General Structure Information
| PDB ID | 3v4v |
| HGNC Gene Label(s) | ITGA4 |
| Structure Name | crystal structure of a4b7 headpiece complexed with fab act-1 and ro0505376 |
| Resolution | 3.1Å |
| Reference | AUTH Y.YU,J.ZHU,L.Z.MI,T.WALZ,H.SUN,J.CHEN,T.A.SPRINGERTITL STRUCTURAL SPECIALIZATIONS OF A4B7, AN INTEGRIN THATTITL 2 MEDIATES ROLLING ADHESIONREF J.CELL BIOL. V. 196 131 2012REFN ISSN 0021-9525PMID 22232704DOI 10.1083/JCB.201110023 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 582 |
| Number Of SNVs | 104 |
| Number Of Permutations | 52208 |
| Optimal Distance Threshold | 14.0 |
| K Statistic | 0.063 |
| p-value | 0.022 |
COSMIC
| Number Of Residues | 582 |
| Number Of SNVs | 13 |
| Number Of Permutations | 24948 |
| Optimal Distance Threshold | 35.0 |
| K Statistic | 0.346 |
| p-value | 0.24 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 104 |
| Number Of COSMIC SNVs | 13 |
| Optimal Distance Threshold | 15.0 |
| K Statistic | 0.052 |
| p-value | 0.593 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 2:182322490 | D>N | A:4 | (25.93, 46.22, 51.50) | |
| 2:182322494 | rs371583061 | T>I | A:5 | (22.30, 47.83, 52.09) |
| 2:182322515 | Q>R | A:12 | (12.74, 48.42, 37.76) | |
| 2:182322523 | rs201830618 | H>N | A:15 | (3.41, 47.98, 35.25) |
| 2:182322527 | N>T | A:16 | (1.43, 44.21, 35.56) | |
| 2:182322550 | rs371276887 | V>M | A:24 | (19.25, 33.15, 39.07) |
| 2:182322559 | S>G | A:27 | (28.40, 32.65, 35.83) | |
| 2:182322566 | G>E | A:29 | (33.17, 33.04, 32.48) | |
| 2:182322948 | rs201919577 | N>D | A:42 | (3.01, 40.14, 27.54) |
| 2:182322961 | N>S | A:46 | (3.33, 36.84, 19.91) | |
| 2:182322976 | rs200955253 | N>S | A:51 | (-0.42, 37.31, 30.11) |
| 2:182323017 | G>S | A:65 | (21.82, 51.72, 34.50) | |
| 2:182323024 | COSM3391330 | T>M | A:67 | (19.03, 47.45, 31.04) |
| 2:182323029 | E>K | A:69 | (17.73, 41.77, 27.69) | |
| 2:182339690 | rs189570672 | S>N | A:75 | (8.38, 29.35, 18.59) |
| 2:182339692 | rs370594590 COSM343301 |
P>S | A:76 | (6.95, 32.65, 18.39) |
| 2:182339704 | rs201604237 | P>S | A:80 | (5.10, 21.17, 16.94) |
| 2:182339711 | G>V | A:82 | (2.07, 16.21, 19.34) | |
| 2:182339734 | D>H | A:90 | (-2.58, 31.56, 27.05) | |
| 2:182339756 | rs372164526 | T>K | A:97 | (11.14, 28.56, 38.48) |
| 2:182339791 | rs201346236 | V>M | A:109 | (15.91, 25.57, 34.46) |
| 2:182339899 | R>I | A:114 | (-1.44, 27.88, 34.56) | |
| 2:182339919 | I>V | A:121 | (-11.42, 21.58, 24.19) | |
| 2:182339924 | COSM441925 | K>N | A:122 | (-12.94, 17.79, 21.37) |
| 2:182339937 | L>I | A:127 | (-4.45, 18.64, 29.92) | |
| 2:182339961 | rs199505436 | V>M | A:135 | (19.13, 27.51, 28.89) |
| 2:182339964 | P>A | A:136 | (22.25, 27.58, 27.07) | |
| 2:182339977 | rs200678526 COSM3574738 |
R>Q | A:140 | (23.31, 30.64, 21.95) |
| 2:182343507 | N>Y | A:161 | (-2.11, 8.99, 35.68) | |
| 2:182343513 | A>T | A:163 | (-2.93, 14.90, 33.24) | |
| 2:182343529 | G>E | A:168 | (7.43, 23.56, 37.36) | |
| 2:182343533 | rs376313842 | I>M | A:169 | (5.54, 24.86, 40.75) |
| 2:182343537 | S>G | A:171 | (13.18, 24.19, 40.01) | |
| 2:182343538 | rs370333613 | S>T | A:171 | (13.18, 24.19, 40.01) |
| 2:182344922 | Y>C | A:195 | (16.34, 15.29, 31.83) | |
| 2:182344925 | rs201276246 | N>S | A:196 | (19.66, 12.10, 33.61) |
| 2:182344928 | rs367624699 | I>T | A:197 | (21.72, 16.06, 31.74) |
| 2:182344947 | COSM1529549 | K>N | A:203 | (14.26, 8.69, 36.73) |
| 2:182344981 | COSM1403746 | G>R | A:215 | (-3.71, 16.89, 47.91) |
| 2:182346351 | COSM1013554 | R>W | A:228 | (22.52, 8.20, 50.62) |
| 2:182346352 | rs148901650 | R>Q | A:228 | (22.52, 8.20, 50.62) |
| 2:182346360 | H>Y | A:231 | (29.98, 8.13, 45.44) | |
| 2:182346361 | H>R | A:231 | (29.98, 8.13, 45.44) | |
| 2:182346363 | T>A | A:232 | (24.68, 9.08, 45.79) | |
| 2:182346366 | rs201013234 | T>A | A:233 | (22.08, 12.28, 44.19) |
| 2:182346367 | T>N | A:233 | (22.08, 12.28, 44.19) | |
| 2:182346372 | V>L | A:235 | (15.51, 14.30, 45.75) | |
| 2:182346378 | G>R | A:237 | (9.87, 17.28, 48.84) | |
| 2:182347090 | rs145010184 | Y>H | A:249 | (7.99, 13.12, 51.67) |
| 2:182347093 | rs202008290 | I>V | A:250 | (14.48, 12.46, 51.51) |
| 2:182347099 | S>C | A:252 | (15.99, 7.40, 46.04) | |
| 2:182347101 | S>R | A:252 | (15.99, 7.40, 46.04) | |
| 2:182347103 | I>T | A:253 | (17.72, 7.64, 42.24) | |
| 2:182347104 | I>M | A:253 | (17.72, 7.64, 42.24) | |
| 2:182347111 | K>E | A:256 | (13.51, 1.85, 36.86) | |
| 2:182347112 | rs200000911 | K>I | A:256 | (13.51, 1.85, 36.86) |
| 2:182347113 | COSM476617 | K>N | A:256 | (13.51, 1.85, 36.86) |
| 2:182347124 | I>T | A:260 | (10.30, 7.56, 50.39) | |
| 2:182347128 | L>F | A:261 | (15.16, 7.40, 51.99) | |
| 2:182347129 | rs201919556 | H>N | A:262 | (13.28, 10.51, 56.44) |
| 2:182347139 | K>R | A:265 | (4.27, 15.79, 60.43) | |
| 2:182347256 | G>R | A:274 | (6.74, 22.26, 52.42) | |
| 2:182347284 | N>S | A:283 | (27.54, 20.64, 60.10) | |
| 2:182347287 | A>G | A:284 | (30.76, 21.04, 57.38) | |
| 2:182347310 | rs200311535 COSM1255006 |
V>M | A:292 | (11.32, 22.83, 55.96) |
| 2:182347331 | T>S | A:299 | (0.87, 32.67, 66.24) | |
| 2:182347368 | N>I | A:311 | (22.48, 14.37, 57.95) | |
| 2:182350627 | rs377146123 | M>K | A:321 | (16.73, 21.68, 65.98) |
| 2:182350641 | rs35419274 | V>I | A:326 | (11.15, 32.99, 63.79) |
| 2:182350648 | rs374319884 | S>T | A:328 | (10.80, 38.91, 63.27) |
| 2:182350650 | rs376305280 | D>N | A:329 | (7.33, 36.32, 64.68) |
| 2:182350695 | rs200585256 | D>N | A:344 | (30.55, 30.39, 52.57) |
| 2:182358063 | G>R | A:356 | (11.91, 34.74, 53.24) | |
| 2:182358087 | rs199973456 | Q>K | A:364 | (7.95, 46.15, 52.91) |
| 2:182358112 | G>D | A:372 | (26.50, 28.21, 59.86) | |
| 2:182358114 | rs200340958 | R>C | A:373 | (27.08, 28.65, 63.56) |
| 2:182358115 | rs199723658 COSM359605 |
R>H | A:373 | (27.08, 28.65, 63.56) |
| 2:182358117 | rs374355635 | A>T | A:374 | (28.92, 23.05, 64.20) |
| 2:182358118 | rs200411275 | A>V | A:374 | (28.92, 23.05, 64.20) |
| 2:182358120 | D>Y | A:375 | (25.80, 24.21, 66.54) | |
| 2:182358121 | rs201076589 | D>G | A:375 | (25.80, 24.21, 66.54) |
| 2:182358130 | S>L | A:378 | (21.89, 30.27, 64.42) | |
| 2:182359468 | I>N | A:390 | (16.91, 49.10, 49.18) | |
| 2:182359485 | rs144469731 | M>V | A:396 | (6.01, 40.96, 47.88) |
| 2:182359534 | Y>F | A:412 | (33.83, 37.40, 50.03) | |
| 2:182360100 | rs185899371 | V>I | A:415 | (22.63, 38.14, 47.40) |
| 2:182360118 | rs201906563 COSM3574745 |
R>W | A:421 | (3.01, 44.28, 44.71) |
| 2:182360523 | rs200550756 | V>I | A:434 | (37.98, 40.12, 59.54) |
| 2:182360532 | D>N | A:437 | (42.68, 35.18, 67.51) | |
| 2:182360560 | V>A | A:446 | (46.56, 37.60, 93.30) | |
| 2:182360572 | rs201163007 | K>T | A:450 | (54.50, 39.66, 94.59) |
| 2:182360583 | V>I | A:454 | (55.74, 51.64, 93.80) | |
| 2:182360587 | rs200133029 | E>G | A:455 | (50.39, 53.59, 94.16) |
| 2:182360614 | D>V | A:464 | (50.52, 43.03, 84.10) | |
| 2:182360638 | K>R | A:472 | (43.17, 35.34, 59.69) | |
| 2:182360655 | G>S | A:478 | (46.10, 44.96, 56.33) | |
| 2:182360656 | rs547068990 | G>A | A:478 | (46.10, 44.96, 56.33) |
| 2:182363354 | L>F | A:482 | (40.22, 46.66, 67.04) | |
| 2:182363368 | S>N | A:487 | (35.94, 45.21, 83.04) | |
| 2:182363391 | rs200957447 | E>Q | A:495 | (26.68, 45.81, 98.57) |
| 2:182363408 | F>L | A:500 | (41.59, 45.35, 91.41) | |
| 2:182363435 | D>E | A:509 | (36.09, 49.62, 86.95) | |
| 2:182363436 | rs201961822 COSM1013562 |
V>M | A:510 | (36.24, 50.63, 82.93) |
| 2:182363455 | rs201929711 | Q>R | A:516 | (46.84, 50.08, 63.96) |
| 2:182363457 | V>L | A:517 | (45.95, 45.07, 64.16) | |
| 2:182363484 | T>A | A:526 | (49.86, 46.16, 78.51) | |
| 2:182363502 | rs201091569 COSM302437 |
R>W | A:532 | (40.31, 49.00, 96.84) |
| 2:182374391 | rs201930987 | V>M | A:535 | (41.58, 45.12, 101.19) |
| 2:182374395 | R>Q | A:536 | (37.22, 44.62, 103.85) | |
| 2:182374403 | L>I | A:539 | (37.27, 34.35, 99.88) | |
| 2:182374412 | rs200533064 | I>V | A:542 | (38.24, 38.91, 90.49) |
| 2:182374467 | rs202138044 | T>I | A:560 | (37.05, 55.03, 42.46) |
| 2:182374469 | COSM333400 | E>Q | A:561 | (36.16, 51.30, 39.60) |
| 2:182374496 | COSM3838072 | L>F | A:570 | (34.21, 41.44, 63.24) |
| 2:182374517 | D>N | A:577 | (33.55, 39.24, 69.99) | |
| 2:182374524 | M>R | A:579 | (37.96, 37.82, 76.24) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 2:182322503 | COSM1255007 | A>V | A:8 | (22.51, 48.45, 45.95) |
| 2:182339925 | COSM1613990 | N>D | A:123 | (-16.11, 16.44, 24.63) |
| 2:182344970 | COSM1613991 | Q>L | A:211 | (3.59, 6.06, 50.79) |
| 2:182346369 | COSM1669565 | E>K | A:234 | (20.14, 12.19, 47.54) |
| 2:182347105 | COSM1306195 | D>N | A:254 | (16.08, 3.31, 42.54) |
| 2:182347137 | COSM3896126 | M>I | A:264 | (10.06, 15.21, 57.04) |
| 2:182359477 | COSM1210994 | S>L | A:393 | (9.16, 51.04, 45.66) |
| 2:182360634 | COSM4410814 | Y>H | A:471 | (44.02, 40.73, 60.72) |
| 2:182363436 | COSM1013562 | V>M | A:510 | (36.24, 50.63, 82.93) |
| 2:182363502 | COSM302437 | R>W | A:532 | (40.31, 49.00, 96.84) |
| 2:182374507 | COSM1752162 | K>N | A:573 | (33.61, 33.27, 66.10) |
| 2:182374515 | COSM2151258 | K>T | A:576 | (29.12, 36.84, 72.24) |
| 2:182374525 | COSM3574758 | M>I | A:579 | (37.96, 37.82, 76.24) |