General Structure Information
| PDB ID | 4bkw |
| HGNC Gene Label(s) | ZFYVE9 |
| Structure Name | crystal structure of the c-terminal region of human zfyve9 |
| Resolution | 2.53Å |
| Reference | AUTH E.WILLIAMSTITL CRYSTAL STRUCTURE OF THE C-TERMINAL REGION OF HUMAN ZFYVE9REF PH D THESIS 2013PUBL NULL: UNIVERSITY OF OXFORD (THESIS) |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 479 |
| Number Of SNVs | 96 |
| Number Of Permutations | 16623 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.022 |
| p-value | 0.936 |
COSMIC
| Number Of Residues | 479 |
| Number Of SNVs | 5 |
| Number Of Permutations | 69 |
| Optimal Distance Threshold | 29.0 |
| K Statistic | 0.1 |
| p-value | 0.046 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 96 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 27.0 |
| K Statistic | -0.391 |
| p-value | 0.006 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:52740193 | rs141085489 | A>T | A:895 | (6.36, 59.03, 58.54) |
| 1:52740196 | M>V | A:896 | (6.50, 54.77, 57.43) | |
| 1:52740215 | D>V | A:902 | (19.20, 64.76, 50.62) | |
| 1:52740229 | rs145187001 | I>F | A:907 | (21.02, 61.16, 65.01) |
| 1:52740236 | I>N | A:909 | (21.04, 61.94, 71.10) | |
| 1:52740238 | S>P | A:910 | (21.06, 59.94, 75.35) | |
| 1:52744191 | Q>R | A:925 | (27.14, 63.76, 55.54) | |
| 1:52744204 | M>I | A:929 | (31.95, 59.70, 58.62) | |
| 1:52744226 | rs546135293 | P>A | A:937 | (32.35, 52.11, 71.51) |
| 1:52744232 | P>S | A:939 | (26.47, 52.38, 68.20) | |
| 1:52744264 | rs149553882 | L>F | A:949 | (15.87, 52.38, 65.44) |
| 1:52744268 | rs144226254 | M>V | A:951 | (22.06, 50.66, 65.08) |
| 1:52744270 | rs568830561 | M>I | A:951 | (22.06, 50.66, 65.08) |
| 1:52744280 | V>L | A:955 | (33.77, 46.49, 62.64) | |
| 1:52747352 | W>C | A:963 | (30.15, 50.81, 56.55) | |
| 1:52747360 | rs142219419 | T>I | A:966 | (21.82, 46.92, 63.17) |
| 1:52747380 | V>M | A:973 | (6.42, 43.95, 62.63) | |
| 1:52747395 | I>V | A:978 | (18.11, 42.58, 59.85) | |
| 1:52747396 | I>T | A:978 | (18.11, 42.58, 59.85) | |
| 1:52747401 | rs555764165 | I>V | A:980 | (23.95, 44.20, 56.93) |
| 1:52747407 | L>I | A:982 | (28.89, 46.44, 53.73) | |
| 1:52747413 | C>G | A:984 | (34.72, 48.82, 53.25) | |
| 1:52747414 | rs61752688 | C>Y | A:984 | (34.72, 48.82, 53.25) |
| 1:52747420 | P>L | A:986 | (38.60, 51.41, 48.69) | |
| 1:52747440 | rs574308757 | K>Q | A:993 | (21.37, 56.57, 52.12) |
| 1:52747446 | rs149699758 | I>V | A:995 | (21.34, 49.49, 53.80) |
| 1:52747459 | rs375430570 | F>S | A:999 | (17.08, 48.03, 57.09) |
| 1:52747461 | V>L | A:1000 | (12.00, 51.02, 55.31) | |
| 1:52747465 | Q>R | A:1001 | (10.43, 47.87, 51.62) | |
| 1:52747473 | R>W | A:1004 | (7.16, 50.14, 53.75) | |
| 1:52747474 | R>Q | A:1004 | (7.16, 50.14, 53.75) | |
| 1:52759133 | V>M | A:1012 | (12.40, 37.62, 55.97) | |
| 1:52759134 | V>A | A:1012 | (12.40, 37.62, 55.97) | |
| 1:52759164 | Q>R | A:1022 | (15.03, 50.45, 42.21) | |
| 1:52759178 | rs148834262 | S>G | A:1027 | (25.09, 47.71, 40.74) |
| 1:52759188 | H>R | A:1030 | (24.32, 44.68, 43.43) | |
| 1:52759209 | T>I | A:1037 | (20.84, 31.88, 61.25) | |
| 1:52759211 | S>P | A:1038 | (24.37, 32.32, 63.29) | |
| 1:52759212 | rs192873630 | S>F | A:1038 | (24.37, 32.32, 63.29) |
| 1:52759218 | Y>C | A:1040 | (29.35, 26.26, 63.58) | |
| 1:52759235 | L>V | A:1046 | (29.53, 42.16, 66.79) | |
| 1:52759242 | rs371180594 | L>H | A:1048 | (24.32, 41.86, 67.98) |
| 1:52759264 | F>L | A:1055 | (23.56, 37.86, 60.06) | |
| 1:52759279 | Q>H | A:1060 | (25.19, 39.24, 42.43) | |
| 1:52759313 | rs569702498 | I>V | A:1072 | (21.14, 25.18, 51.12) |
| 1:52759319 | rs530780120 | L>M | A:1074 | (23.75, 30.63, 47.32) |
| 1:52759323 | M>T | A:1075 | (24.63, 28.97, 52.33) | |
| 1:52759346 | COSM3865765 | R>G | A:1083 | (38.84, 29.57, 51.61) |
| 1:52759347 | rs375050885 | R>Q | A:1083 | (38.84, 29.57, 51.61) |
| 1:52759349 | COSM191296 | L>F | A:1084 | (34.16, 31.02, 56.04) |
| 1:52761575 | C>R | A:1087 | (28.42, 31.11, 55.56) | |
| 1:52761621 | rs202129003 | T>M | A:1102 | (20.24, 27.22, 35.47) |
| 1:52761632 | rs150653407 | I>V | A:1106 | (19.25, 17.27, 38.83) |
| 1:52769509 | Q>R | A:1117 | (5.57, 27.42, 40.57) | |
| 1:52769526 | rs143012855 | V>I | A:1123 | (10.54, 19.25, 56.26) |
| 1:52769545 | D>V | A:1129 | (23.40, 12.11, 57.42) | |
| 1:52769547 | M>V | A:1130 | (26.42, 11.57, 54.06) | |
| 1:52769548 | COSM1237111 | M>T | A:1130 | (26.42, 11.57, 54.06) |
| 1:52769556 | COSM910631 | R>W | A:1133 | (30.19, 1.45, 55.58) |
| 1:52769557 | rs139791435 | R>Q | A:1133 | (30.19, 1.45, 55.58) |
| 1:52769559 | K>E | A:1134 | (25.04, 5.15, 58.07) | |
| 1:52769565 | S>G | A:1136 | (20.50, 9.14, 57.36) | |
| 1:52769573 | rs534801827 | K>N | A:1138 | (17.91, 12.58, 60.78) |
| 1:52769580 | S>G | A:1141 | (8.67, 14.12, 65.77) | |
| 1:52769593 | rs571286212 | N>S | A:1145 | (1.23, 16.81, 59.36) |
| 1:52798440 | rs368989878 | M>V | A:1147 | (6.77, 14.00, 55.43) |
| 1:52798444 | M>T | A:1148 | (2.35, 12.95, 55.53) | |
| 1:52798465 | N>S | A:1155 | (5.06, 9.43, 42.05) | |
| 1:52798482 | G>R | A:1161 | (13.64, 16.50, 49.20) | |
| 1:52798498 | N>S | A:1166 | (23.42, 18.85, 59.39) | |
| 1:52798515 | H>Y | A:1172 | (27.02, 20.24, 54.24) | |
| 1:52798527 | V>L | A:1176 | (30.61, 24.11, 41.82) | |
| 1:52798547 | rs540633246 | N>K | A:1182 | (28.92, 22.05, 33.08) |
| 1:52798576 | rs200871651 | N>S | A:1192 | (39.73, 21.33, 57.19) |
| 1:52798582 | P>L | A:1194 | (39.07, 13.72, 58.43) | |
| 1:52800371 | S>G | A:1201 | (21.00, 19.69, 50.05) | |
| 1:52800387 | S>N | A:1206 | (13.47, 5.39, 43.21) | |
| 1:52803460 | Q>H | A:1229 | (17.22, 3.03, 42.59) | |
| 1:52803461 | I>L | A:1230 | (14.26, 1.41, 46.45) | |
| 1:52803473 | rs376782218 | N>H | A:1234 | (11.62, -1.46, 50.11) |
| 1:52803495 | A>V | A:1241 | (6.42, 3.49, 58.09) | |
| 1:52803503 | rs141578777 | E>K | A:1244 | (2.08, 3.83, 61.48) |
| 1:52803507 | M>K | A:1245 | (5.69, 8.34, 63.39) | |
| 1:52803519 | T>I | A:1249 | (16.10, -0.02, 57.93) | |
| 1:52803583 | D>E | A:1270 | (13.78, 15.48, 67.98) | |
| 1:52803594 | N>I | A:1274 | (10.76, 27.32, 66.42) | |
| 1:52803596 | rs374609564 | V>I | A:1275 | (12.18, 29.38, 69.28) |
| 1:52805802 | COSM4008796 | V>I | A:1280 | (13.57, 35.61, 76.98) |
| 1:52805823 | S>P | A:1287 | (13.59, 30.02, 77.99) | |
| 1:52805824 | S>Y | A:1287 | (13.59, 30.02, 77.99) | |
| 1:52805835 | I>V | A:1291 | (8.37, 26.73, 73.87) | |
| 1:52805874 | A>T | A:1304 | (-4.76, 54.76, 72.25) | |
| 1:52810440 | V>L | A:1314 | (1.43, 32.70, 70.73) | |
| 1:52810499 | S>R | A:1333 | (-7.84, 30.21, 68.80) | |
| 1:52810516 | V>A | A:1339 | (-7.16, 36.60, 75.97) | |
| 1:52810539 | L>V | A:1347 | (-3.41, 48.04, 78.93) | |
| 1:52810582 | K>R | A:1361 | (8.42, 43.06, 74.91) | |
| 1:52810606 | rs369860366 | D>G | A:1369 | (-6.02, 23.24, 84.73) |
| 1:52811739 | Y>F | A:1375 | (-3.86, 36.85, 85.12) | |
| 1:52811762 | P>T | A:1383 | (5.78, 42.79, 87.72) | |
| 1:52811774 | rs376516156 COSM191307 |
Q>K | A:1387 | (-1.23, 51.12, 89.12) |
| 1:52811810 | V>M | A:1399 | (-12.46, 35.49, 79.14) | |
| 1:52811816 | H>D | A:1401 | (-13.59, 32.25, 84.01) | |
| 1:52811817 | H>L | A:1401 | (-13.59, 32.25, 84.01) | |
| 1:52811856 | rs370965958 | M>T | A:1414 | (-1.29, 30.65, 76.65) |
| 1:52811866 | rs182715743 | I>M | A:1417 | (4.04, 38.60, 72.95) |
| 1:52811873 | I>V | A:1420 | (3.45, 49.75, 73.29) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:52744180 | COSM910627 | E>D | A:921 | (15.87, 66.51, 61.83) |
| 1:52759283 | COSM2192800 | W>R | A:1062 | (23.11, 35.59, 36.05) |
| 1:52798442 | COSM4821262 | M>I | A:1147 | (6.77, 14.00, 55.43) |
| 1:52798566 | COSM24279 | S>G | A:1189 | (34.92, 21.56, 56.68) |
| 1:52811772 | COSM426435 | S>L | A:1386 | (-0.24, 47.51, 91.10) |