General Structure Information
| PDB ID | 2d7r |
| HGNC Gene Label(s) | GALNT10 |
| Structure Name | crystal structure of pp-galnac-t10 complexed with galnac-ser on lectin domain |
| Resolution | 2.8Å |
| Reference | AUTH T.KUBOTA,T.SHIBA,S.SUGIOKA,S.FURUKAWA,H.SAWAKI,R.KATO,AUTH 2 S.WAKATSUKI,H.NARIMATSUTITL STRUCTURAL BASIS OF CARBOHYDRATE TRANSFER ACTIVITY BY HUMANTITL 2 UDP-GALNAC: POLYPEPTIDETITL 3 ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE (PP-GALNAC-T10)REF J.MOL.BIOL. V. 359 708 2006REFN ISSN 0022-2836PMID 16650853DOI 10.1016/J.JMB.2006.03.061 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 536 |
| Number Of SNVs | 136 |
| Number Of Permutations | 30058 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.03 |
| p-value | 0.604 |
COSMIC
| Number Of Residues | 536 |
| Number Of SNVs | 8 |
| Number Of Permutations | 6256 |
| Optimal Distance Threshold | 26.0 |
| K Statistic | 0.143 |
| p-value | 0.213 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 136 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 28.0 |
| K Statistic | -0.233 |
| p-value | 0.394 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:153674434 | D>A | A:73 | (10.98, 12.42, 12.04) | |
| 5:153674439 | H>Y | A:75 | (8.34, 16.54, 11.57) | |
| 5:153674454 | rs142239169 | I>V | A:80 | (1.00, 19.38, 12.76) |
| 5:153674458 | R>Q | A:81 | (-3.30, 15.65, 13.01) | |
| 5:153674472 | rs146720050 | R>C | A:86 | (-6.08, 26.15, 17.04) |
| 5:153674473 | rs200653755 | R>H | A:86 | (-6.08, 26.15, 17.04) |
| 5:153674475 | rs140354249 | V>I | A:87 | (-10.68, 27.48, 15.29) |
| 5:153677536 | D>N | A:100 | (-13.12, 51.00, 13.61) | |
| 5:153677539 | A>P | A:101 | (-11.29, 49.26, 17.62) | |
| 5:153677546 | R>T | A:103 | (-9.00, 50.37, 12.09) | |
| 5:153677561 | Y>F | A:108 | (-0.14, 50.72, 16.49) | |
| 5:153677564 | R>Q | A:109 | (1.66, 55.70, 21.57) | |
| 5:153677587 | rs144259960 | V>I | A:117 | (-4.72, 42.74, 17.37) |
| 5:153677590 | S>G | A:118 | (-2.11, 40.72, 20.18) | |
| 5:153677594 | D>V | A:119 | (-4.41, 41.38, 23.42) | |
| 5:153677629 | rs538296822 | R>W | A:131 | (8.27, 23.87, 5.95) |
| 5:153677630 | R>Q | A:131 | (8.27, 23.87, 5.95) | |
| 5:153709145 | rs150192577 | R>C | A:139 | (15.05, 11.43, 8.91) |
| 5:153709146 | COSM269222 COSM3661635 |
R>H | A:139 | (15.05, 11.43, 8.91) |
| 5:153709154 | rs191295808 | E>K | A:142 | (18.26, 9.97, 17.67) |
| 5:153709163 | P>S | A:145 | (23.05, 19.68, 20.82) | |
| 5:153709175 | rs376432659 | I>V | A:149 | (16.16, 29.62, 24.17) |
| 5:153709206 | S>C | A:159 | (0.67, 39.44, 24.31) | |
| 5:153709211 | L>F | A:161 | (6.65, 38.23, 25.83) | |
| 5:153709221 | T>I | A:164 | (7.44, 34.32, 22.00) | |
| 5:153709223 | COSM1064715 | V>I | A:165 | (7.47, 31.76, 25.37) |
| 5:153709227 | H>P | A:166 | (3.07, 29.87, 25.06) | |
| 5:153709242 | rs111378217 | R>H | A:171 | (5.49, 25.43, 17.91) |
| 5:153709245 | S>L | A:172 | (10.26, 23.09, 21.13) | |
| 5:153709262 | COSM1064716 | A>T | A:178 | (17.84, 23.72, 28.64) |
| 5:153709270 | I>M | A:180 | (13.47, 29.63, 28.24) | |
| 5:153709296 | rs200301599 | R>Q | A:189 | (5.96, 49.10, 30.29) |
| 5:153755866 | M>V | A:200 | (6.79, 32.60, 33.38) | |
| 5:153755872 | L>F | A:202 | (3.16, 28.40, 36.25) | |
| 5:153755879 | rs201987167 | P>L | A:204 | (9.33, 24.98, 34.68) |
| 5:153755882 | S>N | A:205 | (11.77, 25.99, 31.47) | |
| 5:153755884 | V>M | A:206 | (10.78, 29.79, 32.13) | |
| 5:153755914 | G>R | A:216 | (20.77, 46.83, 25.97) | |
| 5:153755930 | COSM1435407 | R>Q | A:221 | (21.62, 39.65, 22.63) |
| 5:153755938 | G>R | A:224 | (22.61, 35.52, 28.99) | |
| 5:153755950 | A>S | A:228 | (24.11, 29.76, 29.79) | |
| 5:153755951 | A>V | A:228 | (24.11, 29.76, 29.79) | |
| 5:153755987 | C>S | A:240 | (8.79, 35.87, 17.87) | |
| 5:153755996 | rs116636563 | N>S | A:243 | (6.88, 27.55, 12.38) |
| 5:153756001 | N>H | A:245 | (10.57, 21.14, 13.01) | |
| 5:153756010 | rs139479065 | P>S | A:248 | (15.92, 20.61, 15.04) |
| 5:153760010 | R>C | A:253 | (24.54, 22.35, 9.23) | |
| 5:153760020 | rs372572304 | R>Q | A:256 | (26.73, 17.37, 11.19) |
| 5:153760024 | rs540856217 | N>K | A:257 | (29.73, 22.35, 11.27) |
| 5:153760025 | R>C | A:258 | (32.52, 24.31, 17.40) | |
| 5:153760026 | R>H | A:258 | (32.52, 24.31, 17.40) | |
| 5:153760038 | V>A | A:262 | (22.61, 28.90, 12.42) | |
| 5:153760043 | P>S | A:264 | (16.47, 31.34, 11.03) | |
| 5:153760044 | COSM449163 | P>L | A:264 | (16.47, 31.34, 11.03) |
| 5:153760070 | COSM3853002 COSM3853003 |
D>N | A:273 | (-3.12, 41.87, 10.18) |
| 5:153760071 | D>G | A:273 | (-3.12, 41.87, 10.18) | |
| 5:153760075 | F>L | A:274 | (-0.38, 40.36, 14.29) | |
| 5:153760077 | R>Q | A:275 | (-0.50, 39.78, 7.36) | |
| 5:153760084 | E>D | A:277 | (3.49, 37.13, 5.19) | |
| 5:153760097 | rs377273675 | D>N | A:282 | (12.09, 33.75, 0.82) |
| 5:153760106 | R>W | A:285 | (23.36, 36.16, -0.12) | |
| 5:153760119 | D>G | A:289 | (24.15, 50.27, 2.31) | |
| 5:153760131 | Y>C | A:293 | (20.94, 51.72, 6.48) | |
| 5:153760140 | R>Q | A:296 | (16.75, 40.53, 1.92) | |
| 5:153760143 | I>T | A:297 | (21.05, 40.24, -2.02) | |
| 5:153760160 | rs368896641 | L>V | A:303 | (26.14, 30.49, -4.96) |
| 5:153760170 | A>D | A:306 | (20.19, 21.73, -5.63) | |
| 5:153760175 | COSM3853006 COSM3853007 |
P>A | A:308 | (15.87, 24.31, -2.67) |
| 5:153760181 | rs200736059 COSM2150310 COSM2150311 |
D>N | A:310 | (19.69, 22.34, 1.59) |
| 5:153760187 | F>I | A:312 | (21.43, 29.65, 2.25) | |
| 5:153760190 | E>K | A:313 | (27.02, 29.89, 2.16) | |
| 5:153765901 | rs139262954 | A>T | A:323 | (22.45, 29.90, 16.58) |
| 5:153765904 | V>M | A:324 | (25.95, 29.84, 18.50) | |
| 5:153765907 | D>H | A:325 | (28.76, 26.63, 20.26) | |
| 5:153765913 | K>Q | A:327 | (33.37, 26.88, 23.58) | |
| 5:153765931 | G>S | A:333 | (33.68, 37.65, 22.42) | |
| 5:153765932 | rs144099170 | G>D | A:333 | (33.68, 37.65, 22.42) |
| 5:153765934 | rs374511506 | G>R | A:334 | (31.15, 38.22, 21.37) |
| 5:153765935 | G>E | A:334 | (31.15, 38.22, 21.37) | |
| 5:153765946 | rs376469597 | G>S | A:338 | (30.33, 49.17, 23.37) |
| 5:153765954 | E>D | A:340 | (25.31, 51.38, 23.52) | |
| 5:153765965 | G>E | A:344 | (25.94, 46.33, 14.96) | |
| 5:153765982 | rs202216584 | S>A | A:350 | (28.99, 38.60, 10.73) |
| 5:153765985 | rs148741733 | F>L | A:351 | (32.00, 41.33, 9.49) |
| 5:153783664 | rs201377561 | V>L | A:353 | (32.09, 34.03, 11.79) |
| 5:153783682 | rs142364912 | R>C | A:359 | (30.52, 28.51, 7.33) |
| 5:153783683 | R>H | A:359 | (30.52, 28.51, 7.33) | |
| 5:153783697 | P>A | A:364 | (15.80, 26.85, 4.67) | |
| 5:153783698 | rs371395496 | P>L | A:364 | (15.80, 26.85, 4.67) |
| 5:153783713 | G>A | A:369 | (8.55, 34.93, 13.44) | |
| 5:153783720 | I>M | A:371 | (6.63, 41.73, 15.14) | |
| 5:153783728 | K>T | A:374 | (4.54, 51.27, 12.11) | |
| 5:153783749 | P>L | A:381 | (19.69, 56.82, 26.19) | |
| 5:153783754 | rs540121328 | G>R | A:383 | (24.40, 59.92, 24.08) |
| 5:153783761 | S>N | A:385 | (24.99, 57.09, 18.37) | |
| 5:153783769 | R>W | A:388 | (30.32, 54.89, 19.56) | |
| 5:153789110 | R>W | A:392 | (33.50, 50.65, 18.68) | |
| 5:153789113 | V>M | A:393 | (32.38, 47.79, 13.76) | |
| 5:153789119 | COSM3827498 COSM3827499 |
E>K | A:395 | (38.01, 51.61, 12.92) |
| 5:153789128 | rs140453579 | M>V | A:398 | (35.28, 47.38, 7.67) |
| 5:153789132 | D>G | A:399 | (40.21, 47.28, 7.24) | |
| 5:153789140 | rs202225318 | A>T | A:402 | (35.62, 52.38, 6.16) |
| 5:153789146 | Y>H | A:404 | (34.79, 52.78, 0.41) | |
| 5:153789149 | I>V | A:405 | (31.30, 54.29, 5.74) | |
| 5:153789159 | rs147103681 | R>H | A:408 | (28.39, 57.06, 0.96) |
| 5:153789161 | rs202239148 | R>W | A:409 | (26.71, 58.55, 7.08) |
| 5:153789162 | R>Q | A:409 | (26.71, 58.55, 7.08) | |
| 5:153789173 | R>C | A:413 | (36.04, 61.31, 8.35) | |
| 5:153789178 | H>Q | A:414 | (36.84, 64.62, 14.29) | |
| 5:153789197 | rs369435277 COSM1207841 COSM3373756 |
A>T | A:421 | (41.77, 48.66, 21.94) |
| 5:153789200 | V>I | A:422 | (40.13, 45.75, 23.91) | |
| 5:153789215 | R>C | A:427 | (41.03, 41.71, 13.66) | |
| 5:153789222 | S>C | A:429 | (43.89, 36.87, 19.19) | |
| 5:153789224 | L>I | A:430 | (41.10, 35.30, 16.68) | |
| 5:153789234 | rs139635794 | K>R | A:433 | (41.11, 36.01, 6.98) |
| 5:153789279 | K>R | A:448 | (26.31, 43.10, -8.29) | |
| 5:153789293 | rs117925322 | V>M | A:453 | (32.47, 53.63, -6.15) |
| 5:153789299 | P>S | A:455 | (28.77, 54.14, -11.37) | |
| 5:153789317 | rs373237804 | G>R | A:461 | (17.93, 67.10, -14.54) |
| 5:153789320 | E>K | A:462 | (15.20, 70.02, -17.15) | |
| 5:153792450 | I>T | A:463 | (12.89, 65.57, -17.87) | |
| 5:153792458 | rs200600903 | V>M | A:466 | (9.74, 68.32, -27.29) |
| 5:153792464 | T>A | A:468 | (4.31, 70.37, -24.19) | |
| 5:153792465 | T>I | A:468 | (4.31, 70.37, -24.19) | |
| 5:153792468 | G>E | A:469 | (7.70, 72.06, -23.31) | |
| 5:153792483 | rs143091614 | T>I | A:474 | (7.03, 66.06, -8.50) |
| 5:153792491 | rs577854465 | G>R | A:477 | (5.16, 62.59, -3.81) |
| 5:153792494 | rs373562892 | A>T | A:478 | (6.91, 59.94, -2.15) |
| 5:153792504 | rs201408248 | S>F | A:481 | (2.45, 60.89, -6.39) |
| 5:153792516 | L>P | A:485 | (3.90, 68.21, -16.98) | |
| 5:153792528 | V>G | A:489 | (11.78, 76.44, -12.72) | |
| 5:153792531 | COSM3612889 COSM3612890 |
R>Q | A:490 | (16.53, 77.44, -15.74) |
| 5:153792536 | COSM3853014 COSM3853015 |
R>C | A:492 | (14.99, 81.36, -13.75) |
| 5:153792537 | R>H | A:492 | (14.99, 81.36, -13.75) | |
| 5:153795374 | R>Q | A:512 | (16.78, 57.54, -8.27) | |
| 5:153795413 | D>V | A:525 | (6.87, 52.40, -10.73) | |
| 5:153795415 | A>T | A:526 | (5.42, 51.58, -14.53) | |
| 5:153795428 | T>S | A:530 | (-1.65, 52.52, -20.29) | |
| 5:153795434 | P>R | A:532 | (0.42, 56.27, -14.81) | |
| 5:153795440 | rs35810347 | T>M | A:534 | (4.56, 56.35, -9.81) |
| 5:153795448 | rs200092315 COSM449164 |
D>N | A:537 | (9.92, 52.17, -2.88) |
| 5:153795466 | G>S | A:543 | (11.42, 46.39, -14.10) | |
| 5:153795475 | L>M | A:546 | (13.95, 49.01, -16.80) | |
| 5:153796375 | D>G | A:552 | (14.34, 58.16, -29.97) | |
| 5:153796422 | E>K | A:568 | (-0.81, 68.75, -25.39) | |
| 5:153796456 | rs139580325 | N>S | A:579 | (5.52, 57.34, -32.03) |
| 5:153796464 | S>P | A:582 | (6.37, 62.31, -31.78) | |
| 5:153796494 | T>A | A:592 | (24.45, 63.58, -21.04) | |
| 5:153796495 | rs535948214 | T>S | A:592 | (24.45, 63.58, -21.04) |
| 5:153796520 | F>L | A:600 | (21.11, 48.12, -20.78) | |
| 5:153796521 | N>D | A:601 | (21.71, 50.21, -26.07) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:153709146 | COSM269222 | R>H | A:139 | (15.05, 11.43, 8.91) |
| 5:153709223 | COSM1064715 | V>I | A:165 | (7.47, 31.76, 25.37) |
| 5:153709265 | COSM3612885 | E>K | A:179 | (17.98, 27.39, 29.87) |
| 5:153760070 | COSM3853002 | D>N | A:273 | (-3.12, 41.87, 10.18) |
| 5:153760181 | COSM2150310 | D>Y | A:310 | (19.69, 22.34, 1.59) |
| 5:153789197 | COSM1207841 | A>T | A:421 | (41.77, 48.66, 21.94) |
| 5:153789216 | COSM327580 | R>H | A:427 | (41.03, 41.71, 13.66) |
| 5:153792479 | COSM337154 | D>H | A:473 | (7.17, 68.52, -11.56) |