General Structure Information
| PDB ID | 3ol2 |
| HGNC Gene Label(s) | PLXNB1 |
| Structure Name | receptor-ligand structure of human semaphorin 4d with plexin b1. |
| Resolution | 2.99Å |
| Reference | AUTH B.J.JANSSEN,R.A.ROBINSON,F.PEREZ-BRANGULI,C.H.BELL,AUTH 2 K.J.MITCHELL,C.SIEBOLD,E.Y.JONESTITL STRUCTURAL BASIS OF SEMAPHORIN-PLEXIN SIGNALLING.REF NATURE V. 467 1118 2010REFN ISSN 0028-0836PMID 20877282DOI 10.1038/NATURE09468 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 496 |
| Number Of SNVs | 119 |
| Number Of Permutations | 31047 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.018 |
| p-value | 0.458 |
COSMIC
| Number Of Residues | 496 |
| Number Of SNVs | 5 |
| Number Of Permutations | 786 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.1 |
| p-value | 0.404 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 119 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.082 |
| p-value | 0.467 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:48465942 | rs530386453 | A>T | B:27 | (25.92, -23.11, 3.17) |
| 3:48465935 | T>N | B:29 | (19.86, -21.04, 3.38) | |
| 3:48465929 | rs559719918 | N>S | B:31 | (13.05, -22.39, 2.30) |
| 3:48465926 | rs533198395 | G>V | B:32 | (10.59, -20.43, 5.33) |
| 3:48465920 | rs532663603 | Y>F | B:34 | (13.19, -16.53, 10.35) |
| 3:48465901 | rs375170570 | R>S | B:40 | (29.25, -31.02, 17.62) |
| 3:48465741 | rs374420352 | T>A | B:94 | (0.94, -20.96, 16.75) |
| 3:48465701 | A>V | B:107 | (18.81, -38.09, 22.96) | |
| 3:48465673 | rs144549732 | Q>H | B:116 | (2.84, -24.19, 28.09) |
| 3:48465669 | rs368626600 | V>L | B:118 | (6.58, -29.46, 26.01) |
| 3:48465653 | rs543884018 | R>H | B:123 | (16.84, -42.84, 17.35) |
| 3:48465654 | R>C | B:123 | (16.84, -42.84, 17.35) | |
| 3:48465647 | G>E | B:125 | (20.47, -39.75, 13.31) | |
| 3:48465639 | rs189274296 | E>K | B:128 | (12.26, -38.48, 10.90) |
| 3:48465623 | COSM190216 | R>Q | B:133 | (5.72, -36.74, 21.42) |
| 3:48465624 | rs142798130 | R>W | B:133 | (5.72, -36.74, 21.42) |
| 3:48465620 | P>L | B:134 | (5.07, -36.84, 26.80) | |
| 3:48465614 | R>Q | B:136 | (-2.19, -37.34, 30.38) | |
| 3:48465611 | P>L | B:137 | (1.46, -33.47, 29.55) | |
| 3:48465612 | P>S | B:137 | (1.46, -33.47, 29.55) | |
| 3:48465608 | G>V | B:138 | (2.09, -31.56, 33.10) | |
| 3:48465597 | Y>H | B:142 | (3.99, -27.28, 31.47) | |
| 3:48465593 | V>A | B:143 | (10.59, -27.15, 30.31) | |
| 3:48465575 | A>V | B:149 | (11.13, -13.28, 23.05) | |
| 3:48465566 | T>M | B:152 | (15.49, -21.36, 27.31) | |
| 3:48465555 | V>I | B:156 | (23.20, -32.36, 29.65) | |
| 3:48465536 | COSM228924 | G>E | B:162 | (24.58, -41.58, 35.37) |
| 3:48465524 | L>P | B:166 | (17.90, -30.97, 31.67) | |
| 3:48465518 | V>A | B:168 | (16.40, -25.53, 32.81) | |
| 3:48465449 | P>L | B:191 | (12.74, -41.65, 34.25) | |
| 3:48465450 | rs112441374 | P>T | B:191 | (12.74, -41.65, 34.25) |
| 3:48465441 | P>S | B:194 | (9.31, -43.23, 30.81) | |
| 3:48465438 | rs150395060 | Q>K | B:195 | (5.11, -41.01, 30.13) |
| 3:48465425 | S>F | B:199 | (10.11, -33.94, 36.03) | |
| 3:48465419 | E>G | B:201 | (10.99, -34.91, 42.82) | |
| 3:48465402 | rs35798367 | A>S | B:207 | (12.37, -20.95, 44.82) |
| 3:48465392 | COSM169211 | R>H | B:210 | (7.33, -11.05, 44.55) |
| 3:48465393 | R>C | B:210 | (7.33, -11.05, 44.55) | |
| 3:48465365 | rs34256029 | V>A | B:219 | (22.72, -16.02, 28.49) |
| 3:48465366 | rs146847340 | V>M | B:219 | (22.72, -16.02, 28.49) |
| 3:48465350 | rs200677699 | R>H | B:224 | (34.84, -25.99, 36.62) |
| 3:48465351 | R>C | B:224 | (34.84, -25.99, 36.62) | |
| 3:48465341 | S>N | B:227 | (29.44, -27.56, 39.22) | |
| 3:48465339 | COSM4118197 | A>T | B:228 | (26.34, -25.94, 37.54) |
| 3:48465318 | COSM1423743 | R>W | B:235 | (14.36, -6.36, 37.64) |
| 3:48465306 | rs375084462 | A>S | B:239 | (18.85, -1.92, 44.76) |
| 3:48465302 | Q>P | B:240 | (16.67, 1.74, 46.43) | |
| 3:48465287 | R>H | B:245 | (23.73, -6.62, 38.97) | |
| 3:48465285 | COSM3993121 | A>P | B:246 | (24.96, -9.45, 35.84) |
| 3:48465278 | rs374123799 | V>G | B:248 | (27.42, -16.08, 38.18) |
| 3:48465276 | S>P | B:249 | (24.89, -19.24, 39.20) | |
| 3:48465272 | R>Q | B:250 | (28.51, -22.60, 42.63) | |
| 3:48465260 | R>Q | B:254 | (26.50, -33.47, 44.32) | |
| 3:48465261 | rs566324180 | R>W | B:254 | (26.50, -33.47, 44.32) |
| 3:48465216 | rs547716678 | E>K | B:269 | (34.90, -1.24, 33.53) |
| 3:48465182 | A>G | B:280 | (32.81, -18.82, 26.35) | |
| 3:48465174 | T>A | B:283 | (37.83, -24.66, 23.18) | |
| 3:48465171 | S>T | B:284 | (41.48, -27.12, 21.99) | |
| 3:48465154 | H>Q | B:289 | (36.28, -27.95, 27.69) | |
| 3:48465147 | V>M | B:292 | (38.74, -18.76, 31.51) | |
| 3:48465125 | rs542965215 | S>L | B:299 | (25.96, -0.75, 27.03) |
| 3:48465116 | P>H | B:302 | (17.11, 3.76, 28.21) | |
| 3:48465117 | P>T | B:302 | (17.11, 3.76, 28.21) | |
| 3:48465099 | P>S | B:308 | (13.18, -5.85, 28.10) | |
| 3:48465092 | rs142876524 | S>L | B:310 | (17.93, -3.24, 25.61) |
| 3:48465089 | A>V | B:311 | (21.40, -2.74, 24.22) | |
| 3:48465072 | rs368760694 | G>R | B:317 | (26.93, 1.80, 21.87) |
| 3:48465056 | C>F | B:322 | (35.39, -9.89, 30.27) | |
| 3:48465029 | rs144682293 | R>Q | B:331 | (39.00, -18.03, 44.64) |
| 3:48465030 | rs146977900 | R>W | B:331 | (39.00, -18.03, 44.64) |
| 3:48465017 | R>H | B:335 | (35.90, -16.25, 49.88) | |
| 3:48465018 | rs373706977 | R>C | B:335 | (35.90, -16.25, 49.88) |
| 3:48465014 | T>M | B:336 | (29.61, -16.33, 49.80) | |
| 3:48465011 | R>Q | B:337 | (30.42, -21.89, 51.16) | |
| 3:48465008 | D>G | B:338 | (32.51, -20.06, 53.98) | |
| 3:48464993 | R>Q | B:343 | (32.08, -15.76, 58.68) | |
| 3:48464994 | R>W | B:343 | (32.08, -15.76, 58.68) | |
| 3:48464989 | E>D | B:344 | (25.96, -14.04, 60.94) | |
| 3:48464984 | rs371044732 | R>H | B:346 | (28.82, -10.38, 59.72) |
| 3:48464985 | R>C | B:346 | (28.82, -10.38, 59.72) | |
| 3:48464979 | rs146898727 | E>K | B:348 | (37.50, -11.72, 59.22) |
| 3:48464972 | rs192227026 | G>A | B:350 | (34.77, -6.25, 56.94) |
| 3:48464967 | E>K | B:352 | (27.01, -6.43, 54.86) | |
| 3:48464964 | rs141304166 | V>M | B:353 | (29.89, -10.34, 51.95) |
| 3:48464955 | rs571891500 | I>V | B:356 | (19.35, -15.10, 51.90) |
| 3:48464952 | E>Q | B:357 | (18.40, -13.14, 47.08) | |
| 3:48464939 | N>S | B:361 | (12.02, -16.98, 55.90) | |
| 3:48464927 | COSM4118196 | A>G | B:365 | (24.89, -18.30, 60.22) |
| 3:48464346 | D>G | B:373 | (34.66, -29.65, 55.51) | |
| 3:48464347 | D>Y | B:373 | (34.66, -29.65, 55.51) | |
| 3:48464341 | Y>H | B:375 | (26.99, -30.72, 55.84) | |
| 3:48464338 | rs200514394 | P>S | B:376 | (30.07, -29.17, 50.85) |
| 3:48464326 | D>H | B:380 | (18.27, -29.59, 56.32) | |
| 3:48464314 | S>G | B:384 | (19.04, -21.26, 50.97) | |
| 3:48464301 | S>I | B:388 | (27.37, -11.68, 46.88) | |
| 3:48464302 | S>C | B:388 | (27.37, -11.68, 46.88) | |
| 3:48464298 | R>Q | B:389 | (25.63, -7.86, 49.78) | |
| 3:48464299 | rs34050056 | R>W | B:389 | (25.63, -7.86, 49.78) |
| 3:48464296 | V>I | B:390 | (31.13, -8.88, 46.88) | |
| 3:48464292 | rs199576492 COSM1287259 |
P>L | B:391 | (31.22, -7.84, 43.15) |
| 3:48464278 | rs112016313 | P>S | B:396 | (37.98, -4.86, 29.86) |
| 3:48464259 | G>E | B:402 | (29.85, 0.40, 17.98) | |
| 3:48464260 | G>R | B:402 | (29.85, 0.40, 17.98) | |
| 3:48464233 | T>A | B:411 | (40.33, -21.17, 20.35) | |
| 3:48464229 | M>K | B:412 | (44.01, -22.11, 22.78) | |
| 3:48464223 | D>G | B:414 | (50.93, -22.38, 19.56) | |
| 3:48464212 | I>V | B:418 | (42.17, -17.00, 19.02) | |
| 3:48464208 | A>V | B:419 | (38.32, -14.70, 19.45) | |
| 3:48464209 | COSM3660589 | A>T | B:419 | (38.32, -14.70, 19.45) |
| 3:48464200 | G>S | B:422 | (29.48, -11.68, 17.36) | |
| 3:48464193 | S>N | B:424 | (23.87, -7.12, 15.63) | |
| 3:48464178 | H>L | B:429 | (34.27, -9.46, 14.40) | |
| 3:48463856 | rs142527941 | P>S | B:435 | (50.79, -11.28, 24.70) |
| 3:48463853 | rs373864177 | G>R | B:436 | (49.98, -7.26, 23.80) |
| 3:48463841 | H>Y | B:440 | (42.93, -5.25, 16.84) | |
| 3:48463832 | rs139956646 | S>A | B:443 | (39.18, -10.23, 10.81) |
| 3:48463828 | T>I | B:444 | (35.72, -8.30, 10.01) | |
| 3:48463822 | rs148423378 | S>N | B:446 | (29.44, -10.74, 6.48) |
| 3:48463813 | Q>R | B:449 | (23.19, -8.69, 5.54) | |
| 3:48463807 | S>C | B:451 | (21.46, -10.89, 11.15) | |
| 3:48463799 | rs114964512 | S>R | B:454 | (23.88, -17.25, 17.38) |
| 3:48463791 | D>E | B:456 | (24.55, -21.43, 19.26) | |
| 3:48463790 | L>F | B:457 | (29.60, -19.57, 18.08) | |
| 3:48463757 | V>F | B:468 | (28.55, -19.04, 11.93) | |
| 3:48463599 | V>L | B:479 | (39.74, -21.22, 11.78) | |
| 3:48463587 | A>T | B:483 | (47.00, -21.75, 1.94) | |
| 3:48463577 | L>P | B:486 | (51.54, -19.32, -2.54) | |
| 3:48463554 | H>Y | B:494 | (48.85, -10.98, 4.26) | |
| 3:48463544 | rs377195859 | P>L | B:497 | (47.25, -15.62, 14.57) |
| 3:48463542 | Y>H | B:498 | (45.00, -19.81, 13.50) | |
| 3:48463526 | V>G | B:503 | (61.06, -23.39, 5.84) | |
| 3:48463527 | rs140699424 | V>M | B:503 | (61.06, -23.39, 5.84) |
| 3:48463207 | COSM3824059 | R>H | B:510 | (47.40, -24.50, 11.87) |
| 3:48463208 | rs527420911 | R>C | B:510 | (47.40, -24.50, 11.87) |
| 3:48463204 | R>H | B:511 | (54.48, -23.79, 15.15) | |
| 3:48463205 | R>C | B:511 | (54.48, -23.79, 15.15) | |
| 3:48463201 | S>F | B:512 | (50.59, -28.11, 13.75) | |
| 3:48463192 | rs560284322 | S>L | B:515 | (56.24, -31.97, 10.68) |
| 3:48463177 | P>R | B:520 | (58.86, -29.98, 15.56) | |
| 3:48463157 | F>V | B:527 | (51.00, -11.84, 14.65) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:48465260 | COSM4391918 | R>Q | B:254 | (26.50, -33.47, 44.32) |
| 3:48464292 | COSM1287259 | P>L | B:391 | (31.22, -7.84, 43.15) |
| 3:48464209 | COSM3660589 | A>T | B:419 | (38.32, -14.70, 19.45) |
| 3:48464174 | COSM359798 | R>S | B:430 | (38.61, -14.01, 12.43) |
| 3:48463752 | COSM3714641 | M>I | B:469 | (23.47, -19.46, 13.29) |