General Structure Information
| PDB ID | 1t77 |
| HGNC Gene Label(s) | LRBA |
| Structure Name | crystal structure of the ph-beach domains of human lrba/bgl |
| Resolution | 2.4Å |
| Reference | AUTH D.GEBAUER,J.LI,G.JOGL,Y.SHEN,D.G.MYSZKA,L.TONGTITL CRYSTAL STRUCTURE OF THE PH-BEACH DOMAINS OF HUMANTITL 2 LRBA/BGLREF BIOCHEMISTRY V. 43 14873 2004REFN ISSN 0006-2960PMID 15554694DOI 10.1021/BI049498Y |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 414 |
| Number Of SNVs | 111 |
| Number Of Permutations | 48369 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.077 |
| p-value | 0.473 |
COSMIC
| Number Of Residues | 414 |
| Number Of SNVs | 10 |
| Number Of Permutations | 2305 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.067 |
| p-value | 0.723 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 111 |
| Number Of COSMIC SNVs | 8 |
| Optimal Distance Threshold | 31.0 |
| K Statistic | -0.128 |
| p-value | 0.603 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:151509331 | V>I | A:2078 | (45.80, 69.52, 13.08) | |
| 4:151509316 | rs140681994 | P>S | A:2083 | (44.65, 68.76, 26.45) |
| 4:151509304 | rs151337867 | V>M | A:2087 | (35.41, 58.97, 29.66) |
| 4:151509300 | A>G | A:2088 | (35.32, 54.94, 29.90) | |
| 4:151509297 | rs201667311 | P>L | A:2089 | (33.40, 52.25, 31.05) |
| 4:151509294 | S>F | A:2090 | (37.34, 51.19, 31.76) | |
| 4:151509277 | T>A | A:2096 | (46.02, 64.36, 22.65) | |
| 4:151509264 | T>N | A:2100 | (40.86, 67.27, 11.34) | |
| 4:151509249 | Y>C | A:2105 | (43.22, 62.34, 15.93) | |
| 4:151509232 | E>Q | A:2111 | (55.62, 59.16, 29.57) | |
| 4:151509226 | P>T | A:2113 | (52.12, 58.34, 35.48) | |
| 4:151509206 | rs375803883 | D>E | A:2119 | (45.91, 47.00, 35.15) |
| 4:151509205 | P>S | A:2120 | (46.79, 45.31, 31.14) | |
| 4:151412186 | I>S | A:2122 | (41.28, 47.25, 32.23) | |
| 4:151412155 | K>N | A:2132 | (40.43, 57.44, 13.49) | |
| 4:151412140 | rs377051616 | E>D | A:2137 | (29.51, 58.08, 10.74) |
| 4:151412137 | I>M | A:2138 | (29.13, 62.60, 13.93) | |
| 4:151412135 | R>L | A:2139 | (24.77, 60.96, 12.94) | |
| 4:151412130 | rs373680922 | I>V | A:2141 | (27.55, 66.62, 19.70) |
| 4:151412120 | COSM1196960 | R>H | A:2144 | (27.38, 65.22, 28.73) |
| 4:151412118 | COSM170657 | R>C | A:2145 | (27.91, 67.70, 32.89) |
| 4:151412114 | Y>C | A:2146 | (34.51, 63.77, 34.83) | |
| 4:151412115 | Y>H | A:2146 | (34.51, 63.77, 34.83) | |
| 4:151412103 | rs369815651 | N>D | A:2150 | (30.18, 72.00, 32.27) |
| 4:151412075 | rs143949228 | N>S | A:2159 | (27.93, 52.80, 14.98) |
| 4:151412076 | N>D | A:2159 | (27.93, 52.80, 14.98) | |
| 4:151408978 | M>V | A:2164 | (32.93, 60.88, 27.41) | |
| 4:151408973 | F>L | A:2165 | (36.45, 62.71, 24.83) | |
| 4:151408963 | rs145663124 | D>N | A:2169 | (38.32, 74.55, 30.11) |
| 4:151408956 | A>V | A:2171 | (36.33, 76.85, 26.69) | |
| 4:151408954 | T>A | A:2172 | (37.97, 73.53, 25.44) | |
| 4:151408948 | K>E | A:2174 | (32.12, 76.77, 22.33) | |
| 4:151408939 | V>I | A:2177 | (31.57, 72.35, 19.39) | |
| 4:151408933 | Y>H | A:2179 | (37.03, 73.29, 15.18) | |
| 4:151408923 | rs572317255 | R>P | A:2182 | (24.99, 71.90, 11.87) |
| 4:151408924 | rs541771508 | R>C | A:2182 | (24.99, 71.90, 11.87) |
| 4:151408915 | V>I | A:2185 | (21.19, 66.45, 20.25) | |
| 4:151408908 | rs528350950 | T>R | A:2187 | (17.09, 63.71, 14.84) |
| 4:151408909 | T>A | A:2187 | (17.09, 63.71, 14.84) | |
| 4:151408894 | P>T | A:2192 | (17.16, 72.18, 17.17) | |
| 4:151392889 | COSM732425 | R>H | A:2196 | (22.34, 77.34, 19.88) |
| 4:151392890 | R>C | A:2196 | (22.34, 77.34, 19.88) | |
| 4:151392868 | rs372513836 | R>H | A:2203 | (16.18, 74.25, 33.20) |
| 4:151392869 | rs200164280 | R>C | A:2203 | (16.18, 74.25, 33.20) |
| 4:151392848 | N>H | A:2210 | (9.01, 66.52, 21.17) | |
| 4:151392805 | E>A | A:2224 | (11.80, 55.18, 24.79) | |
| 4:151392797 | M>V | A:2227 | (17.21, 56.55, 28.66) | |
| 4:151392784 | T>M | A:2231 | (20.53, 61.59, 27.80) | |
| 4:151392781 | rs116526975 | I>T | A:2232 | (18.94, 65.62, 28.38) |
| 4:151392779 | COSM1485727 | A>T | A:2233 | (21.01, 65.07, 32.34) |
| 4:151388935 | R>W | A:2235 | (23.58, 60.48, 34.30) | |
| 4:151388925 | N>S | A:2238 | (30.86, 56.03, 28.48) | |
| 4:151388923 | D>Y | A:2239 | (30.61, 58.03, 33.65) | |
| 4:151388887 | rs202061746 COSM162212 |
T>A | A:2251 | (7.70, 45.65, 46.01) |
| 4:151388883 | N>S | A:2252 | (6.35, 41.06, 45.44) | |
| 4:151388876 | E>D | A:2254 | (8.60, 37.23, 48.58) | |
| 4:151358007 | A>S | A:2275 | (10.55, 56.93, 52.40) | |
| 4:151357997 | P>Q | A:2278 | (8.32, 53.70, 57.95) | |
| 4:151357992 | R>G | A:2280 | (15.11, 53.52, 56.39) | |
| 4:151357985 | rs142655006 | A>G | A:2282 | (12.63, 58.37, 61.13) |
| 4:151357970 | rs200802435 COSM1291841 |
R>H | A:2287 | (20.97, 61.86, 59.84) |
| 4:151357968 | Y>H | A:2288 | (17.49, 67.55, 57.68) | |
| 4:151357951 | rs138518902 | D>E | A:2293 | (24.87, 73.65, 59.47) |
| 4:151357952 | D>G | A:2293 | (24.87, 73.65, 59.47) | |
| 4:151357949 | rs147096866 | D>V | A:2294 | (29.09, 74.47, 61.15) |
| 4:151357947 | COSM1309802 | Q>E | A:2295 | (30.84, 74.96, 57.15) |
| 4:151357935 | F>V | A:2299 | (22.73, 65.12, 55.34) | |
| 4:151357928 | Y>C | A:2301 | (19.33, 60.24, 52.18) | |
| 4:151357919 | COSM71467 | H>R | A:2304 | (23.29, 59.02, 45.56) |
| 4:151357910 | rs151286835 | T>N | A:2307 | (27.49, 54.63, 42.38) |
| 4:151357907 | A>E | A:2308 | (30.12, 53.13, 40.18) | |
| 4:151357902 | F>L | A:2310 | (25.75, 51.20, 43.66) | |
| 4:151357899 | V>I | A:2311 | (27.13, 49.67, 38.16) | |
| 4:151357876 | rs201643144 | I>M | A:2318 | (28.48, 41.27, 32.54) |
| 4:151356841 | F>Y | A:2325 | (34.41, 44.14, 41.25) | |
| 4:151356816 | rs149154150 | F>L | A:2333 | (35.02, 38.17, 43.03) |
| 4:151356814 | D>G | A:2334 | (33.40, 41.25, 47.78) | |
| 4:151356811 | H>R | A:2335 | (32.00, 38.59, 52.10) | |
| 4:151356809 | rs61742065 | A>S | A:2336 | (29.62, 36.68, 49.53) |
| 4:151356769 | rs144189042 | N>S | A:2349 | (19.37, 45.59, 52.15) |
| 4:151356770 | N>H | A:2349 | (19.37, 45.59, 52.15) | |
| 4:151356766 | rs183574413 | S>I | A:2350 | (16.78, 49.07, 49.90) |
| 4:151356760 | rs371873204 COSM258711 |
R>H | A:2352 | (15.05, 46.00, 56.34) |
| 4:151356746 | rs199674409 | I>V | A:2357 | (19.04, 54.81, 49.34) |
| 4:151336718 | L>I | A:2367 | (20.60, 42.75, 30.23) | |
| 4:151336707 | rs146268782 | M>I | A:2370 | (22.37, 41.27, 34.91) |
| 4:151336700 | N>H | A:2373 | (27.52, 32.74, 36.57) | |
| 4:151336692 | N>K | A:2375 | (31.42, 33.50, 32.92) | |
| 4:151336694 | N>D | A:2375 | (31.42, 33.50, 32.92) | |
| 4:151336684 | N>T | A:2378 | (33.88, 31.43, 42.75) | |
| 4:151336672 | M>T | A:2382 | (26.66, 33.53, 51.78) | |
| 4:151336664 | G>R | A:2385 | (26.17, 28.44, 52.56) | |
| 4:151336657 | V>A | A:2387 | (26.44, 28.99, 46.49) | |
| 4:151336643 | rs372702422 COSM1051990 |
E>K | A:2392 | (18.76, 34.02, 44.61) |
| 4:151336607 | rs202243949 | V>I | A:2404 | (13.52, 41.30, 32.23) |
| 4:151336603 | H>R | A:2405 | (8.54, 40.12, 29.96) | |
| 4:151336597 | rs149731019 | N>S | A:2407 | (10.77, 43.88, 35.47) |
| 4:151271293 | V>I | A:2416 | (4.19, 53.33, 36.21) | |
| 4:151271282 | Q>H | A:2419 | (1.81, 58.33, 39.59) | |
| 4:151271283 | Q>R | A:2419 | (1.81, 58.33, 39.59) | |
| 4:151271278 | H>Y | A:2421 | (4.33, 62.36, 37.56) | |
| 4:151271250 | rs376374926 | Y>S | A:2430 | (8.79, 70.10, 42.30) |
| 4:151271248 | K>E | A:2431 | (9.91, 67.14, 44.70) | |
| 4:151271236 | P>A | A:2435 | (11.98, 73.56, 50.23) | |
| 4:151271221 | A>S | A:2440 | (10.28, 64.36, 50.37) | |
| 4:151271217 | rs374717449 | L>R | A:2441 | (12.68, 62.44, 53.01) |
| 4:151271209 | F>I | A:2444 | (20.46, 63.03, 48.53) | |
| 4:151271190 | E>G | A:2450 | (24.41, 71.07, 39.61) | |
| 4:151271182 | V>I | A:2453 | (32.81, 71.73, 44.00) | |
| 4:151271167 | COSM75269 | I>V | A:2458 | (41.91, 72.42, 43.85) |
| 4:151271160 | D>V | A:2460 | (47.43, 70.34, 45.38) | |
| 4:151271157 | P>L | A:2461 | (47.48, 68.10, 42.35) | |
| 4:151271148 | rs377302910 | R>K | A:2464 | (41.70, 68.23, 40.97) |
| 4:151247049 | rs542791563 | A>G | A:2466 | (40.82, 63.67, 46.78) |
| 4:151247037 | rs369733391 | Q>R | A:2470 | (35.09, 61.83, 48.55) |
| 4:151247025 | F>S | A:2474 | (30.30, 61.03, 48.65) | |
| 4:151247016 | rs376476747 | T>S | A:2477 | (22.54, 64.49, 41.59) |
| 4:151247010 | S>F | A:2479 | (21.05, 67.55, 35.89) | |
| 4:151247001 | L>H | A:2482 | (11.96, 70.39, 35.65) | |
| 4:151246998 | I>T | A:2483 | (11.75, 74.51, 38.33) | |
| 4:151246984 | P>S | A:2488 | (0.69, 63.98, 34.02) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:151509256 | COSM1052007 | E>K | A:2103 | (39.13, 62.71, 11.35) |
| 4:151509207 | COSM3396551 | D>A | A:2119 | (45.91, 47.00, 35.15) |
| 4:151412120 | COSM1196960 | R>L | A:2144 | (27.38, 65.22, 28.73) |
| 4:151412118 | COSM170657 | R>C | A:2145 | (27.91, 67.70, 32.89) |
| 4:151392889 | COSM732425 | R>H | A:2196 | (22.34, 77.34, 19.88) |
| 4:151392883 | COSM1695067 | S>L | A:2198 | (25.38, 70.78, 21.61) |
| 4:151356802 | COSM3127540 | R>Q | A:2338 | (29.93, 42.60, 51.02) |
| 4:151356784 | COSM3600847 | S>F | A:2344 | (14.89, 39.73, 47.66) |
| 4:151336643 | COSM1051990 | E>K | A:2392 | (18.76, 34.02, 44.61) |
| 4:151271167 | COSM75269 | I>V | A:2458 | (41.91, 72.42, 43.85) |