | (33.90, 16.39, -5.81) |
| 17:1674326 | COSM76384 | A>V | A:76 | (52.03, 27.94, 1.29) |
| 17:1674335 | COSM3818937 | R>Q | A:79 | (50.82, 20.30, 2.97) |