General Structure Information
| PDB ID | 3s2k |
| HGNC Gene Label(s) | LRP6 |
| Structure Name | structural basis of wnt signaling inhibition by dickkopf binding to lrp5/6. |
| Resolution | 2.8Å |
| Reference | AUTH V.E.AHN,M.L.CHU,H.J.CHOI,D.TRAN,A.ABO,W.I.WEISTITL STRUCTURAL BASIS OF WNT SIGNALING INHIBITION BY DICKKOPFTITL 2 BINDING TO LRP5/6.REF DEV.CELL V. 21 862 2011REFN ISSN 1534-5807PMID 22000856DOI 10.1016/J.DEVCEL.2011.09.003 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 610 |
| Number Of SNVs | 113 |
| Number Of Permutations | 31649 |
| Optimal Distance Threshold | 32.0 |
| K Statistic | 0.477 |
| p-value | 0.109 |
COSMIC
| Number Of Residues | 610 |
| Number Of SNVs | 8 |
| Number Of Permutations | 5835 |
| Optimal Distance Threshold | 5.0 |
| K Statistic | 0.036 |
| p-value | 0.447 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 113 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | -0.113 |
| p-value | 0.955 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:12317347 | R>W | A:638 | (36.29, -2.17, -14.25) | |
| 12:12317337 | D>V | A:641 | (37.67, -7.01, -16.47) | |
| 12:12317314 | T>A | A:649 | (42.70, -12.82, 1.83) | |
| 12:12317299 | V>M | A:654 | (42.63, -12.29, -9.31) | |
| 12:12317293 | I>V | A:656 | (38.37, -14.52, -14.31) | |
| 12:12317249 | rs370529299 | D>E | A:670 | (26.94, -23.35, -11.97) |
| 12:12317250 | D>G | A:670 | (26.94, -23.35, -11.97) | |
| 12:12317238 | rs560695053 | N>S | A:674 | (33.36, -24.36, -12.06) |
| 12:12317235 | rs376188127 COSM168429 |
R>Q | A:675 | (30.46, -23.40, -16.83) |
| 12:12317233 | rs188649737 | I>V | A:676 | (31.31, -17.50, -15.21) |
| 12:12315337 | F>S | A:690 | (34.52, -24.08, -17.48) | |
| 12:12315323 | A>T | A:695 | (35.04, -23.15, -22.66) | |
| 12:12315299 | G>S | A:703 | (18.25, -10.17, -29.79) | |
| 12:12315275 | A>T | A:711 | (19.97, -15.64, -13.86) | |
| 12:12315229 | T>M | A:726 | (13.89, -5.78, -25.94) | |
| 12:12315223 | R>L | A:728 | (11.60, -9.39, -25.29) | |
| 12:12315215 | rs200627221 | V>L | A:731 | (14.11, -18.76, -21.00) |
| 12:12315207 | K>N | A:733 | (18.56, -24.92, -21.41) | |
| 12:12315208 | K>M | A:733 | (18.56, -24.92, -21.41) | |
| 12:12315202 | D>V | A:735 | (23.07, -24.71, -24.11) | |
| 12:12315203 | rs149258721 | D>N | A:735 | (23.07, -24.71, -24.11) |
| 12:12315190 | R>Q | A:739 | (15.74, -17.42, -27.12) | |
| 12:12315185 | V>L | A:741 | (9.42, -14.97, -24.34) | |
| 12:12315179 | V>L | A:743 | (7.69, -11.39, -19.82) | |
| 12:12315161 | S>C | A:749 | (13.08, -1.23, -17.92) | |
| 12:12315145 | rs138465296 | A>V | A:754 | (15.91, -12.83, -8.98) |
| 12:12315146 | A>T | A:754 | (15.91, -12.83, -8.98) | |
| 12:12312896 | F>Y | A:761 | (7.79, -17.35, -6.94) | |
| 12:12312841 | D>E | A:779 | (6.02, -19.77, -16.09) | |
| 12:12312830 | R>H | A:783 | (3.42, -9.49, -14.25) | |
| 12:12312780 | Y>D | A:800 | (17.93, -17.73, -1.39) | |
| 12:12312777 | rs143673928 | A>T | A:801 | (17.50, -18.34, 4.70) |
| 12:12312731 | E>A | A:816 | (14.95, -0.79, 0.66) | |
| 12:12312728 | rs2302686 | S>C | A:817 | (14.48, -4.96, 3.04) |
| 12:12312081 | R>C | A:825 | (9.53, -1.39, 2.47) | |
| 12:12312072 | rs368501687 | I>V | A:828 | (19.41, -1.73, 5.89) |
| 12:12312038 | T>S | A:839 | (25.27, -9.11, -2.61) | |
| 12:12312021 | I>V | A:845 | (25.01, -6.39, 3.17) | |
| 12:12311996 | rs572509429 | R>H | A:853 | (36.92, 4.95, -6.50) |
| 12:12311997 | R>C | A:853 | (36.92, 4.95, -6.50) | |
| 12:12311973 | T>S | A:861 | (19.90, -6.77, 10.02) | |
| 12:12311958 | R>C | A:866 | (29.18, 0.34, 7.95) | |
| 12:12311955 | rs141458215 | T>A | A:867 | (34.07, -3.03, 6.61) |
| 12:12311950 | I>M | A:868 | (36.44, -0.99, 3.28) | |
| 12:12311952 | I>V | A:868 | (36.44, -0.99, 3.28) | |
| 12:12311913 | COSM87966 COSM1561792 |
V>I | A:881 | (29.00, -14.25, -3.36) |
| 12:12311862 | G>R | A:898 | (10.33, -33.51, -15.99) | |
| 12:12311837 | A>G | A:906 | (9.32, -23.28, -11.92) | |
| 12:12311825 | G>E | A:910 | (7.98, -26.18, -6.21) | |
| 12:12311810 | G>E | A:915 | (8.39, -25.76, -21.99) | |
| 12:12311785 | rs201126262 | N>K | A:923 | (2.00, -31.29, -27.20) |
| 12:12303966 | COSM3457328 | T>M | A:933 | (2.64, -25.21, -38.70) |
| 12:12303955 | L>I | A:937 | (8.76, -15.21, -42.56) | |
| 12:12303934 | I>V | A:944 | (15.28, -13.42, -41.28) | |
| 12:12303930 | N>S | A:945 | (12.17, -11.64, -38.48) | |
| 12:12303927 | R>H | A:946 | (9.34, -17.15, -36.36) | |
| 12:12303907 | Q>K | A:953 | (-0.73, -11.56, -28.12) | |
| 12:12303896 | D>E | A:956 | (8.61, -10.80, -33.04) | |
| 12:12303892 | I>L | A:958 | (15.76, -12.49, -34.48) | |
| 12:12303889 | L>F | A:959 | (15.57, -16.46, -37.31) | |
| 12:12303876 | S>N | A:963 | (25.98, -14.63, -42.49) | |
| 12:12303861 | R>Q | A:968 | (17.03, -7.78, -53.25) | |
| 12:12303862 | R>W | A:968 | (17.03, -7.78, -53.25) | |
| 12:12303837 | rs368801975 | D>G | A:976 | (12.16, -30.33, -46.15) |
| 12:12303825 | rs375132066 | Y>C | A:980 | (15.26, -21.65, -49.45) |
| 12:12303819 | rs144397003 | I>T | A:982 | (18.24, -13.21, -52.44) |
| 12:12303820 | rs201612233 | I>V | A:982 | (18.24, -13.21, -52.44) |
| 12:12303795 | R>Q | A:990 | (23.09, -17.64, -48.86) | |
| 12:12303796 | R>G | A:990 | (23.09, -17.64, -48.86) | |
| 12:12303792 | rs202168933 | K>R | A:991 | (19.49, -23.49, -47.20) |
| 12:12303789 | A>E | A:992 | (18.45, -22.45, -43.79) | |
| 12:12302081 | T>A | A:1001 | (25.04, -22.16, -51.18) | |
| 12:12302074 | V>G | A:1003 | (22.80, -19.71, -56.48) | |
| 12:12302032 | Y>C | A:1017 | (14.90, -8.24, -57.97) | |
| 12:12302027 | L>V | A:1019 | (12.92, -16.05, -54.77) | |
| 12:12302005 | rs146852380 | R>H | A:1026 | (11.19, -29.80, -54.43) |
| 12:12302006 | rs140679529 | R>C | A:1026 | (11.19, -29.80, -54.43) |
| 12:12301981 | A>V | A:1034 | (21.99, -8.64, -65.24) | |
| 12:12301975 | rs143873199 | N>S | A:1036 | (17.41, -9.27, -67.79) |
| 12:12301951 | D>V | A:1044 | (20.34, -29.65, -55.40) | |
| 12:12301952 | rs140182370 | D>N | A:1044 | (20.34, -29.65, -55.40) |
| 12:12301933 | V>A | A:1050 | (16.61, -20.42, -68.97) | |
| 12:12301898 | rs2302685 | V>I | A:1062 | (8.60, -14.29, -59.55) |
| 12:12300488 | Y>C | A:1070 | (-0.48, -20.74, -65.31) | |
| 12:12300486 | M>V | A:1071 | (5.05, -17.91, -64.37) | |
| 12:12300477 | rs370421599 | T>A | A:1074 | (7.02, -7.96, -62.85) |
| 12:12300473 | rs202124188 | N>S | A:1075 | (8.13, -6.88, -67.74) |
| 12:12300474 | N>D | A:1075 | (8.13, -6.88, -67.74) | |
| 12:12300444 | rs143966208 | R>W | A:1085 | (-0.61, -15.86, -67.01) |
| 12:12300434 | L>S | A:1088 | (6.22, -23.29, -64.75) | |
| 12:12300420 | R>W | A:1093 | (5.26, -14.45, -72.61) | |
| 12:12300399 | G>S | A:1100 | (-1.13, 1.50, -63.99) | |
| 12:12300387 | P>S | A:1104 | (5.71, -3.12, -60.87) | |
| 12:12300384 | I>V | A:1105 | (8.32, -3.93, -56.38) | |
| 12:12300368 | D>G | A:1110 | (-4.86, -16.84, -52.23) | |
| 12:12300364 | rs376932334 | S>R | A:1111 | (-5.94, -19.97, -54.40) |
| 12:12300353 | K>R | A:1115 | (-7.89, -12.18, -55.86) | |
| 12:12300333 | D>H | A:1122 | (6.39, 4.97, -58.48) | |
| 12:12300326 | R>Q | A:1124 | (3.29, 6.82, -53.18) | |
| 12:12300327 | rs147411481 | R>W | A:1124 | (3.29, 6.82, -53.18) |
| 12:12300323 | R>L | A:1125 | (-1.68, 2.08, -56.53) | |
| 12:12300321 | I>V | A:1126 | (-1.90, -2.10, -52.74) | |
| 12:12300317 | rs560813860 | E>G | A:1127 | (-3.60, -2.67, -57.66) |
| 12:12300314 | S>N | A:1128 | (-6.46, -6.68, -56.82) | |
| 12:12300308 | D>G | A:1130 | (-9.38, -12.12, -60.52) | |
| 12:12300309 | rs142845287 | D>N | A:1130 | (-9.38, -12.12, -60.52) |
| 12:12291459 | R>Q | A:1136 | (-6.99, -3.45, -62.22) | |
| 12:12291460 | rs140962861 | R>W | A:1136 | (-6.99, -3.45, -62.22) |
| 12:12291434 | rs148108074 | I>M | A:1144 | (1.13, 3.98, -49.26) |
| 12:12291406 | E>K | A:1154 | (-5.11, -16.68, -42.28) | |
| 12:12291388 | I>V | A:1160 | (6.64, -4.45, -46.16) | |
| 12:12291382 | K>E | A:1162 | (12.08, 0.34, -47.09) | |
| 12:12291367 | I>F | A:1167 | (4.17, -4.55, -40.87) | |
| 12:12291351 | M>K | A:1172 | (-9.52, -9.43, -48.19) | |
| 12:12291342 | rs372175738 COSM1180224 |
R>Q | A:1175 | (-16.52, -8.92, -41.91) |
| 12:12291339 | rs145672862 | E>A | A:1176 | (-11.50, -5.86, -38.54) |
| 12:12291310 | A>S | A:1186 | (14.49, -1.15, -40.27) | |
| 12:12291297 | D>G | A:1190 | (10.28, -9.75, -48.23) | |
| 12:12291295 | I>L | A:1191 | (6.45, -10.23, -46.08) | |
| 12:12291264 | rs185244696 | E>G | A:1201 | (-4.20, -31.72, -50.57) |
| 12:12288225 | P>L | A:1206 | (1.09, -34.80, -60.59) | |
| 12:12288219 | A>V | A:1208 | (5.65, -34.44, -56.83) | |
| 12:12288220 | A>T | A:1208 | (5.65, -34.44, -56.83) | |
| 12:12288213 | rs368248844 | D>G | A:1210 | (9.96, -39.17, -58.72) |
| 12:12288214 | rs372538850 | D>N | A:1210 | (9.96, -39.17, -58.72) |
| 12:12288196 | H>Y | A:1216 | (14.97, -30.93, -66.96) | |
| 12:12288193 | I>V | A:1217 | (10.30, -28.58, -66.49) | |
| 12:12288175 | D>N | A:1223 | (-6.78, -29.23, -68.10) | |
| 12:12288172 | G>S | A:1224 | (-4.97, -31.93, -65.75) | |
| 12:12288168 | T>I | A:1225 | (-2.92, -31.58, -68.67) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:12317346 | COSM180998 | R>Q | A:638 | (36.29, -2.17, -14.25) |
| 12:12317235 | COSM168429 | R>Q | A:675 | (30.46, -23.40, -16.83) |
| 12:12311913 | COSM1561792 | V>I | A:881 | (29.00, -14.25, -3.36) |
| 12:12303810 | COSM1605690 | R>Q | A:985 | (28.18, -7.57, -50.21) |
| 12:12303771 | COSM24314 | Q>R | A:998 | (20.85, -27.71, -42.69) |
| 12:12302087 | COSM24309 | G>S | A:999 | (23.65, -24.53, -44.48) |
| 12:12302006 | COSM180991 | R>C | A:1026 | (11.19, -29.80, -54.43) |
| 12:12301904 | COSM1676731 | R>G | A:1060 | (13.16, -7.50, -62.46) |