General Structure Information
| PDB ID | 2ffu |
| HGNC Gene Label(s) | GALNT2 |
| Structure Name | crystal structure of human ppgalnact-2 complexed with udp and ea2 |
| Resolution | 1.64Å |
| Reference | AUTH T.A.FRITZ,J.RAMAN,L.A.TABAKTITL DYNAMIC ASSOCIATION BETWEEN THE CATALYTIC ANDTITL 2 LECTIN DOMAINS OF HUMAN UDP-GALNAC:POLYPEPTIDETITL 3 {ALPHA}-N-ACETYLGALACTOSAMINYLTRANSFERASE-2REF J.BIOL.CHEM. V. 281 8613 2006REFN ISSN 0021-9258PMID 16434399DOI 10.1074/JBC.M513590200 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 494 |
| Number Of SNVs | 119 |
| Number Of Permutations | 33583 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.119 |
| p-value | 0.002 |
COSMIC
| Number Of Residues | 494 |
| Number Of SNVs | 4 |
| Number Of Permutations | 266 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | 0.167 |
| p-value | 1.0 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 119 |
| Number Of COSMIC SNVs | 4 |
| Optimal Distance Threshold | 44.0 |
| K Statistic | 0.39 |
| p-value | 0.595 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:230338891 | COSM905335 | R>W | A:77 | (-17.52, -35.69, 31.15) |
| 1:230338892 | rs184261638 | R>Q | A:77 | (-17.52, -35.69, 31.15) |
| 1:230338905 | F>L | A:81 | (-19.08, -26.00, 28.32) | |
| 1:230338909 | rs200978844 | Q>E | A:83 | (-22.56, -24.13, 23.99) |
| 1:230338925 | G>A | A:88 | (-22.78, -15.01, 24.52) | |
| 1:230338927 | G>R | A:89 | (-20.38, -12.92, 25.59) | |
| 1:230338975 | N>Y | A:105 | (-19.43, -14.95, 9.72) | |
| 1:230338976 | rs557579820 | N>S | A:105 | (-19.43, -14.95, 9.72) |
| 1:230338981 | V>L | A:107 | (-23.07, -14.83, 13.02) | |
| 1:230338984 | E>Q | A:108 | (-23.06, -18.30, 10.40) | |
| 1:230338993 | COSM3360732 | K>E | A:111 | (-25.85, -19.74, 13.74) |
| 1:230339003 | M>R | A:114 | (-20.11, -27.97, 21.00) | |
| 1:230339005 | D>N | A:115 | (-21.59, -31.32, 18.88) | |
| 1:230339011 | A>T | A:117 | (-22.30, -32.61, 12.21) | |
| 1:230339020 | rs143344842 | D>H | A:120 | (-17.02, -39.09, 6.07) |
| 1:230371767 | R>W | A:128 | (-10.75, -53.09, 4.14) | |
| 1:230371768 | rs556141120 | R>Q | A:128 | (-10.75, -53.09, 4.14) |
| 1:230371773 | Q>E | A:130 | (-6.72, -51.38, 9.96) | |
| 1:230371774 | Q>L | A:130 | (-6.72, -51.38, 9.96) | |
| 1:230371780 | rs151140953 | R>Q | A:132 | (0.37, -49.85, 15.51) |
| 1:230371803 | rs570007994 | V>M | A:140 | (-3.46, -31.54, 21.56) |
| 1:230371821 | N>D | A:146 | (-7.94, -12.55, 19.78) | |
| 1:230371851 | V>M | A:156 | (-11.75, -28.57, 22.01) | |
| 1:230371857 | S>R | A:158 | (-13.45, -32.05, 17.68) | |
| 1:230372112 | rs545023670 | S>C | A:163 | (-10.61, -38.76, 19.60) |
| 1:230372122 | H>L | A:166 | (-6.78, -44.52, 24.26) | |
| 1:230372161 | N>S | A:179 | (-8.34, -8.62, 24.90) | |
| 1:230372411 | D>N | A:183 | (-11.62, -16.36, 25.74) | |
| 1:230372427 | G>E | A:188 | (-10.55, -25.31, 31.91) | |
| 1:230372433 | rs374087942 | I>T | A:190 | (-13.37, -28.74, 29.57) |
| 1:230372445 | R>Q | A:194 | (-2.19, -27.27, 30.95) | |
| 1:230372447 | rs552559804 | V>I | A:195 | (-4.98, -22.98, 30.08) |
| 1:230372451 | L>P | A:196 | (-0.67, -22.43, 29.13) | |
| 1:230379060 | R>C | A:206 | (7.94, -17.20, 20.47) | |
| 1:230379061 | R>H | A:206 | (7.94, -17.20, 20.47) | |
| 1:230379066 | R>W | A:208 | (2.98, -23.84, 17.40) | |
| 1:230379073 | rs376870425 | R>Q | A:210 | (4.26, -22.14, 27.11) |
| 1:230379078 | rs145628006 | A>T | A:212 | (5.69, -28.69, 23.59) |
| 1:230379092 | rs142046356 | Q>H | A:216 | (3.80, -34.65, 29.84) |
| 1:230379098 | K>N | A:218 | (6.28, -39.73, 24.40) | |
| 1:230379117 | S>G | A:225 | (-8.18, -22.11, 16.82) | |
| 1:230379133 | N>S | A:230 | (-13.66, -36.11, 10.53) | |
| 1:230379135 | E>K | A:231 | (-14.81, -40.47, 11.82) | |
| 1:230379137 | E>D | A:231 | (-14.81, -40.47, 11.82) | |
| 1:230379140 | rs370170142 COSM1738507 |
H>Q | A:232 | (-11.63, -42.96, 12.98) |
| 1:230379151 | P>H | A:236 | (-4.30, -42.51, 10.83) | |
| 1:230379169 | rs201212164 | A>V | A:242 | (4.86, -45.48, 15.42) |
| 1:230381819 | R>Q | A:247 | (7.10, -41.54, 9.20) | |
| 1:230381839 | COSM905339 | D>N | A:254 | (-11.17, -30.60, 4.85) |
| 1:230381852 | M>T | A:258 | (-15.01, -17.18, 5.41) | |
| 1:230381854 | D>N | A:259 | (-18.81, -16.62, 4.35) | |
| 1:230381858 | rs150471503 | N>S | A:260 | (-22.14, -19.59, 5.51) |
| 1:230384933 | F>C | A:274 | (7.74, -23.64, -2.54) | |
| 1:230384945 | L>S | A:278 | (9.25, -18.55, -0.20) | |
| 1:230384948 | V>G | A:279 | (4.05, -18.28, -0.58) | |
| 1:230384974 | E>K | A:288 | (2.94, -40.82, -13.25) | |
| 1:230384987 | S>F | A:292 | (1.11, -43.97, -8.90) | |
| 1:230384989 | R>W | A:293 | (-1.68, -42.39, -5.00) | |
| 1:230385007 | rs199925000 | A>T | A:299 | (-1.41, -43.61, 0.36) |
| 1:230386236 | rs565300791 | M>I | A:313 | (6.48, -34.34, 15.36) |
| 1:230386238 | rs78164071 | D>A | A:314 | (8.24, -37.79, 18.06) |
| 1:230386246 | Y>H | A:317 | (12.41, -35.86, 14.96) | |
| 1:230386259 | L>R | A:321 | (15.16, -31.62, 14.31) | |
| 1:230386261 | G>R | A:322 | (14.67, -27.69, 16.75) | |
| 1:230386262 | G>E | A:322 | (14.67, -27.69, 16.75) | |
| 1:230386265 | COSM1560198 COSM74726 |
K>R | A:323 | (12.10, -27.14, 19.40) |
| 1:230386278 | M>I | A:327 | (14.61, -15.37, 16.75) | |
| 1:230390966 | I>V | A:338 | (9.66, -27.59, 9.94) | |
| 1:230390970 | COSM3484980 | S>L | A:339 | (9.60, -28.37, 5.81) |
| 1:230390978 | rs372846843 | V>M | A:342 | (12.37, -32.53, 8.22) |
| 1:230391021 | R>L | A:356 | (-10.04, -35.78, 5.48) | |
| 1:230391051 | P>R | A:366 | (-7.40, -10.81, 12.42) | |
| 1:230391057 | COSM140403 | T>M | A:368 | (-1.57, -7.24, 15.43) |
| 1:230391063 | rs376128700 COSM4029372 |
P>L | A:370 | (4.58, -6.08, 15.15) |
| 1:230391090 | R>Q | A:379 | (11.57, -10.54, 10.54) | |
| 1:230398329 | rs374726944 | R>W | A:383 | (15.84, -16.22, 10.82) |
| 1:230398362 | N>D | A:394 | (19.74, -15.51, -4.46) | |
| 1:230398367 | COSM1295981 COSM1339994 |
F>L | A:395 | (16.50, -17.91, -7.36) |
| 1:230398390 | A>V | A:403 | (13.37, -8.69, 1.27) | |
| 1:230398393 | COSM3484981 | R>I | A:404 | (18.13, -7.65, -0.79) |
| 1:230398398 | V>I | A:406 | (14.32, -7.04, 6.01) | |
| 1:230398702 | S>G | A:422 | (24.37, -33.71, 8.81) | |
| 1:230398710 | K>N | A:424 | (21.02, -33.66, 3.08) | |
| 1:230398711 | P>S | A:425 | (22.16, -29.94, 0.31) | |
| 1:230398715 | F>C | A:426 | (17.39, -26.28, -1.09) | |
| 1:230398717 | K>E | A:427 | (21.32, -29.37, -5.54) | |
| 1:230398735 | rs540616116 | V>I | A:433 | (11.60, -33.43, -2.27) |
| 1:230398741 | rs574340854 | P>S | A:435 | (11.26, -32.18, -8.54) |
| 1:230398751 | R>T | A:438 | (11.53, -24.88, -14.06) | |
| 1:230401006 | rs201830158 | I>V | A:445 | (18.97, -7.15, -20.85) |
| 1:230401025 | Q>R | A:451 | (3.68, -2.84, -27.97) | |
| 1:230401026 | Q>H | A:451 | (3.68, -2.84, -27.97) | |
| 1:230401031 | G>A | A:453 | (-1.20, -0.76, -29.88) | |
| 1:230401034 | T>I | A:454 | (-1.82, -3.14, -32.85) | |
| 1:230401036 | N>D | A:455 | (1.34, -0.92, -34.19) | |
| 1:230401038 | N>K | A:455 | (1.34, -0.92, -34.19) | |
| 1:230401088 | E>G | A:472 | (0.58, -5.18, -36.92) | |
| 1:230401097 | N>S | A:475 | (5.36, -12.09, -31.37) | |
| 1:230410197 | rs140514370 | A>T | A:483 | (16.74, -3.07, -26.11) |
| 1:230410204 | T>M | A:485 | (20.28, -0.32, -22.69) | |
| 1:230410207 | rs377338023 | K>M | A:486 | (21.87, -0.94, -17.90) |
| 1:230410216 | S>L | A:489 | (19.89, 2.56, -25.48) | |
| 1:230410219 | V>A | A:490 | (16.65, 2.22, -28.07) | |
| 1:230410231 | D>G | A:494 | (25.05, -3.31, -33.17) | |
| 1:230410234 | L>S | A:495 | (21.73, -0.12, -35.03) | |
| 1:230410239 | rs149595757 | L>V | A:497 | (16.83, 5.00, -31.61) |
| 1:230410242 | T>P | A:498 | (19.86, 8.69, -33.24) | |
| 1:230410243 | T>I | A:498 | (19.86, 8.69, -33.24) | |
| 1:230410255 | rs144216012 | R>Q | A:502 | (17.60, 17.96, -29.05) |
| 1:230410257 | A>S | A:503 | (13.98, 19.91, -33.82) | |
| 1:230410261 | P>L | A:504 | (10.74, 20.18, -32.80) | |
| 1:230410284 | rs370275711 | G>S | A:512 | (25.57, 3.41, -34.06) |
| 1:230410291 | rs527685112 | R>Q | A:514 | (27.61, 5.84, -31.29) |
| 1:230410297 | N>S | A:516 | (30.20, 8.69, -26.30) | |
| 1:230410309 | rs544481491 | Q>R | A:520 | (22.25, 7.10, -29.06) |
| 1:230410310 | rs372150000 | Q>H | A:520 | (22.25, 7.10, -29.06) |
| 1:230415064 | rs149914257 | E>K | A:526 | (4.20, 9.04, -18.01) |
| 1:230415068 | rs528256081 | G>D | A:527 | (4.69, 4.07, -16.45) |
| 1:230415071 | N>S | A:528 | (7.25, 2.43, -18.00) | |
| 1:230415088 | rs141375194 | V>M | A:534 | (17.93, 12.23, -21.90) |
| 1:230415099 | N>K | A:537 | (10.16, 17.94, -23.20) | |
| 1:230415112 | S>G | A:542 | (4.00, 8.15, -34.55) | |
| 1:230415116 | rs201604838 | R>H | A:543 | (2.45, 13.25, -34.42) |
| 1:230415145 | E>K | A:553 | (7.15, 16.47, -30.77) | |
| 1:230415148 | rs2273970 | V>M | A:554 | (6.83, 18.41, -27.44) |
| 1:230415158 | P>L | A:557 | (-1.32, 14.22, -24.64) | |
| 1:230415163 | L>I | A:559 | (-2.44, 8.06, -28.67) | |
| 1:230415167 | COSM1207850 | S>L | A:560 | (1.81, 9.24, -30.88) |
| 1:230415188 | rs371254497 | L>R | A:567 | (9.40, -8.77, -21.98) |
| 1:230415192 | N>K | A:568 | (9.19, -11.47, -26.84) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 1:230371783 | COSM4594372 | V>G | A:133 | (-3.90, -51.53, 19.35) |
| 1:230372463 | COSM905338 | R>Q | A:200 | (5.68, -11.54, 26.67) |
| 1:230391060 | COSM1668550 | F>S | A:369 | (1.45, -8.95, 12.00) |
| 1:230398367 | COSM1295981 | F>L | A:395 | (16.50, -17.91, -7.36) |
| 1:230398700 | COSM145442 | L>P | A:421 | (21.33, -32.22, 12.35) |