General Structure Information
| PDB ID | 4bx9 |
| HGNC Gene Label(s) | VPS33A |
| Structure Name | human vps33a in complex with a fragment of human vps16 |
| Resolution | 2.6Å |
| Reference | AUTH S.C.GRAHAM,L.WARTOSCH,S.R.GRAY,E.J.SCOURFIELD,J.E.DEANE,AUTH 2 J.P.LUZIO,D.J.OWENTITL STRUCTURAL BASIS OF VPS33A RECRUITMENT TO THE HUMAN HOPSTITL 2 COMPLEX BY VPS16.REF PROC.NATL.ACAD.SCI.USA V. 110 13345 2013REFN ISSN 0027-8424PMID 23901104DOI 10.1073/PNAS.1307074110 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 574 |
| Number Of SNVs | 132 |
| Number Of Permutations | 69863 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.006 |
| p-value | 0.236 |
COSMIC
| Number Of Residues | 574 |
| Number Of SNVs | 3 |
| Number Of Permutations | 278 |
| Optimal Distance Threshold | 50.0 |
| K Statistic | 0.333 |
| p-value | 0.228 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 132 |
| Number Of COSMIC SNVs | 3 |
| Optimal Distance Threshold | 37.0 |
| K Statistic | -0.569 |
| p-value | 0.153 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:122750948 | COSM4039570 | A>V | A:3 | (54.81, 59.98, 314.63) |
| 12:122750949 | rs141072842 | A>T | A:3 | (54.81, 59.98, 314.63) |
| 12:122750946 | rs539322852 | H>Y | A:4 | (50.81, 61.63, 313.86) |
| 12:122750928 | rs571511630 | V>M | A:10 | (52.16, 56.49, 303.96) |
| 12:122750912 | L>W | A:15 | (54.98, 65.62, 302.24) | |
| 12:122750909 | R>L | A:16 | (55.42, 68.10, 308.19) | |
| 12:122750910 | R>C | A:16 | (55.42, 68.10, 308.19) | |
| 12:122750881 | E>D | A:25 | (65.70, 76.12, 301.52) | |
| 12:122748745 | A>V | A:35 | (58.68, 90.30, 309.17) | |
| 12:122748743 | I>V | A:36 | (56.01, 87.25, 308.23) | |
| 12:122748226 | M>I | A:63 | (53.96, 87.36, 312.85) | |
| 12:122748222 | T>A | A:65 | (47.76, 91.03, 309.34) | |
| 12:122748209 | N>S | A:69 | (47.45, 102.17, 305.20) | |
| 12:122748206 | R>H | A:70 | (53.14, 103.71, 307.55) | |
| 12:122748200 | P>L | A:72 | (53.90, 98.00, 311.24) | |
| 12:122748201 | P>T | A:72 | (53.90, 98.00, 311.24) | |
| 12:122748180 | I>L | A:79 | (59.19, 93.00, 305.32) | |
| 12:122748177 | COSM202596 | I>V | A:80 | (58.50, 88.31, 304.16) |
| 12:122748155 | L>P | A:87 | (44.42, 91.39, 291.47) | |
| 12:122748153 | E>K | A:88 | (42.12, 91.99, 296.32) | |
| 12:122748143 | D>V | A:91 | (46.44, 97.05, 295.13) | |
| 12:122748140 | rs374894067 | I>T | A:92 | (47.00, 95.94, 300.11) |
| 12:122748141 | rs114821540 | I>L | A:92 | (47.00, 95.94, 300.11) |
| 12:122748135 | A>T | A:94 | (51.69, 98.65, 297.25) | |
| 12:122748126 | rs143335526 | V>M | A:97 | (55.95, 99.38, 299.65) |
| 12:122748120 | rs573977857 | S>G | A:99 | (53.89, 103.93, 302.84) |
| 12:122745983 | R>Q | A:103 | (63.04, 109.62, 307.32) | |
| 12:122745960 | I>V | A:111 | (56.69, 88.09, 297.55) | |
| 12:122745956 | L>R | A:112 | (56.06, 83.50, 299.40) | |
| 12:122745951 | rs147687101 | V>L | A:114 | (50.68, 80.63, 298.69) |
| 12:122745944 | rs376590100 | R>H | A:116 | (50.06, 80.20, 290.97) |
| 12:122745945 | rs145366138 | R>C | A:116 | (50.06, 80.20, 290.97) |
| 12:122745942 | R>C | A:117 | (55.23, 83.23, 290.38) | |
| 12:122745923 | Q>R | A:123 | (51.97, 93.46, 285.00) | |
| 12:122745920 | R>Q | A:124 | (48.28, 95.90, 289.22) | |
| 12:122745893 | COSM1732992 | S>F | A:133 | (61.04, 96.78, 295.69) |
| 12:122745869 | S>N | A:141 | (53.55, 74.41, 296.31) | |
| 12:122745861 | COSM3457303 | L>F | A:144 | (47.87, 67.83, 299.41) |
| 12:122745857 | I>T | A:145 | (47.87, 69.90, 304.03) | |
| 12:122745848 | D>V | A:148 | (46.56, 62.07, 310.55) | |
| 12:122745840 | L>V | A:151 | (43.95, 62.73, 306.28) | |
| 12:122745831 | M>L | A:154 | (43.43, 71.19, 299.09) | |
| 12:122745818 | G>V | A:158 | (35.21, 76.55, 297.17) | |
| 12:122745811 | rs554163858 | F>L | A:160 | (30.66, 71.91, 295.53) |
| 12:122735642 | rs149732743 | C>Y | A:163 | (33.40, 73.34, 290.11) |
| 12:122735612 | Y>C | A:173 | (46.69, 73.32, 288.26) | |
| 12:122735607 | rs200143325 COSM936196 |
A>T | A:175 | (44.90, 68.47, 292.61) |
| 12:122735567 | rs150571876 | T>M | A:188 | (54.09, 56.25, 289.80) |
| 12:122735561 | P>H | A:190 | (49.87, 52.45, 288.68) | |
| 12:122735562 | P>A | A:190 | (49.87, 52.45, 288.68) | |
| 12:122735557 | Q>H | A:191 | (45.45, 51.34, 288.37) | |
| 12:122735535 | A>S | A:199 | (37.61, 63.27, 287.86) | |
| 12:122735531 | rs200032973 | R>P | A:200 | (38.34, 62.15, 282.87) |
| 12:122735532 | R>W | A:200 | (38.34, 62.15, 282.87) | |
| 12:122734585 | A>V | A:203 | (43.08, 62.61, 285.14) | |
| 12:122734561 | R>K | A:211 | (52.22, 63.75, 278.25) | |
| 12:122734562 | R>G | A:211 | (52.22, 63.75, 278.25) | |
| 12:122734535 | rs568695865 | I>V | A:220 | (60.35, 56.10, 293.69) |
| 12:122734525 | rs139224941 | V>A | A:223 | (53.35, 53.48, 298.10) |
| 12:122734526 | rs373733055 | V>I | A:223 | (53.35, 53.48, 298.10) |
| 12:122734517 | N>D | A:226 | (45.07, 52.10, 293.38) | |
| 12:122734498 | R>Q | A:232 | (30.64, 64.84, 297.44) | |
| 12:122734460 | T>S | A:245 | (30.89, 59.48, 314.86) | |
| 12:122734456 | COSM1511384 | Y>C | A:246 | (33.92, 61.39, 320.09) |
| 12:122734427 | rs34996966 | I>L | A:256 | (37.11, 70.11, 313.92) |
| 12:122729294 | rs558127298 | P>L | A:264 | (32.86, 74.75, 326.34) |
| 12:122729285 | K>R | A:267 | (33.02, 70.26, 331.94) | |
| 12:122729276 | P>L | A:270 | (41.76, 75.92, 334.83) | |
| 12:122729277 | P>S | A:270 | (41.76, 75.92, 334.83) | |
| 12:122729240 | rs201831186 COSM936194 |
T>M | A:282 | (36.71, 83.11, 330.60) |
| 12:122729228 | K>R | A:286 | (42.68, 75.41, 321.60) | |
| 12:122729211 | rs373704049 COSM3935789 |
A>S | A:292 | (48.76, 61.13, 318.86) |
| 12:122729198 | Y>C | A:296 | (40.48, 61.17, 319.19) | |
| 12:122729169 | A>T | A:306 | (30.57, 52.91, 322.19) | |
| 12:122729165 | rs553698385 | V>A | A:307 | (32.37, 56.01, 323.82) |
| 12:122729154 | L>I | A:311 | (35.52, 56.25, 328.69) | |
| 12:122729137 | rs369560611 | K>N | A:316 | (37.50, 50.46, 336.10) |
| 12:122729116 | E>D | A:323 | (44.26, 52.89, 345.14) | |
| 12:122729117 | E>A | A:323 | (44.26, 52.89, 345.14) | |
| 12:122727033 | V>A | A:331 | (62.76, 51.52, 348.57) | |
| 12:122727034 | rs138934995 | V>M | A:331 | (62.76, 51.52, 348.57) |
| 12:122727025 | I>V | A:334 | (58.69, 53.82, 345.71) | |
| 12:122727006 | Q>R | A:340 | (54.66, 53.49, 336.00) | |
| 12:122726964 | rs138405241 | H>R | A:354 | (38.25, 62.81, 325.36) |
| 12:122726956 | rs142464282 | I>V | A:357 | (34.14, 65.96, 325.03) |
| 12:122726937 | D>G | A:363 | (23.97, 67.43, 327.15) | |
| 12:122726931 | T>S | A:365 | (22.50, 63.11, 321.96) | |
| 12:122724484 | D>H | A:369 | (15.50, 68.62, 318.43) | |
| 12:122724481 | F>V | A:370 | (19.53, 64.42, 318.16) | |
| 12:122724463 | rs371664986 | V>M | A:376 | (13.09, 63.00, 309.91) |
| 12:122724444 | S>C | A:382 | (14.21, 54.58, 304.57) | |
| 12:122724435 | rs374204973 | D>V | A:385 | (6.67, 60.04, 303.69) |
| 12:122724433 | T>A | A:386 | (10.35, 61.47, 300.35) | |
| 12:122724429 | D>G | A:387 | (6.41, 63.12, 298.65) | |
| 12:122723264 | N>S | A:391 | (4.76, 68.36, 310.07) | |
| 12:122723258 | I>T | A:393 | (10.81, 70.71, 308.34) | |
| 12:122723244 | rs186215132 | A>T | A:398 | (8.08, 78.48, 312.83) |
| 12:122723237 | rs576248840 | K>T | A:400 | (13.67, 81.92, 313.19) |
| 12:122723231 | rs377687330 COSM316479 |
S>L | A:402 | (19.05, 77.21, 312.06) |
| 12:122723193 | COSM3416564 | V>M | A:415 | (18.44, 63.86, 297.50) |
| 12:122723172 | Q>E | A:422 | (7.06, 72.83, 291.57) | |
| 12:122723139 | rs376097037 COSM1232375 |
L>I | A:433 | (11.93, 83.71, 301.48) |
| 12:122720464 | G>S | A:437 | (14.43, 86.40, 303.80) | |
| 12:122720455 | rs143287106 | H>Y | A:440 | (18.41, 83.78, 302.23) |
| 12:122720452 | I>L | A:441 | (16.15, 83.84, 296.38) | |
| 12:122720440 | rs144105987 | H>N | A:445 | (18.05, 80.33, 292.96) |
| 12:122720434 | rs371402962 | L>M | A:447 | (20.82, 74.81, 297.06) |
| 12:122720422 | G>S | A:451 | (21.17, 69.37, 293.35) | |
| 12:122720403 | T>M | A:457 | (11.98, 65.57, 286.43) | |
| 12:122720391 | N>S | A:461 | (12.61, 58.35, 292.45) | |
| 12:122720386 | rs574910295 | Y>H | A:463 | (17.62, 56.84, 297.32) |
| 12:122720380 | T>A | A:465 | (17.04, 51.55, 292.47) | |
| 12:122720377 | rs556251997 | I>V | A:466 | (20.50, 53.87, 294.13) |
| 12:122720373 | R>Q | A:467 | (17.30, 52.59, 299.07) | |
| 12:122720374 | R>W | A:467 | (17.30, 52.59, 299.07) | |
| 12:122720362 | COSM1476265 | R>C | A:471 | (23.61, 46.37, 301.43) |
| 12:122720353 | M>V | A:474 | (21.04, 48.30, 307.07) | |
| 12:122720344 | V>I | A:477 | (23.05, 48.47, 312.83) | |
| 12:122720333 | Q>H | A:480 | (28.59, 48.58, 320.49) | |
| 12:122717488 | S>G | A:490 | (22.88, 54.30, 312.64) | |
| 12:122717467 | V>L | A:497 | (32.37, 54.21, 301.03) | |
| 12:122717464 | COSM936189 | R>W | A:498 | (28.65, 50.40, 299.99) |
| 12:122717442 | R>Q | A:505 | (36.10, 42.38, 297.36) | |
| 12:122717436 | G>D | A:507 | (33.47, 45.38, 290.85) | |
| 12:122717430 | rs200715881 COSM271599 |
R>Q | A:509 | (31.91, 46.33, 285.17) |
| 12:122717423 | I>M | A:511 | (27.43, 48.42, 289.86) | |
| 12:122717422 | E>K | A:512 | (27.34, 49.49, 284.50) | |
| 12:122717416 | rs143321630 | V>F | A:514 | (23.66, 52.08, 289.44) |
| 12:122717409 | R>H | A:516 | (25.07, 53.36, 282.36) | |
| 12:122717410 | R>C | A:516 | (25.07, 53.36, 282.36) | |
| 12:122717406 | I>T | A:517 | (21.59, 56.34, 287.35) | |
| 12:122717407 | I>L | A:517 | (21.59, 56.34, 287.35) | |
| 12:122717400 | P>Q | A:519 | (26.67, 61.79, 288.30) | |
| 12:122717394 | P>L | A:521 | (32.20, 59.81, 283.83) | |
| 12:122717383 | E>K | A:525 | (43.29, 55.70, 282.55) | |
| 12:122717380 | R>W | A:526 | (46.74, 50.81, 283.36) | |
| 12:122717367 | P>L | A:530 | (59.64, 51.86, 284.91) | |
| 12:122716956 | R>Q | A:543 | (44.90, 46.21, 296.90) | |
| 12:122716945 | I>L | A:547 | (40.05, 57.99, 298.21) | |
| 12:122716927 | V>I | A:553 | (35.23, 64.59, 303.28) | |
| 12:122716918 | A>T | A:556 | (32.12, 59.56, 308.70) | |
| 12:122716890 | S>F | A:565 | (41.35, 49.61, 306.10) | |
| 12:122716879 | D>N | A:569 | (39.28, 41.12, 304.02) | |
| 12:122716869 | T>I | A:572 | (42.01, 47.82, 300.31) | |
| 12:122716861 | V>I | A:575 | (45.12, 57.08, 301.93) | |
| 12:122716815 | A>G | A:590 | (29.74, 77.85, 301.23) | |
| 12:122716801 | rs200158890 | P>T | A:595 | (24.97, 88.69, 304.23) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:122748207 | COSM692587 | R>C | A:70 | (53.14, 103.71, 307.55) |
| 12:122735567 | COSM936195 | T>M | A:188 | (54.09, 56.25, 289.80) |
| 12:122723193 | COSM3416564 | V>M | A:415 | (18.44, 63.86, 297.50) |