General Structure Information
| PDB ID | 3nyo |
| HGNC Gene Label(s) | GRK6 |
| Structure Name | crystal structure of g protein-coupled receptor kinase 6 in complex with amp |
| Resolution | 2.92Å |
| Reference | AUTH C.A.BOGUTH,P.SINGH,C.C.HUANG,J.J.TESMERTITL MOLECULAR BASIS FOR ACTIVATION OF G PROTEIN-COUPLED RECEPTORTITL 2 KINASES.REF EMBO J. V. 29 3249 2010REFN ISSN 0261-4189PMID 20729810DOI 10.1038/EMBOJ.2010.206 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 553 |
| Number Of SNVs | 115 |
| Number Of Permutations | 76680 |
| Optimal Distance Threshold | 33.0 |
| K Statistic | 0.379 |
| p-value | 0.006 |
COSMIC
| Number Of Residues | 553 |
| Number Of SNVs | 3 |
| Number Of Permutations | 17 |
| Optimal Distance Threshold | 25.0 |
| K Statistic | 0.333 |
| p-value | 1.0 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 115 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.088 |
| p-value | 0.462 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:176853883 | L>I | A:13 | (-63.29, 7.35, 11.41) | |
| 5:176857878 | rs182443546 | G>S | A:20 | (-63.29, 11.42, -1.16) |
| 5:176857879 | G>V | A:20 | (-63.29, 11.42, -1.16) | |
| 5:176857888 | rs547540433 | R>H | A:23 | (-64.93, 13.76, -3.84) |
| 5:176857912 | rs141014084 | R>Q | A:31 | (-68.56, 23.22, -9.22) |
| 5:176857915 | Q>R | A:32 | (-74.96, 21.72, -10.56) | |
| 5:176857917 | M>L | A:33 | (-75.77, 21.76, -5.17) | |
| 5:176857928 | F>L | A:36 | (-73.70, 31.95, -8.28) | |
| 5:176857935 | rs539625494 | I>V | A:39 | (-78.32, 39.61, -11.28) |
| 5:176857942 | Q>R | A:41 | (-83.18, 35.49, -9.03) | |
| 5:176857947 | rs557978680 | E>K | A:43 | (-83.36, 43.98, -7.20) |
| 5:176858999 | rs370990784 | R>H | A:51 | (-77.45, 50.95, 1.46) |
| 5:176859019 | E>K | A:58 | (-67.21, 45.00, 10.37) | |
| 5:176859023 | R>Q | A:59 | (-71.40, 40.63, 12.43) | |
| 5:176859037 | R>C | A:64 | (-63.97, 41.46, 6.55) | |
| 5:176859038 | R>H | A:64 | (-63.97, 41.46, 6.55) | |
| 5:176859050 | R>Q | A:68 | (-60.18, 42.61, 2.90) | |
| 5:176859052 | E>K | A:69 | (-61.98, 40.81, -2.74) | |
| 5:176859065 | rs56382815 | T>M | A:73 | (-58.78, 47.86, -6.54) |
| 5:176859071 | P>L | A:75 | (-54.43, 52.25, -3.91) | |
| 5:176859082 | R>C | A:79 | (-52.17, 52.70, 2.42) | |
| 5:176859083 | rs571235637 | R>H | A:79 | (-52.17, 52.70, 2.42) |
| 5:176859085 | C>R | A:80 | (-56.47, 51.50, 4.78) | |
| 5:176859088 | V>I | A:81 | (-57.12, 47.34, 4.81) | |
| 5:176859091 | COSM3783897 COSM3783896 |
A>T | A:82 | (-53.34, 46.87, 5.91) |
| 5:176859235 | A>V | A:88 | (-55.01, 43.84, 15.00) | |
| 5:176859237 | rs139370245 | E>K | A:89 | (-50.81, 41.59, 14.34) |
| 5:176859253 | P>L | A:94 | (-46.65, 39.89, 22.66) | |
| 5:176859260 | COSM1736194 | D>E | A:96 | (-41.62, 40.90, 24.37) |
| 5:176859264 | R>W | A:98 | (-46.91, 45.49, 22.27) | |
| 5:176859265 | R>Q | A:98 | (-46.91, 45.49, 22.27) | |
| 5:176859270 | A>T | A:100 | (-40.95, 46.21, 17.24) | |
| 5:176859274 | C>Y | A:101 | (-44.43, 45.59, 15.53) | |
| 5:176859289 | rs76705113 | T>M | A:106 | (-45.06, 53.97, 12.67) |
| 5:176859708 | G>D | A:114 | (-45.47, 59.52, 1.71) | |
| 5:176859735 | rs139248624 | R>Q | A:123 | (-50.01, 67.74, 9.91) |
| 5:176859747 | T>M | A:127 | (-46.69, 63.79, 16.48) | |
| 5:176859762 | rs2230881 | R>Q | A:132 | (-48.62, 56.86, 24.98) |
| 5:176859773 | G>C | A:136 | (-45.77, 52.99, 26.51) | |
| 5:176859780 | C>F | A:138 | (-50.69, 51.16, 24.72) | |
| 5:176859806 | R>W | A:147 | (-62.15, 56.99, 15.88) | |
| 5:176859807 | R>Q | A:147 | (-62.15, 56.99, 15.88) | |
| 5:176860158 | rs528670739 | E>K | A:151 | (-65.22, 57.91, 10.62) |
| 5:176860159 | E>G | A:151 | (-65.22, 57.91, 10.62) | |
| 5:176860170 | rs542185009 | V>M | A:155 | (-68.87, 57.16, 3.86) |
| 5:176860191 | L>I | A:162 | (-72.94, 49.27, -1.90) | |
| 5:176860200 | I>V | A:165 | (-69.33, 43.81, -9.51) | |
| 5:176860210 | N>S | A:168 | (-73.90, 42.51, -7.55) | |
| 5:176860212 | rs200416754 | R>C | A:169 | (-70.35, 37.30, -7.23) |
| 5:176860240 | R>T | A:178 | (-82.01, 34.41, 2.61) | |
| 5:176860400 | G>S | A:196 | (-84.77, 15.29, 25.03) | |
| 5:176860546 | C>R | A:203 | (-73.97, 15.82, 9.81) | |
| 5:176860555 | R>W | A:206 | (-75.40, 16.56, -0.47) | |
| 5:176860568 | K>R | A:210 | (-68.17, 21.63, 7.74) | |
| 5:176860598 | K>R | A:220 | (-95.23, 13.14, 17.60) | |
| 5:176860600 | rs530467814 | R>W | A:221 | (-90.45, 12.29, 22.28) |
| 5:176860601 | R>Q | A:221 | (-90.45, 12.29, 22.28) | |
| 5:176860625 | A>D | A:229 | (-90.39, 27.24, 24.07) | |
| 5:176860631 | COSM449396 | A>V | A:231 | (-86.99, 24.91, 21.63) |
| 5:176860930 | rs551229599 | A>T | A:252 | (-82.91, 25.45, 11.02) |
| 5:176860936 | E>Q | A:254 | (-89.28, 21.23, 8.83) | |
| 5:176860939 | T>A | A:255 | (-88.36, 16.65, 9.15) | |
| 5:176860948 | rs35270792 | A>T | A:258 | (-88.34, 16.75, 13.13) |
| 5:176860970 | L>Q | A:265 | (-68.96, 18.18, 15.30) | |
| 5:176860978 | G>R | A:268 | (-64.56, 14.84, 22.11) | |
| 5:176860984 | D>N | A:270 | (-69.33, 14.08, 26.88) | |
| 5:176860999 | rs371992461 | I>V | A:275 | (-65.05, 12.24, 34.25) |
| 5:176861020 | G>S | A:282 | (-60.57, 12.03, 36.54) | |
| 5:176861035 | R>W | A:287 | (-57.50, 17.63, 31.91) | |
| 5:176861036 | R>Q | A:287 | (-57.50, 17.63, 31.91) | |
| 5:176861041 | rs551864050 | V>I | A:289 | (-57.82, 24.31, 35.93) |
| 5:176861050 | rs74796961 | A>T | A:292 | (-62.82, 25.91, 34.23) |
| 5:176861053 | rs368436043 | A>T | A:293 | (-61.06, 28.50, 32.69) |
| 5:176861078 | rs150356729 | D>A | A:301 | (-69.17, 35.35, 26.67) |
| 5:176861086 | R>W | A:304 | (-69.71, 40.54, 28.22) | |
| 5:176861092 | rs138392836 | R>C | A:306 | (-78.04, 40.46, 30.90) |
| 5:176862036 | rs560434892 | H>R | A:324 | (-59.84, 23.85, 22.94) |
| 5:176862065 | rs143935970 | V>M | A:334 | (-83.03, 32.75, 30.29) |
| 5:176862077 | rs200924933 | E>K | A:338 | (-80.24, 46.26, 32.48) |
| 5:176862079 | rs373013135 | E>D | A:338 | (-80.24, 46.26, 32.48) |
| 5:176862081 | G>D | A:339 | (-82.50, 45.53, 36.29) | |
| 5:176862089 | I>V | A:342 | (-85.35, 35.61, 37.07) | |
| 5:176862110 | rs376452319 COSM1195888 |
V>M | A:349 | (-80.56, 17.16, 40.49) |
| 5:176863077 | P>L | A:354 | (-79.18, 27.00, 46.84) | |
| 5:176863097 | R>W | A:361 | (-86.98, 36.65, 41.96) | |
| 5:176863098 | rs200876617 | R>Q | A:361 | (-86.98, 36.65, 41.96) |
| 5:176863104 | rs200013126 | T>M | A:363 | (-79.18, 36.80, 38.27) |
| 5:176863110 | rs149423489 | S>T | A:365 | (-75.92, 32.88, 40.77) |
| 5:176863125 | A>V | A:370 | (-72.05, 24.91, 38.69) | |
| 5:176863145 | rs371241210 | E>K | A:377 | (-67.94, 16.08, 39.04) |
| 5:176863154 | rs202175190 | A>T | A:380 | (-63.02, 14.24, 42.86) |
| 5:176863196 | R>W | A:394 | (-86.58, 14.26, 44.02) | |
| 5:176863244 | rs200401278 | E>K | A:410 | (-55.97, 13.97, 50.66) |
| 5:176863247 | rs146135301 | R>C | A:411 | (-57.81, 13.46, 44.34) |
| 5:176863257 | P>L | A:414 | (-53.93, 24.39, 48.72) | |
| 5:176863262 | A>S | A:416 | (-58.31, 23.99, 44.96) | |
| 5:176863265 | rs139154979 | R>C | A:417 | (-60.36, 23.52, 50.57) |
| 5:176863266 | R>H | A:417 | (-60.36, 23.52, 50.57) | |
| 5:176863271 | L>F | A:419 | (-62.07, 28.37, 43.74) | |
| 5:176863278 | S>L | A:421 | (-65.36, 27.02, 48.76) | |
| 5:176863402 | C>W | A:425 | (-71.11, 29.93, 48.88) | |
| 5:176863413 | A>V | A:429 | (-74.44, 37.65, 47.87) | |
| 5:176863415 | E>K | A:430 | (-70.89, 36.37, 50.47) | |
| 5:176863419 | COSM3827783 COSM3827782 |
R>H | A:431 | (-72.35, 32.28, 45.22) |
| 5:176863430 | rs374437384 | R>C | A:435 | (-68.24, 38.37, 46.06) |
| 5:176863437 | G>D | A:437 | (-67.10, 41.15, 39.41) | |
| 5:176863446 | rs199662008 | R>H | A:440 | (-62.48, 40.71, 35.69) |
| 5:176863514 | rs199647408 | P>S | A:463 | (-54.67, 22.14, 25.20) |
| 5:176863518 | P>L | A:464 | (-53.50, 19.85, 28.67) | |
| 5:176867734 | I>L | A:480 | (-77.87, 4.51, 23.35) | |
| 5:176867750 | rs369487775 | T>M | A:485 | (-92.77, 5.81, 20.37) |
| 5:176867761 | rs540859187 | V>M | A:489 | (-100.38, 12.18, 18.98) |
| 5:176867776 | T>A | A:494 | (-101.70, 25.41, 15.89) | |
| 5:176867783 | Q>R | A:496 | (-98.08, 23.85, 10.42) | |
| 5:176867795 | Q>R | A:500 | (-93.56, 29.32, 9.72) | |
| 5:176867813 | S>I | A:506 | (-79.36, 29.34, 7.01) | |
| 5:176867932 | E>K | A:519 | (-61.36, 26.26, -0.16) | |
| 5:176867959 | G>R | A:528 | (-61.81, 35.52, -15.05) | |
| 5:176867965 | D>N | A:530 | (-62.02, 29.74, -15.78) | |
| 5:176867981 | rs148914663 | P>L | A:535 | (-59.74, 32.99, -28.86) |
| 5:176867999 | rs200510977 COSM3697165 COSM3697164 |
G>V | A:541 | (-62.46, 31.19, -38.35) |
| 5:176868005 | P>L | A:543 | (-57.01, 34.24, -37.99) | |
| 5:176868008 | rs199969070 | P>L | A:544 | (-55.98, 36.95, -35.13) |
| 5:176868017 | rs142613356 | P>R | A:547 | (-51.77, 35.23, -36.40) |
| 5:176868025 | G>R | A:550 | (-49.01, 28.41, -31.87) | |
| 5:176868035 | Q>R | A:553 | (-45.88, 25.71, -34.07) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:176857912 | COSM20611 | R>Q | A:31 | (-68.56, 23.22, -9.22) |
| 5:176860543 | COSM1066370 | A>T | A:202 | (-73.66, 13.14, 12.57) |
| 5:176863212 | COSM4999478 | R>Q | A:399 | (-80.63, 17.75, 53.63) |
| 5:176863227 | COSM4999460 | V>D | A:404 | (-74.26, 20.01, 54.12) |
| 5:176868034 | COSM3715179 | Q>K | A:553 | (-45.88, 25.71, -34.07) |