General Structure Information
| PDB ID | 3vi4 |
| HGNC Gene Label(s) | ITGA5 |
| Structure Name | crystal structure of alpha5beta1 integrin headpiece in complex with rgd peptide |
| Resolution | 2.9Å |
| Reference | AUTH M.NAGAE,S.RE,E.MIHARA,T.NOGI,Y.SUGITA,J.TAKAGITITL CRYSTAL STRUCTURE OF ALPHA5BETA1 INTEGRIN ECTODOMAIN: ATOMICTITL 2 DETAILS OF THE FIBRONECTIN RECEPTORREF J.CELL BIOL. V. 197 131 2012REFN ISSN 0021-9525PMID 22451694DOI 10.1083/JCB.201111077 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 601 |
| Number Of SNVs | 150 |
| Number Of Permutations | 88503 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | 0.117 |
| p-value | 0.416 |
COSMIC
| Number Of Residues | 601 |
| Number Of SNVs | 6 |
| Number Of Permutations | 2536 |
| Optimal Distance Threshold | 25.0 |
| K Statistic | 0.067 |
| p-value | 0.084 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 150 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 21.0 |
| K Statistic | -0.21 |
| p-value | 0.822 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:54812855 | N>S | A:2 | (5.95, 17.00, 15.84) | |
| 12:54812848 | D>E | A:4 | (9.88, 10.71, 19.75) | |
| 12:54812816 | COSM4043204 | P>L | A:15 | (7.45, -15.29, 16.48) |
| 12:54812790 | E>Q | A:24 | (-7.01, 1.17, 15.94) | |
| 12:54812777 | P>Q | A:28 | (-13.02, 2.64, 26.54) | |
| 12:54812778 | P>S | A:28 | (-13.02, 2.64, 26.54) | |
| 12:54812768 | D>A | A:31 | (-8.89, 8.09, 28.39) | |
| 12:54805747 | V>I | A:33 | (-5.78, 4.64, 26.13) | |
| 12:54805743 | rs201444911 COSM1193947 |
S>N | A:34 | (-5.31, 1.15, 24.09) |
| 12:54805668 | P>R | A:59 | (-2.42, -1.49, 27.50) | |
| 12:54805669 | P>S | A:59 | (-2.42, -1.49, 27.50) | |
| 12:54805666 | rs200580175 | W>R | A:60 | (0.71, 4.07, 26.02) |
| 12:54805663 | G>C | A:61 | (0.40, 2.46, 30.46) | |
| 12:54805644 | C>F | A:67 | (0.29, -7.29, 24.87) | |
| 12:54805624 | S>G | A:74 | (-12.68, -19.48, 22.35) | |
| 12:54803379 | S>A | A:77 | (-15.05, -24.96, 13.89) | |
| 12:54803361 | S>P | A:83 | (-24.12, -34.98, 9.75) | |
| 12:54803349 | S>P | A:87 | (-22.50, -42.26, 9.02) | |
| 12:54803331 | V>M | A:93 | (-19.63, -25.82, 8.63) | |
| 12:54803305 | COSM941145 | F>L | A:101 | (-9.18, -12.53, 13.60) |
| 12:54803306 | F>S | A:101 | (-9.18, -12.53, 13.60) | |
| 12:54803298 | T>A | A:104 | (-8.90, -5.66, 9.49) | |
| 12:54803285 | H>R | A:108 | (-16.68, 4.28, 17.05) | |
| 12:54803282 | G>D | A:109 | (-15.50, 3.56, 20.88) | |
| 12:54803279 | S>F | A:110 | (-16.86, 0.72, 22.97) | |
| 12:54803273 | I>S | A:112 | (-13.54, -3.56, 18.80) | |
| 12:54803135 | rs200931801 | A>V | A:114 | (-12.30, -7.85, 13.72) |
| 12:54803111 | R>H | A:122 | (-19.73, -27.61, 3.75) | |
| 12:54803112 | R>C | A:122 | (-19.73, -27.61, 3.75) | |
| 12:54803075 | T>I | A:134 | (-15.76, -13.24, 9.43) | |
| 12:54803058 | rs368421506 | D>H | A:140 | (-20.70, -2.06, 25.14) |
| 12:54803048 | T>I | A:143 | (-20.71, -6.70, 27.10) | |
| 12:54803045 | rs540145150 | R>Q | A:144 | (-23.45, -9.15, 22.70) |
| 12:54803040 | COSM1210996 | L>V | A:146 | (-21.63, -9.39, 17.72) |
| 12:54803022 | R>S | A:152 | (-21.83, -16.65, 6.73) | |
| 12:54802688 | rs200109874 | E>K | A:171 | (-13.37, 2.57, 8.36) |
| 12:54802585 | T>A | A:175 | (-22.49, 6.78, 13.76) | |
| 12:54802579 | R>C | A:177 | (-23.53, 2.20, 9.42) | |
| 12:54802575 | V>A | A:178 | (-20.06, -1.38, 9.91) | |
| 12:54802554 | S>N | A:185 | (-18.29, -10.46, -4.83) | |
| 12:54802548 | F>Y | A:187 | (-17.23, -14.53, -11.12) | |
| 12:54801977 | Y>S | A:204 | (-25.30, -13.20, 16.52) | |
| 12:54801967 | E>D | A:207 | (-28.03, -21.66, 17.13) | |
| 12:54801969 | COSM1512428 | E>K | A:207 | (-28.03, -21.66, 17.13) |
| 12:54801951 | V>I | A:213 | (-28.87, -8.08, 8.12) | |
| 12:54801938 | L>R | A:217 | (-26.69, -0.97, 2.82) | |
| 12:54801934 | rs374695746 | Q>H | A:218 | (-26.20, -5.04, -0.31) |
| 12:54801933 | T>A | A:219 | (-23.20, -3.04, -3.89) | |
| 12:54801923 | A>D | A:222 | (-23.08, -6.40, -12.44) | |
| 12:54801920 | S>I | A:223 | (-22.57, -7.08, -16.01) | |
| 12:54801912 | Y>H | A:226 | (-18.80, -3.96, -14.92) | |
| 12:54801646 | V>I | A:237 | (-15.30, 7.27, 5.70) | |
| 12:54801627 | rs150405444 | D>V | A:243 | (-25.71, 14.76, 3.71) |
| 12:54801468 | A>T | A:250 | (-14.05, 2.51, -2.84) | |
| 12:54801443 | rs529704616 | T>I | A:258 | (-6.24, -2.79, -15.19) |
| 12:54801438 | G>S | A:260 | (-8.33, 2.55, -11.94) | |
| 12:54799710 | COSM694651 | V>L | A:262 | (-12.06, 5.60, -6.53) |
| 12:54799682 | rs200642938 | R>Q | A:271 | (-28.42, 4.88, -4.84) |
| 12:54799677 | rs564976660 | L>F | A:273 | (-22.17, 10.04, -5.75) |
| 12:54799670 | N>S | A:275 | (-16.26, 7.55, -10.50) | |
| 12:54799659 | COSM3462807 COSM3462806 |
E>Q | A:279 | (-2.11, 7.86, -14.61) |
| 12:54799470 | rs375602887 COSM1362790 |
A>T | A:291 | (-10.58, 10.77, 4.06) |
| 12:54799466 | T>I | A:292 | (-8.81, 14.19, 5.24) | |
| 12:54799461 | COSM287536 | V>I | A:294 | (-5.83, 18.87, 3.72) |
| 12:54799457 | N>S | A:295 | (-7.78, 22.72, 2.88) | |
| 12:54799449 | rs141341610 | G>R | A:298 | (-14.88, 21.63, 6.13) |
| 12:54799153 | rs202050846 | D>G | A:300 | (-13.88, 15.83, 3.79) |
| 12:54799135 | A>V | A:306 | (-0.66, 4.04, -6.67) | |
| 12:54799112 | P>S | A:314 | (15.47, 12.10, -16.23) | |
| 12:54799105 | rs146614663 | G>E | A:316 | (14.57, 6.97, -19.28) |
| 12:54799106 | G>R | A:316 | (14.57, 6.97, -19.28) | |
| 12:54799102 | R>Q | A:317 | (16.21, 3.83, -15.64) | |
| 12:54799103 | COSM1299611 | R>W | A:317 | (16.21, 3.83, -15.64) |
| 12:54799091 | V>L | A:321 | (7.83, 4.83, -7.59) | |
| 12:54799075 | V>A | A:326 | (-4.88, 14.95, -3.65) | |
| 12:54799063 | H>P | A:330 | (-13.80, 22.69, -3.97) | |
| 12:54799055 | rs377645220 | G>S | A:333 | (-17.46, 19.66, -5.53) |
| 12:54799052 | I>V | A:334 | (-15.14, 16.46, -6.01) | |
| 12:54799049 | E>Q | A:335 | (-10.90, 18.74, -8.99) | |
| 12:54799042 | T>M | A:337 | (-8.74, 16.40, -12.24) | |
| 12:54799030 | T>I | A:341 | (0.62, 14.36, -7.75) | |
| 12:54799031 | rs554050434 | T>S | A:341 | (0.62, 14.36, -7.75) |
| 12:54799028 | L>V | A:342 | (2.72, 12.90, -4.02) | |
| 12:54799016 | COSM3462800 | D>H | A:346 | (12.81, 4.72, -3.09) |
| 12:54799003 | R>Q | A:350 | (5.05, -1.50, -3.35) | |
| 12:54798994 | S>T | A:353 | (0.80, 1.21, 0.26) | |
| 12:54798991 | S>F | A:354 | (-0.30, 3.37, 3.28) | |
| 12:54798983 | P>S | A:357 | (-5.59, 10.46, 8.61) | |
| 12:54798979 | L>Q | A:358 | (-1.77, 12.34, 11.22) | |
| 12:54798980 | COSM1362789 | L>V | A:358 | (-1.77, 12.34, 11.22) |
| 12:54798976 | COSM1705724 | G>E | A:359 | (-4.69, 15.31, 11.73) |
| 12:54798971 | L>V | A:361 | (1.15, 16.52, 13.99) | |
| 12:54798967 | D>G | A:362 | (1.63, 21.03, 13.36) | |
| 12:54798962 | rs578020993 | D>N | A:364 | (-0.98, 24.42, 12.03) |
| 12:54798959 | G>S | A:365 | (-4.88, 24.29, 11.54) | |
| 12:54798952 | N>S | A:367 | (-5.68, 18.40, 8.90) | |
| 12:54798953 | rs200918284 | N>D | A:367 | (-5.68, 18.40, 8.90) |
| 12:54798670 | I>V | A:371 | (2.27, 8.43, 2.94) | |
| 12:54798664 | rs202005757 | A>S | A:373 | (7.25, 2.89, 1.70) |
| 12:54798643 | rs538916711 | Q>E | A:380 | (15.05, -2.10, 0.97) |
| 12:54798625 | rs200940770 | V>I | A:386 | (4.86, 13.40, 7.39) |
| 12:54798603 | G>E | A:393 | (-3.04, 22.21, 0.34) | |
| 12:54798597 | G>D | A:395 | (2.26, 19.19, 0.92) | |
| 12:54798586 | S>A | A:399 | (7.55, 17.20, 7.83) | |
| 12:54798581 | Q>H | A:400 | (9.11, 13.70, 10.07) | |
| 12:54798580 | V>L | A:401 | (11.40, 10.78, 7.32) | |
| 12:54798573 | rs531610716 | Q>P | A:403 | (13.76, 5.51, 8.58) |
| 12:54798561 | A>V | A:407 | (18.64, -3.97, 11.77) | |
| 12:54798546 | P>Q | A:412 | (11.20, -8.28, 4.60) | |
| 12:54798547 | rs149010571 | P>S | A:412 | (11.20, -8.28, 4.60) |
| 12:54798541 | F>I | A:414 | (6.59, -5.68, 4.98) | |
| 12:54798538 | F>L | A:415 | (8.40, 0.73, 8.99) | |
| 12:54798535 | G>S | A:416 | (4.46, 1.05, 6.83) | |
| 12:54798526 | L>F | A:419 | (-0.43, 3.72, 8.84) | |
| 12:54798522 | rs376218631 | R>Q | A:420 | (-5.51, 4.35, 12.06) |
| 12:54798513 | rs181020771 | R>Q | A:423 | (-7.76, 8.63, 17.55) |
| 12:54798492 | Y>C | A:430 | (0.61, 18.31, 20.37) | |
| 12:54798253 | rs577974426 | I>T | A:434 | (0.08, 3.40, 15.32) |
| 12:54798245 | S>P | A:437 | (6.70, -3.78, 11.21) | |
| 12:54798227 | A>S | A:443 | (4.53, -1.86, 16.61) | |
| 12:54798025 | R>H | A:449 | (8.24, 16.46, 20.54) | |
| 12:54798026 | R>C | A:449 | (8.24, 16.46, 20.54) | |
| 12:54798022 | P>L | A:450 | (5.63, 19.72, 22.65) | |
| 12:54798011 | rs112896207 | A>T | A:454 | (11.30, 31.16, 18.21) |
| 12:54797999 | rs147794441 | L>F | A:458 | (21.97, 40.20, 16.99) |
| 12:54797993 | I>V | A:460 | (25.90, 45.66, 16.56) | |
| 12:54797984 | rs181997225 | A>T | A:463 | (29.11, 48.98, 13.86) |
| 12:54797980 | M>T | A:464 | (31.79, 52.13, 13.17) | |
| 12:54797962 | R>Q | A:470 | (40.83, 53.85, 23.63) | |
| 12:54797963 | rs527756302 | R>W | A:470 | (40.83, 53.85, 23.63) |
| 12:54797950 | rs370538855 | L>S | A:474 | (38.98, 46.65, 31.83) |
| 12:54797945 | G>R | A:476 | (43.89, 50.77, 32.99) | |
| 12:54797739 | S>N | A:485 | (21.71, 43.55, 21.63) | |
| 12:54797710 | rs140478060 | V>I | A:495 | (4.01, 24.58, 26.25) |
| 12:54797697 | I>T | A:499 | (10.24, 28.57, 27.65) | |
| 12:54797555 | V>M | A:503 | (22.10, 31.89, 24.45) | |
| 12:54797551 | E>G | A:504 | (26.63, 30.00, 22.16) | |
| 12:54797549 | L>F | A:505 | (27.05, 35.17, 21.93) | |
| 12:54797535 | W>C | A:509 | (31.50, 32.82, 12.53) | |
| 12:54797512 | R>Q | A:517 | (38.66, 34.93, 18.90) | |
| 12:54797513 | rs143754928 | R>W | A:517 | (38.66, 34.93, 18.90) |
| 12:54797510 | R>W | A:518 | (39.86, 40.62, 15.84) | |
| 12:54797499 | F>L | A:521 | (32.14, 39.35, 25.75) | |
| 12:54797500 | F>S | A:521 | (32.14, 39.35, 25.75) | |
| 12:54797494 | A>V | A:523 | (32.93, 40.80, 31.71) | |
| 12:54797485 | Q>R | A:526 | (36.75, 34.93, 27.51) | |
| 12:54797473 | T>I | A:530 | (27.15, 30.39, 27.49) | |
| 12:54797443 | R>Q | A:540 | (7.80, 43.28, 25.91) | |
| 12:54797441 | E>K | A:541 | (11.65, 41.69, 21.94) | |
| 12:54797418 | I>M | A:548 | (31.92, 44.19, 22.80) | |
| 12:54797105 | E>K | A:553 | (46.57, 44.02, 20.71) | |
| 12:54797086 | K>R | A:559 | (43.82, 46.33, 11.16) | |
| 12:54797077 | P>L | A:562 | (35.39, 41.28, 9.13) | |
| 12:54797066 | rs138215416 | A>T | A:566 | (27.25, 34.29, 16.52) |
| 12:54797063 | L>F | A:567 | (22.85, 34.28, 18.33) | |
| 12:54797042 | rs144650038 | Q>K | A:574 | (18.77, 20.22, 31.58) |
| 12:54797023 | H>R | A:580 | (3.10, 11.61, 30.10) | |
| 12:54797024 | H>D | A:580 | (3.10, 11.61, 30.10) | |
| 12:54797021 | G>S | A:581 | (8.09, 12.11, 28.86) | |
| 12:54797002 | H>R | A:587 | (8.65, 25.46, 13.90) | |
| 12:54796999 | Y>C | A:588 | (10.30, 23.11, 10.23) | |
| 12:54796984 | rs142874592 | R>Q | A:593 | (23.62, 30.26, 13.80) |
| 12:54796981 | I>R | A:594 | (21.49, 35.32, 14.02) | |
| 12:54796976 | D>Y | A:596 | (26.12, 40.67, 12.54) | |
| 12:54796973 | rs138386543 | K>E | A:597 | (29.54, 41.52, 9.60) |
| 12:54796833 | rs202210895 | A>G | A:598 | (32.06, 44.15, 13.02) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:54801909 | COSM1747114 | D>N | A:227 | (-16.36, -9.69, -13.91) |
| 12:54799461 | COSM287536 | V>I | A:294 | (-5.83, 18.87, 3.72) |
| 12:54799103 | COSM1299611 | R>W | A:317 | (16.21, 3.83, -15.64) |
| 12:54798228 | COSM1677034 | K>N | A:442 | (8.30, -5.10, 15.74) |
| 12:54797727 | COSM4411238 | N>S | A:489 | (9.96, 36.48, 20.84) |
| 12:54797021 | COSM4382441 | G>S | A:581 | (8.09, 12.11, 28.86) |