General Structure Information
| PDB ID | 1n52 |
| HGNC Gene Label(s) | NCBP1 |
| Structure Name | cap binding complex |
| Resolution | 2.11Å |
| Reference | AUTH G.CALERO,K.WILSON,T.LY,J.RIOS-STEINER,J.CLARDY,R.CERIONETITL STRUCTURAL BASIS OF M7GPPPG BINDING TO THE NUCLEARTITL 2 CAP-BINDING PROTEIN COMPLEX.REF NAT.STRUCT.BIOL. V. 9 912 2002REFN ISSN 1072-8368PMID 12434151DOI 10.1038/NSB874 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 732 |
| Number Of SNVs | 117 |
| Number Of Permutations | 68991 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.012 |
| p-value | 0.777 |
COSMIC
| Number Of Residues | 732 |
| Number Of SNVs | 3 |
| Number Of Permutations | 268 |
| Optimal Distance Threshold | 4.0 |
| K Statistic | 0.333 |
| p-value | 0.056 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 117 |
| Number Of COSMIC SNVs | 3 |
| Optimal Distance Threshold | 4.0 |
| K Statistic | 0.333 |
| p-value | 0.65 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 9:100403119 | E>D | A:26 | (-6.68, 72.79, -6.76) | |
| 9:100403153 | V>L | A:38 | (-5.34, 77.59, 12.05) | |
| 9:100403853 | S>P | A:45 | (2.44, 82.58, 16.09) | |
| 9:100403904 | P>S | A:62 | (-14.93, 87.49, -4.15) | |
| 9:100403905 | rs199768033 | P>R | A:62 | (-14.93, 87.49, -4.15) |
| 9:100403909 | N>K | A:63 | (-14.74, 84.08, -6.59) | |
| 9:100403911 | COSM3902437 | Y>F | A:64 | (-13.55, 80.84, -3.93) |
| 9:100403930 | R>S | A:70 | (-20.25, 75.99, 2.53) | |
| 9:100405488 | A>G | A:76 | (-18.30, 75.17, 14.41) | |
| 9:100405491 | rs368904475 | R>H | A:77 | (-21.04, 70.89, 12.85) |
| 9:100405523 | rs561132889 | T>A | A:88 | (-10.77, 84.90, 16.28) |
| 9:100405530 | rs200044823 | V>A | A:90 | (-15.42, 85.00, 12.36) |
| 9:100405557 | rs375702222 | N>S | A:99 | (-21.86, 92.58, 4.74) |
| 9:100405560 | F>C | A:100 | (-18.33, 87.15, 5.84) | |
| 9:100405579 | E>D | A:106 | (-28.03, 84.84, 8.67) | |
| 9:100405589 | R>C | A:110 | (-29.72, 78.90, 8.07) | |
| 9:100405590 | R>H | A:110 | (-29.72, 78.90, 8.07) | |
| 9:100405623 | rs201055450 | Y>C | A:121 | (-30.95, 68.88, 20.88) |
| 9:100405634 | rs143745791 | V>M | A:125 | (-24.16, 73.09, 22.53) |
| 9:100407402 | R>C | A:129 | (-20.42, 76.34, 23.70) | |
| 9:100407444 | P>S | A:143 | (-26.89, 92.83, 24.01) | |
| 9:100407445 | COSM403880 | P>L | A:143 | (-26.89, 92.83, 24.01) |
| 9:100407450 | M>V | A:145 | (-26.54, 86.15, 23.12) | |
| 9:100407452 | M>I | A:145 | (-26.54, 86.15, 23.12) | |
| 9:100407459 | M>V | A:148 | (-31.05, 83.46, 22.40) | |
| 9:100407460 | rs570584263 | M>T | A:148 | (-31.05, 83.46, 22.40) |
| 9:100407477 | rs148430361 | S>G | A:154 | (-38.20, 80.47, 28.79) |
| 9:100407480 | rs199742053 | V>I | A:155 | (-38.10, 76.23, 28.07) |
| 9:100407494 | rs367832805 | E>D | A:159 | (-46.64, 73.99, 30.72) |
| 9:100407501 | P>S | A:162 | (-40.00, 66.86, 28.49) | |
| 9:100407502 | P>L | A:162 | (-40.00, 66.86, 28.49) | |
| 9:100407897 | R>Q | A:165 | (-37.42, 70.93, 25.81) | |
| 9:100407900 | R>Q | A:166 | (-38.37, 71.95, 31.06) | |
| 9:100407911 | V>L | A:170 | (-30.15, 75.38, 31.30) | |
| 9:100407924 | L>R | A:174 | (-25.10, 77.29, 32.38) | |
| 9:100407970 | rs369507099 | D>E | A:189 | (-27.44, 93.21, 35.35) |
| 9:100407983 | rs144152800 | R>C | A:194 | (-36.05, 87.96, 34.93) |
| 9:100407984 | COSM307501 | R>H | A:194 | (-36.05, 87.96, 34.93) |
| 9:100407999 | T>I | A:199 | (-32.14, 78.90, 36.75) | |
| 9:100408004 | S>G | A:201 | (-36.24, 77.98, 40.49) | |
| 9:100408014 | K>R | A:204 | (-34.39, 74.81, 43.85) | |
| 9:100409790 | H>Y | A:210 | (-31.67, 60.88, 37.21) | |
| 9:100409794 | V>G | A:211 | (-28.71, 60.04, 40.27) | |
| 9:100409799 | M>V | A:213 | (-29.72, 54.30, 37.05) | |
| 9:100409812 | W>L | A:217 | (-17.61, 55.36, 42.11) | |
| 9:100409817 | rs146305083 | A>S | A:219 | (-19.96, 56.87, 47.62) |
| 9:100409827 | P>L | A:222 | (-13.67, 60.19, 48.15) | |
| 9:100410342 | rs547285420 | Q>R | A:245 | (-12.00, 86.69, 36.66) |
| 9:100410422 | T>S | A:272 | (-38.58, 80.91, 18.91) | |
| 9:100410458 | rs377142866 | M>V | A:284 | (-29.81, 60.71, 28.47) |
| 9:100412821 | F>L | A:312 | (-17.01, 72.12, 31.92) | |
| 9:100412827 | I>V | A:314 | (-9.86, 70.70, 31.03) | |
| 9:100412832 | E>D | A:315 | (-13.14, 67.17, 31.78) | |
| 9:100412843 | H>R | A:319 | (-14.73, 64.20, 26.83) | |
| 9:100412851 | I>V | A:322 | (-11.68, 61.36, 22.33) | |
| 9:100412860 | H>Y | A:325 | (-9.12, 62.56, 16.49) | |
| 9:100412866 | K>E | A:327 | (-12.02, 56.76, 13.45) | |
| 9:100413630 | I>S | A:345 | (-2.79, 71.40, 33.62) | |
| 9:100413650 | rs146487190 | V>I | A:352 | (-6.71, 58.92, 32.98) |
| 9:100416113 | P>T | A:365 | (-19.94, 54.18, 26.44) | |
| 9:100416123 | I>T | A:368 | (-16.01, 50.47, 20.97) | |
| 9:100416140 | T>A | A:374 | (-5.86, 50.74, 22.49) | |
| 9:100416162 | K>R | A:381 | (3.69, 53.55, 22.92) | |
| 9:100417189 | rs201715578 | M>L | A:400 | (-9.22, 50.53, 47.35) |
| 9:100417192 | COSM1464328 | R>G | A:401 | (-12.21, 54.59, 45.10) |
| 9:100417193 | rs191669699 | R>H | A:401 | (-12.21, 54.59, 45.10) |
| 9:100417198 | D>N | A:403 | (-16.74, 48.17, 48.19) | |
| 9:100417201 | rs377011060 | T>A | A:404 | (-19.55, 51.59, 46.05) |
| 9:100417988 | rs562093927 | I>V | A:414 | (-13.11, 43.05, 34.88) |
| 9:100418028 | rs529407443 | R>H | A:427 | (4.67, 41.94, 35.08) |
| 9:100418301 | C>F | A:436 | (-8.81, 40.14, 48.99) | |
| 9:100418313 | D>G | A:440 | (-16.90, 37.11, 51.57) | |
| 9:100418321 | S>G | A:443 | (-16.63, 40.79, 48.49) | |
| 9:100418330 | P>S | A:446 | (-12.56, 39.36, 46.14) | |
| 9:100418331 | rs77602722 | P>L | A:446 | (-12.56, 39.36, 46.14) |
| 9:100418348 | V>I | A:452 | (-9.49, 39.72, 36.31) | |
| 9:100418361 | C>F | A:456 | (-6.45, 36.49, 31.95) | |
| 9:100420932 | H>Y | A:462 | (-5.02, 27.11, 34.22) | |
| 9:100420936 | Q>L | A:463 | (-0.25, 26.94, 34.38) | |
| 9:100420939 | COSM1103043 | R>H | A:464 | (0.99, 32.79, 31.77) |
| 9:100420957 | P>L | A:470 | (0.94, 35.37, 44.20) | |
| 9:100420992 | rs543815167 | T>A | A:482 | (-12.12, 20.32, 32.42) |
| 9:100421011 | rs565223329 | G>A | A:488 | (-17.83, 8.12, 31.31) |
| 9:100423231 | S>F | A:494 | (-26.41, 3.38, 37.89) | |
| 9:100423251 | A>T | A:501 | (-24.17, 6.50, 25.35) | |
| 9:100423254 | L>V | A:502 | (-21.79, 3.56, 25.71) | |
| 9:100423294 | D>G | A:515 | (-31.11, 8.47, 10.33) | |
| 9:100423317 | D>N | A:523 | (-33.21, 1.88, 22.27) | |
| 9:100424344 | P>T | A:541 | (-35.74, 13.81, 29.08) | |
| 9:100424345 | P>L | A:541 | (-35.74, 13.81, 29.08) | |
| 9:100424354 | rs141653335 | I>T | A:544 | (-31.79, 15.51, 25.53) |
| 9:100424381 | H>R | A:553 | (-16.59, 13.56, 25.56) | |
| 9:100424393 | K>T | A:557 | (-9.29, 19.00, 21.01) | |
| 9:100425239 | F>L | A:569 | (-24.99, 14.92, 14.39) | |
| 9:100425246 | V>I | A:572 | (-30.91, 15.25, 16.28) | |
| 9:100425269 | rs576031865 | S>R | A:579 | (-39.72, 21.64, 23.16) |
| 9:100425271 | D>G | A:580 | (-39.83, 25.33, 25.07) | |
| 9:100425300 | M>V | A:590 | (-24.38, 22.85, 27.90) | |
| 9:100425301 | M>T | A:590 | (-24.38, 22.85, 27.90) | |
| 9:100425320 | rs200307901 | N>K | A:596 | (-15.50, 23.87, 34.63) |
| 9:100426647 | M>T | A:608 | (-27.21, 26.61, 20.36) | |
| 9:100426649 | I>V | A:609 | (-29.46, 31.30, 19.34) | |
| 9:100426652 | R>C | A:610 | (-26.26, 33.17, 15.49) | |
| 9:100426653 | rs189780807 | R>H | A:610 | (-26.26, 33.17, 15.49) |
| 9:100426664 | V>I | A:614 | (-32.03, 27.30, 21.31) | |
| 9:100426674 | A>V | A:617 | (-36.63, 32.38, 25.88) | |
| 9:100426686 | N>S | A:621 | (-36.17, 30.74, 31.24) | |
| 9:100426690 | W>C | A:622 | (-29.35, 28.49, 31.15) | |
| 9:100426712 | rs199656608 | R>C | A:630 | (-24.09, 27.26, 43.49) |
| 9:100426713 | rs76139042 | R>L | A:630 | (-24.09, 27.26, 43.49) |
| 9:100429046 | rs563025088 | L>V | A:635 | (-19.14, 38.34, 34.53) |
| 9:100429053 | V>A | A:637 | (-24.48, 34.60, 33.29) | |
| 9:100429073 | rs530473497 | T>S | A:644 | (-29.22, 36.61, 23.63) |
| 9:100429080 | rs372649867 | R>H | A:646 | (-26.19, 42.08, 21.71) |
| 9:100429106 | I>F | A:655 | (-36.39, 41.86, 9.31) | |
| 9:100429112 | rs35694910 | K>Q | A:657 | (-33.01, 46.40, 6.20) |
| 9:100431186 | I>T | A:692 | (-43.71, 43.69, 1.13) | |
| 9:100431187 | rs564435323 | I>M | A:692 | (-43.71, 43.69, 1.13) |
| 9:100431203 | rs369608673 | K>E | A:698 | (-39.76, 37.95, 9.36) |
| 9:100431213 | S>Y | A:701 | (-42.83, 37.67, 14.63) | |
| 9:100431887 | I>V | A:720 | (-35.61, 36.75, 42.00) | |
| 9:100431908 | rs201932796 | R>G | A:727 | (-36.36, 35.14, 52.01) |
| 9:100431944 | rs148698789 | W>R | A:739 | (-28.76, 37.72, 45.19) |
| 9:100431952 | K>N | A:741 | (-24.79, 45.03, 44.53) | |
| 9:100431954 | N>S | A:742 | (-25.68, 41.23, 41.01) | |
| 9:100431960 | I>T | A:744 | (-30.87, 45.49, 41.94) | |
| 9:100433390 | Y>F | A:761 | (-41.92, 47.13, 25.20) | |
| 9:100433434 | rs142212526 | P>T | A:776 | (-40.29, 49.88, 46.83) |
| 9:100433449 | rs377264051 | V>M | A:781 | (-35.26, 50.27, 38.86) |
| 9:100433465 | C>S | A:786 | (-38.80, 56.68, 33.34) | |
| 9:100433477 | A>G | A:790 | (-38.45, 63.23, 31.61) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 9:100423288 | COSM1286519 | T>S | A:513 | (-25.86, 8.87, 10.21) |
| 9:100423298 | COSM3432686 | E>D | A:516 | (-26.97, 5.59, 11.97) |
| 9:100431908 | COSM4368986 | R>G | A:727 | (-36.36, 35.14, 52.01) |