General Structure Information
| PDB ID | 2qqm |
| HGNC Gene Label(s) | NRP1 |
| Structure Name | crystal structure of the a2b1b2 domains from human neuropilin-1 |
| Resolution | 2.0Å |
| Reference | AUTH B.A.APPLETON,P.WU,J.MALONEY,J.YIN,W.C.LIANG,S.STAWICKI,AUTH 2 K.MORTARA,K.K.BOWMAN,J.M.ELLIOTT,W.DESMARAIS,J.F.BAZAN,AUTH 3 A.BAGRI,M.TESSIER-LAVIGNE,A.W.KOCH,Y.WU,R.J.WATTS,C.WIESMANNTITL STRUCTURAL STUDIES OF NEUROPILIN/ANTIBODY COMPLEXES PROVIDETITL 2 INSIGHTS INTO SEMAPHORIN AND VEGF BINDINGREF EMBO J. V. 26 4902 2007REFN ISSN 0261-4189PMID 17989695DOI 10.1038/SJ.EMBOJ.7601906 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 436 |
| Number Of SNVs | 125 |
| Number Of Permutations | 23474 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.007 |
| p-value | 0.883 |
COSMIC
| Number Of Residues | 436 |
| Number Of SNVs | 5 |
| Number Of Permutations | 302 |
| Optimal Distance Threshold | 19.0 |
| K Statistic | 0.1 |
| p-value | 0.925 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 125 |
| Number Of COSMIC SNVs | 4 |
| Optimal Distance Threshold | 30.0 |
| K Statistic | -0.344 |
| p-value | 0.392 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:33552793 | C>R | A:147 | (-15.24, 8.08, 3.52) | |
| 10:33552772 | P>S | A:154 | (3.38, 15.08, 10.99) | |
| 10:33552767 | rs559961807 | S>R | A:155 | (-0.04, 16.69, 11.78) |
| 10:33552768 | S>N | A:155 | (-0.04, 16.69, 11.78) | |
| 10:33552763 | V>M | A:157 | (-7.69, 16.66, 11.57) | |
| 10:33552756 | rs138480424 | K>R | A:159 | (-13.64, 15.34, 9.93) |
| 10:33552757 | K>E | A:159 | (-13.64, 15.34, 9.93) | |
| 10:33552748 | G>R | A:162 | (-19.49, 16.68, 7.86) | |
| 10:33552718 | E>Q | A:172 | (-17.35, 0.64, 6.02) | |
| 10:33552706 | I>V | A:176 | (-4.97, 4.64, 7.75) | |
| 10:33552696 | rs7079053 | V>A | A:179 | (4.05, 7.39, 10.99) |
| 10:33552689 | COSM40396 | K>N | A:181 | (10.65, 8.95, 11.32) |
| 10:33552691 | K>E | A:181 | (10.65, 8.95, 11.32) | |
| 10:33552687 | M>T | A:182 | (8.36, 4.03, 11.69) | |
| 10:33552675 | I>N | A:186 | (-0.70, 11.17, 20.18) | |
| 10:33552676 | I>F | A:186 | (-0.70, 11.17, 20.18) | |
| 10:33552646 | P>A | A:196 | (-26.40, 5.61, 21.75) | |
| 10:33552624 | G>A | A:203 | (-24.40, -7.82, 25.15) | |
| 10:33552612 | rs148308681 | R>H | A:207 | (-26.53, -2.86, 19.26) |
| 10:33552610 | Y>H | A:208 | (-27.51, 0.60, 17.43) | |
| 10:33552603 | R>Q | A:210 | (-19.10, 0.23, 15.13) | |
| 10:33552604 | R>W | A:210 | (-19.10, 0.23, 15.13) | |
| 10:33545394 | rs143227333 | P>T | A:222 | (-3.30, -4.11, 18.11) |
| 10:33545387 | I>T | A:224 | (-7.21, 0.46, 20.98) | |
| 10:33545388 | I>V | A:224 | (-7.21, 0.46, 20.98) | |
| 10:33545381 | rs201034499 | R>H | A:226 | (-16.48, -1.79, 19.91) |
| 10:33545382 | R>C | A:226 | (-16.48, -1.79, 19.91) | |
| 10:33545369 | Q>P | A:230 | (-21.74, 11.62, 24.44) | |
| 10:33545367 | K>E | A:231 | (-17.38, 6.66, 26.70) | |
| 10:33545339 | COSM917837 | S>L | A:240 | (2.75, 0.27, 15.25) |
| 10:33545333 | rs146442068 | I>S | A:242 | (0.08, 2.00, 11.54) |
| 10:33545325 | rs375021532 COSM162993 |
M>V | A:245 | (-9.99, 4.85, 12.90) |
| 10:33545312 | T>S | A:249 | (-23.01, 4.03, 10.25) | |
| 10:33545303 | A>V | A:252 | (-30.53, 5.08, 11.10) | |
| 10:33545264 | L>S | A:265 | (6.12, 11.52, 19.30) | |
| 10:33545258 | rs113722704 | S>N | A:267 | (13.56, 11.44, 19.15) |
| 10:33543084 | E>K | A:285 | (1.11, 11.16, 30.24) | |
| 10:33543080 | rs577020617 | I>S | A:286 | (-0.74, 7.57, 33.51) |
| 10:33543078 | H>N | A:287 | (-6.69, 8.06, 32.53) | |
| 10:33543074 | S>F | A:288 | (-7.07, 7.04, 36.31) | |
| 10:33543070 | D>E | A:289 | (-9.13, 4.33, 33.66) | |
| 10:33543072 | D>N | A:289 | (-9.13, 4.33, 33.66) | |
| 10:33543066 | I>F | A:291 | (-4.40, 3.48, 38.09) | |
| 10:33543053 | S>C | A:295 | (-8.13, -3.21, 47.50) | |
| 10:33543041 | T>I | A:299 | (-13.17, 7.19, 48.26) | |
| 10:33543024 | R>C | A:305 | (-6.40, 9.83, 46.83) | |
| 10:33543017 | R>L | A:307 | (-1.69, 10.13, 40.06) | |
| 10:33543018 | R>C | A:307 | (-1.69, 10.13, 40.06) | |
| 10:33543006 | P>S | A:311 | (-2.57, 16.31, 47.58) | |
| 10:33543002 | E>G | A:312 | (-5.93, 14.53, 50.34) | |
| 10:33542985 | G>R | A:318 | (-8.42, -2.96, 53.08) | |
| 10:33515198 | R>H | A:334 | (6.46, 2.48, 26.91) | |
| 10:33515199 | COSM917835 | R>C | A:334 | (6.46, 2.48, 26.91) |
| 10:33515193 | V>L | A:336 | (10.69, 0.20, 32.94) | |
| 10:33515190 | rs367928513 | T>A | A:337 | (14.34, 1.89, 34.65) |
| 10:33515181 | rs553769055 COSM917834 |
G>R | A:340 | (8.66, 5.64, 42.97) |
| 10:33515169 | COSM4013917 COSM4013919 COSM4013918 COSM4013920 |
A>T | A:344 | (0.87, 9.04, 53.58) |
| 10:33515165 | I>T | A:345 | (0.05, 12.14, 56.21) | |
| 10:33515158 | K>N | A:347 | (-6.60, 15.81, 55.95) | |
| 10:33515147 | K>R | A:351 | (-2.32, 8.10, 62.06) | |
| 10:33515136 | rs571665973 | V>I | A:355 | (5.79, 1.02, 51.96) |
| 10:33515129 | rs374630762 | T>N | A:357 | (9.86, -3.01, 51.51) |
| 10:33515123 | rs149966206 | K>M | A:359 | (8.01, -7.95, 46.21) |
| 10:33515118 | D>H | A:361 | (5.20, -8.38, 39.46) | |
| 10:33515103 | rs370551432 COSM1702246 COSM1702248 COSM1702247 |
G>R | A:366 | (-1.85, -8.53, 32.47) |
| 10:33515090 | rs199673539 | I>T | A:370 | (7.40, -12.14, 35.49) |
| 10:33515087 | rs530168426 | T>I | A:371 | (8.77, -11.53, 39.82) |
| 10:33515088 | T>A | A:371 | (8.77, -11.53, 39.82) | |
| 10:33515085 | I>V | A:372 | (11.82, -8.12, 39.34) | |
| 10:33515072 | COSM3415000 COSM3415002 COSM3415001 COSM3415003 |
N>S | A:376 | (16.35, -17.90, 41.95) |
| 10:33515064 | V>I | A:379 | (13.87, -7.67, 44.06) | |
| 10:33510777 | N>K | A:384 | (9.51, 5.06, 51.92) | |
| 10:33510776 | T>P | A:385 | (11.89, 6.22, 55.95) | |
| 10:33510767 | T>S | A:388 | (6.86, 13.07, 52.80) | |
| 10:33510761 | V>I | A:390 | (10.64, 10.62, 46.76) | |
| 10:33510730 | I>T | A:400 | (10.49, -4.36, 27.50) | |
| 10:33510724 | COSM3437401 COSM3437403 COSM3437402 COSM3437404 |
R>Q | A:402 | (0.74, -2.58, 28.57) |
| 10:33510715 | R>Q | A:405 | (0.83, -6.16, 39.99) | |
| 10:33510703 | A>E | A:409 | (6.46, -6.23, 52.13) | |
| 10:33510704 | A>T | A:409 | (6.46, -6.23, 52.13) | |
| 10:33510685 | I>T | A:415 | (-0.42, -0.51, 52.98) | |
| 10:33510686 | I>V | A:415 | (-0.42, -0.51, 52.98) | |
| 10:33510667 | COSM3368021 COSM3368023 COSM3368022 COSM3368024 |
V>A | A:421 | (6.90, 4.64, 36.63) |
| 10:33510652 | I>T | A:426 | (11.08, 2.09, 22.41) | |
| 10:33510649 | T>R | A:427 | (10.46, 6.11, 20.06) | |
| 10:33502643 | Y>N | A:429 | (16.57, 5.42, 22.67) | |
| 10:33502633 | rs145954532 | S>F | A:432 | (13.63, 2.70, 17.40) |
| 10:33502627 | M>T | A:434 | (7.50, -0.76, 15.58) | |
| 10:33502619 | M>V | A:437 | (5.54, -7.95, 12.61) | |
| 10:33502601 | S>P | A:443 | (2.43, -9.28, 4.98) | |
| 10:33502589 | I>L | A:447 | (6.01, -13.90, 7.36) | |
| 10:33502586 | rs199883581 | T>A | A:448 | (8.84, -17.05, 5.49) |
| 10:33502570 | rs375128788 | G>E | A:453 | (5.34, -27.18, 5.91) |
| 10:33502568 | D>Y | A:454 | (5.13, -27.65, 9.50) | |
| 10:33502556 | rs529636463 | M>V | A:458 | (-0.51, -19.69, 11.19) |
| 10:33502553 | P>T | A:459 | (1.95, -16.39, 9.54) | |
| 10:33502537 | rs200660300 | L>R | A:464 | (4.90, -8.61, 19.41) |
| 10:33502535 | rs540725422 | V>I | A:465 | (1.00, -7.72, 20.81) |
| 10:33502532 | T>S | A:466 | (-1.34, -10.01, 18.19) | |
| 10:33502525 | R>H | A:468 | (-4.22, -16.26, 19.63) | |
| 10:33502526 | rs532348709 | R>C | A:468 | (-4.22, -16.26, 19.63) |
| 10:33502510 | L>P | A:473 | (11.05, -24.93, 16.61) | |
| 10:33502499 | P>S | A:477 | (18.97, -33.36, 20.74) | |
| 10:33502476 | COSM4013909 COSM4013911 COSM4013910 COSM4013912 |
W>C | A:484 | (14.63, -20.17, 7.46) |
| 10:33502467 | rs376390429 | I>M | A:487 | (11.02, -10.88, 7.71) |
| 10:33502469 | rs182437025 | I>V | A:487 | (11.02, -10.88, 7.71) |
| 10:33502466 | D>H | A:488 | (10.12, -9.23, 2.80) | |
| 10:33502459 | G>E | A:490 | (9.78, -4.89, 0.42) | |
| 10:33502450 | COSM1560800 | K>R | A:493 | (13.26, -0.50, 5.38) |
| 10:33502445 | COSM255266 | V>M | A:495 | (17.35, -3.05, 10.68) |
| 10:33502433 | I>V | A:499 | (11.31, -6.79, 20.23) | |
| 10:33502415 | H>Y | A:505 | (1.01, -21.53, 24.95) | |
| 10:33502411 | rs554892989 COSM3437385 COSM3437387 COSM3437386 COSM3437388 |
R>Q | A:506 | (1.15, -20.64, 32.81) |
| 10:33502406 | N>Y | A:508 | (5.49, -26.14, 27.72) | |
| 10:33502397 | F>L | A:511 | (12.22, -19.42, 26.47) | |
| 10:33502394 | M>V | A:512 | (14.82, -17.82, 21.41) | |
| 10:33502379 | I>V | A:517 | (20.72, -11.94, 12.86) | |
| 10:33502376 | G>R | A:518 | (20.41, -12.27, 8.79) | |
| 10:33502370 | rs543390398 | S>G | A:520 | (19.51, -9.94, 2.01) |
| 10:33502357 | rs117525057 | S>L | A:524 | (19.62, -15.51, -2.34) |
| 10:33502332 | D>E | A:532 | (32.98, -8.79, 18.94) | |
| 10:33502334 | rs371533986 | D>Y | A:532 | (32.98, -8.79, 18.94) |
| 10:33502325 | R>C | A:535 | (37.13, -14.67, 14.26) | |
| 10:33502318 | COSM684446 COSM1646301 COSM1646300 COSM3686723 |
A>V | A:537 | (28.21, -15.58, 13.92) |
| 10:33496628 | COSM538806 COSM1648689 COSM1648688 |
N>S | A:544 | (15.55, -14.91, 30.50) |
| 10:33496622 | Y>F | A:546 | (5.87, -16.73, 29.62) | |
| 10:33496616 | rs201841993 | T>I | A:548 | (9.78, -10.44, 29.53) |
| 10:33496608 | L>V | A:551 | (16.03, -4.76, 22.64) | |
| 10:33496604 | R>Q | A:552 | (18.52, -8.31, 22.43) | |
| 10:33496605 | R>W | A:552 | (18.52, -8.31, 22.43) | |
| 10:33496601 | T>I | A:553 | (20.82, -3.96, 19.36) | |
| 10:33496602 | T>S | A:553 | (20.82, -3.96, 19.36) | |
| 10:33496599 | F>L | A:554 | (21.25, -5.18, 15.12) | |
| 10:33496590 | rs190763052 | L>F | A:557 | (21.51, -3.52, 8.89) |
| 10:33496583 | rs143124682 | T>M | A:559 | (18.17, -4.77, 4.55) |
| 10:33496580 | R>Q | A:560 | (13.64, -6.62, 0.50) | |
| 10:33496581 | rs374062923 | R>G | A:560 | (13.64, -6.62, 0.50) |
| 10:33496576 | rs78398035 | F>L | A:561 | (15.09, -9.89, 2.36) |
| 10:33496578 | rs376983601 | F>I | A:561 | (15.09, -9.89, 2.36) |
| 10:33496566 | Y>H | A:565 | (19.29, -18.27, 10.90) | |
| 10:33496560 | COSM4013906 COSM4013908 COSM4013907 |
E>K | A:567 | (21.80, -21.26, 17.94) |
| 10:33496547 | H>L | A:571 | (13.60, -29.68, 27.65) | |
| 10:33496542 | G>R | A:573 | (11.30, -25.55, 23.10) | |
| 10:33496539 | rs569952285 | L>V | A:574 | (11.17, -22.18, 19.97) |
| 10:33496505 | V>A | A:585 | (16.38, 4.83, 3.65) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:33552596 | COSM917838 | E>D | A:212 | (-13.74, -0.18, 15.88) |
| 10:33545339 | COSM1955751 | S>L | A:240 | (2.75, 0.27, 15.25) |
| 10:33510678 | COSM3437397 | M>I | A:417 | (1.87, 3.50, 48.10) |
| 10:33510662 | COSM1347665 | G>S | A:423 | (11.59, 5.69, 31.64) |
| 10:33502318 | COSM1646301 | A>V | A:537 | (28.21, -15.58, 13.92) |