General Structure Information
| PDB ID | 4b3z |
| HGNC Gene Label(s) | CRMP1 |
| Structure Name | structure of the human collapsin response mediator protein-1, a lung cancer suppressor |
| Resolution | 3.05Å |
| Reference | AUTH S.H.LIU,S.F.HUANG,Y.L.HSU,S.H.PAN,Y.J.CHEN,Y.H.LINTITL STRUCTURE OF HUMAN COLLAPSIN RESPONSE MEDIATOR PROTEIN 1: ATITL 2 POSSIBLE ROLE OF ITS C-TERMINAL TAIL.REF ACTA CRYSTALLOGR.,SECT.F V. 71 938 2015REFN ISSN 1744-3091PMID 26249678DOI 10.1107/S2053230X15009243 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 469 |
| Number Of SNVs | 109 |
| Number Of Permutations | 24692 |
| Optimal Distance Threshold | 19.0 |
| K Statistic | 0.206 |
| p-value | 0.2 |
COSMIC
| Number Of Residues | 469 |
| Number Of SNVs | 11 |
| Number Of Permutations | 7156 |
| Optimal Distance Threshold | 20.0 |
| K Statistic | 0.145 |
| p-value | 0.461 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 109 |
| Number Of COSMIC SNVs | 9 |
| Optimal Distance Threshold | 11.0 |
| K Statistic | -0.054 |
| p-value | 0.318 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:5868455 | R>Q | B:23 | (159.28, 7.78, 54.29) | |
| 4:5868456 | R>W | B:23 | (159.28, 7.78, 54.29) | |
| 4:5868444 | rs545458583 | D>Y | B:27 | (161.85, 9.25, 41.70) |
| 4:5868432 | L>F | B:31 | (165.46, 9.32, 53.05) | |
| 4:5868420 | rs377482181 | V>I | B:35 | (163.82, 19.00, 55.33) |
| 4:5868401 | L>H | B:41 | (166.07, 27.00, 48.11) | |
| 4:5868399 | I>V | B:42 | (165.96, 22.38, 49.77) | |
| 4:5862915 | V>I | B:51 | (169.13, 24.31, 63.78) | |
| 4:5862878 | rs373508403 COSM1540663 |
R>Q | B:63 | (152.73, 11.39, 59.09) |
| 4:5862879 | rs147608754 | R>W | B:63 | (152.73, 11.39, 59.09) |
| 4:5862846 | T>S | B:74 | (145.98, 23.91, 33.15) | |
| 4:5862801 | F>I | B:89 | (145.37, 31.91, 37.26) | |
| 4:5862797 | F>Y | B:90 | (143.44, 33.70, 43.79) | |
| 4:5862793 | Q>H | B:91 | (140.01, 30.65, 43.50) | |
| 4:5862795 | rs549636760 | Q>K | B:91 | (140.01, 30.65, 43.50) |
| 4:5862782 | COSM1738975 | A>V | B:95 | (143.01, 24.72, 44.71) |
| 4:5862776 | L>Q | B:97 | (148.41, 25.16, 46.73) | |
| 4:5862777 | L>V | B:97 | (148.41, 25.16, 46.73) | |
| 4:5858025 | rs138323311 | V>A | B:108 | (147.96, 30.10, 25.62) |
| 4:5858003 | S>R | B:115 | (149.43, 37.01, 17.83) | |
| 4:5858004 | S>N | B:115 | (149.43, 37.01, 17.83) | |
| 4:5858002 | L>I | B:116 | (151.03, 33.37, 19.29) | |
| 4:5857995 | T>N | B:118 | (149.39, 39.20, 21.72) | |
| 4:5857987 | E>K | B:121 | (152.57, 39.11, 27.01) | |
| 4:5857982 | rs371476843 | K>N | B:122 | (145.94, 38.46, 27.71) |
| 4:5857979 | W>C | B:123 | (146.47, 33.68, 28.70) | |
| 4:5857933 | rs548835481 | V>M | B:139 | (151.44, 28.17, 23.38) |
| 4:5857923 | rs189022086 | T>I | B:142 | (144.99, 27.68, 16.91) |
| 4:5857912 | COSM1430385 | D>N | B:146 | (152.05, 33.78, 6.94) |
| 4:5857909 | rs114376030 | G>R | B:147 | (154.07, 34.17, 10.73) |
| 4:5857902 | COSM1249130 COSM4135414 |
R>Q | B:149 | (157.86, 29.10, 10.54) |
| 4:5857903 | rs373503083 | R>W | B:149 | (157.86, 29.10, 10.54) |
| 4:5857896 | E>A | B:151 | (155.22, 34.75, 16.35) | |
| 4:5857887 | V>A | B:154 | (160.15, 34.95, 20.00) | |
| 4:5853194 | rs200972738 | V>I | B:161 | (157.85, 28.80, 25.94) |
| 4:5853190 | N>S | B:162 | (159.43, 24.24, 26.21) | |
| 4:5853173 | M>L | B:168 | (144.29, 16.12, 15.04) | |
| 4:5853166 | Y>F | B:170 | (138.17, 21.10, 17.97) | |
| 4:5853154 | Y>C | B:174 | (141.00, 25.44, 17.28) | |
| 4:5853152 | Q>K | B:175 | (141.61, 20.37, 11.89) | |
| 4:5853147 | M>I | B:176 | (146.67, 21.25, 11.95) | |
| 4:5853143 | COSM734027 | D>N | B:178 | (148.07, 15.21, 7.65) |
| 4:5853140 | S>G | B:179 | (150.45, 18.64, 5.54) | |
| 4:5851195 | Y>C | B:182 | (156.13, 16.55, 7.97) | |
| 4:5851193 | rs556396914 | E>K | B:183 | (155.11, 22.59, 8.27) |
| 4:5851189 | rs200982795 | A>G | B:184 | (154.88, 21.71, 12.79) |
| 4:5851181 | rs142860765 | F>L | B:187 | (159.69, 25.26, 13.07) |
| 4:5851171 | G>D | B:190 | (164.34, 22.76, 15.78) | |
| 4:5851160 | V>M | B:194 | (157.52, 19.79, 23.94) | |
| 4:5851151 | V>I | B:197 | (148.76, 16.25, 20.54) | |
| 4:5851144 | A>G | B:199 | (143.95, 13.42, 19.73) | |
| 4:5851145 | A>T | B:199 | (143.95, 13.42, 19.73) | |
| 4:5851121 | rs148566004 | Q>K | B:207 | (130.56, 13.49, 9.41) |
| 4:5844878 | R>Q | B:211 | (124.75, 9.65, 13.21) | |
| 4:5844865 | rs146352571 | M>I | B:215 | (118.90, 10.50, 15.19) |
| 4:5844857 | rs142255876 | T>M | B:218 | (120.26, 17.15, 22.29) |
| 4:5844828 | P>S | B:228 | (134.05, 7.81, 19.59) | |
| 4:5843133 | COSM1202301 COSM1718509 |
R>Q | B:238 | (146.78, 10.81, 12.24) |
| 4:5843124 | rs138991048 | T>I | B:241 | (153.10, 7.97, 12.31) |
| 4:5843118 | A>G | B:243 | (156.89, 11.61, 14.90) | |
| 4:5843112 | rs200099288 | R>Q | B:245 | (158.94, 8.31, 10.03) |
| 4:5843113 | rs149255467 | R>W | B:245 | (158.94, 8.31, 10.03) |
| 4:5843109 | I>T | B:246 | (159.97, 13.99, 11.68) | |
| 4:5843092 | I>L | B:252 | (149.42, 12.31, 23.69) | |
| 4:5843089 | T>A | B:253 | (147.01, 15.69, 25.43) | |
| 4:5843062 | rs372823825 COSM3767925 |
D>N | B:262 | (146.74, 0.11, 24.27) |
| 4:5843059 | COSM1158297 | I>V | B:263 | (148.13, 3.03, 20.29) |
| 4:5843050 | L>V | B:266 | (152.57, -0.89, 20.59) | |
| 4:5843038 | rs150121214 | K>E | B:270 | (157.52, -0.70, 17.61) |
| 4:5841378 | A>V | B:280 | (142.17, 12.79, 36.87) | |
| 4:5841363 | T>N | B:285 | (135.45, 8.99, 36.63) | |
| 4:5841361 | rs376257908 COSM1430381 |
D>N | B:286 | (133.18, 6.60, 34.31) |
| 4:5841354 | T>N | B:288 | (128.29, 6.47, 33.01) | |
| 4:5841351 | H>R | B:289 | (128.27, 9.95, 35.35) | |
| 4:5841330 | A>G | B:296 | (123.69, 19.60, 35.25) | |
| 4:5841321 | A>V | B:299 | (127.34, 18.85, 31.66) | |
| 4:5841319 | A>T | B:300 | (130.00, 18.68, 34.12) | |
| 4:5841315 | F>S | B:301 | (130.98, 14.58, 34.00) | |
| 4:5841291 | rs367815553 | P>L | B:309 | (131.56, 5.02, 28.38) |
| 4:5841286 | P>S | B:311 | (133.42, 1.04, 33.43) | |
| 4:5841282 | T>I | B:312 | (137.04, -0.90, 32.62) | |
| 4:5841274 | rs577291213 | D>N | B:315 | (141.18, 0.42, 36.83) |
| 4:5841264 | rs373607371 | T>I | B:318 | (145.98, 3.19, 36.75) |
| 4:5841252 | rs372231548 | A>V | B:322 | (152.39, 1.48, 36.91) |
| 4:5838621 | Q>H | B:327 | (154.74, 8.73, 31.26) | |
| 4:5838608 | rs374326359 | G>S | B:332 | (142.05, 19.71, 32.65) |
| 4:5838599 | rs183322981 | P>S | B:335 | (136.43, 26.29, 35.17) |
| 4:5838577 | rs371310830 COSM4125346 |
A>V | B:342 | (123.16, 26.20, 29.80) |
| 4:5838566 | D>H | B:346 | (118.77, 23.01, 23.30) | |
| 4:5838539 | V>I | B:355 | (136.44, 19.15, 33.89) | |
| 4:5838535 | rs141437952 | N>I | B:356 | (136.72, 19.11, 38.11) |
| 4:5838512 | rs370480340 | V>I | B:364 | (142.42, 10.75, 42.50) |
| 4:5838501 | COSM215949 | D>E | B:367 | (142.57, 6.17, 46.00) |
| 4:5837763 | N>S | B:387 | (158.18, 12.05, 35.16) | |
| 4:5837725 | rs377414609 | R>W | B:400 | (164.88, 15.37, 43.72) |
| 4:5837716 | V>M | B:403 | (170.51, 20.27, 48.28) | |
| 4:5837712 | rs373011172 | G>D | B:404 | (168.71, 23.32, 45.67) |
| 4:5837698 | V>M | B:409 | (157.36, 20.58, 50.26) | |
| 4:5837686 | D>N | B:413 | (148.62, 11.47, 55.82) | |
| 4:5837678 | rs190668040 | D>E | B:415 | (146.44, 6.92, 56.69) |
| 4:5837680 | rs145169573 | D>N | B:415 | (146.44, 6.92, 56.69) |
| 4:5837675 | K>N | B:416 | (144.07, 12.75, 56.11) | |
| 4:5837659 | COSM1056400 COSM1056399 |
A>T | B:422 | (130.61, 20.45, 46.19) |
| 4:5837643 | COSM447985 | S>L | B:427 | (135.14, 26.02, 43.31) |
| 4:5830394 | COSM1486024 | A>V | B:428 | (132.14, 28.05, 42.07) |
| 4:5830389 | E>Q | B:430 | (127.40, 24.50, 40.94) | |
| 4:5830352 | rs139579016 | S>F | B:442 | (145.72, 13.67, 52.10) |
| 4:5830320 | COSM1430378 | V>I | B:453 | (150.28, 27.75, 51.78) |
| 4:5830298 | N>S | B:460 | (148.16, 31.86, 54.15) | |
| 4:5830299 | N>D | B:460 | (148.16, 31.86, 54.15) | |
| 4:5830296 | rs34611001 | V>I | B:461 | (147.27, 32.27, 49.66) |
| 4:5830282 | M>I | B:465 | (153.91, 35.31, 45.57) | |
| 4:5830283 | M>T | B:465 | (153.91, 35.31, 45.57) | |
| 4:5830284 | rs140124818 | M>V | B:465 | (153.91, 35.31, 45.57) |
| 4:5830278 | rs146163071 | R>C | B:467 | (158.55, 32.38, 40.92) |
| 4:5830268 | rs370759908 | P>L | B:470 | (161.69, 30.03, 32.76) |
| 4:5830269 | rs201976585 COSM239442 |
P>S | B:470 | (161.69, 30.03, 32.76) |
| 4:5830266 | COSM3428575 | R>W | B:471 | (159.43, 25.86, 29.95) |
| 4:5830259 | COSM88528 | A>V | B:473 | (165.24, 24.25, 24.89) |
| 4:5830260 | rs141992841 | A>T | B:473 | (165.24, 24.25, 24.89) |
| 4:5830249 | E>D | B:476 | (168.97, 15.55, 28.74) | |
| 4:5830233 | rs149485730 | V>I | B:482 | (166.49, 13.15, 18.84) |
| 4:5827379 | G>E | B:490 | (171.77, 8.69, 7.64) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:5868434 | COSM1694113 | S>F | B:30 | (162.94, 6.58, 50.51) |
| 4:5862882 | COSM3302443 | G>R | B:62 | (156.16, 9.78, 59.56) |
| 4:5862782 | COSM1738975 | A>V | B:95 | (143.01, 24.72, 44.71) |
| 4:5857975 | COSM1202305 | E>K | B:125 | (149.01, 40.58, 33.07) |
| 4:5857888 | COSM1540666 | V>M | B:154 | (160.15, 34.95, 20.00) |
| 4:5843133 | COSM1202301 | R>Q | B:238 | (146.78, 10.81, 12.24) |
| 4:5843059 | COSM1158297 | I>V | B:263 | (148.13, 3.03, 20.29) |
| 4:5838577 | COSM4125346 | A>V | B:342 | (123.16, 26.20, 29.80) |
| 4:5838496 | COSM1310164 | A>V | B:369 | (147.64, 3.84, 42.47) |
| 4:5837779 | COSM1056401 | A>T | B:382 | (156.80, 10.39, 39.22) |
| 4:5830320 | COSM1430378 | V>I | B:453 | (150.28, 27.75, 51.78) |
| 4:5830269 | COSM239442 | P>S | B:470 | (161.69, 30.03, 32.76) |