General Structure Information
| PDB ID | 2cfy |
| HGNC Gene Label(s) | TXNRD1 |
| Structure Name | crystal structure of human thioredoxin reductase 1 |
| Resolution | 2.7Å |
| Reference | AUTH J.E.DEBRECZENI,C.JOHANSSON,K.KAVANAGH,P.SAVITSKY,AUTH 2 M.SUNDSTROM,C.ARROWSMITH,J.WEIGELT,A.EDWARDS,F.VON DELFT,AUTH 3 U.OPPERMANNTITL CRYSTAL STRUCTURE OF HUMAN THIOREDOXIN REDUCTASE 1REF TO BE PUBLISHEDREFN |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 484 |
| Number Of SNVs | 119 |
| Number Of Permutations | 52709 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.009 |
| p-value | 0.702 |
COSMIC
| Number Of Residues | 484 |
| Number Of SNVs | 5 |
| Number Of Permutations | 500 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.1 |
| p-value | 0.63 |
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 | 7.0 |
| K Statistic | 0.151 |
| p-value | 0.561 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:104705132 | rs371761559 | S>C | A:10 | (91.62, -34.09, 66.24) |
| 12:104705135 | COSM546013 COSM1648874 COSM546012 |
Y>C | A:11 | (88.25, -31.88, 66.67) |
| 12:104705149 | I>V | A:16 | (79.53, -29.02, 62.09) | |
| 12:104705150 | I>T | A:16 | (79.53, -29.02, 62.09) | |
| 12:104705156 | rs367795908 | I>T | A:18 | (73.29, -26.92, 62.95) |
| 12:104705173 | G>C | A:24 | (74.69, -21.93, 56.15) | |
| 12:104705179 | A>T | A:26 | (76.91, -19.22, 52.99) | |
| 12:104707026 | A>T | A:31 | (84.67, -22.31, 54.26) | |
| 12:104707047 | rs201402862 | V>M | A:38 | (82.59, -28.37, 55.92) |
| 12:104707069 | rs374176114 | T>I | A:45 | (60.64, -30.84, 60.76) |
| 12:104707071 | COSM147596 | P>A | A:46 | (57.40, -32.36, 59.30) |
| 12:104707078 | rs376722303 | P>R | A:48 | (51.43, -30.46, 61.28) |
| 12:104709557 | L>V | A:55 | (68.66, -28.13, 50.54) | |
| 12:104709569 | C>R | A:59 | (63.87, -18.45, 51.28) | |
| 12:104709578 | V>M | A:62 | (58.65, -21.70, 52.78) | |
| 12:104709585 | C>Y | A:64 | (61.26, -15.21, 49.72) | |
| 12:104709587 | I>V | A:65 | (61.52, -17.40, 46.08) | |
| 12:104709615 | A>V | A:74 | (49.05, -10.77, 41.07) | |
| 12:104709624 | G>A | A:77 | (46.64, -9.43, 36.61) | |
| 12:104709626 | Q>K | A:78 | (46.38, -4.99, 37.46) | |
| 12:104709629 | A>T | A:79 | (48.62, -6.40, 33.63) | |
| 12:104709640 | rs368438379 | D>E | A:82 | (46.59, -2.28, 33.01) |
| 12:104709641 | S>P | A:83 | (46.40, -4.27, 28.60) | |
| 12:104709642 | S>F | A:83 | (46.40, -4.27, 28.60) | |
| 12:104709665 | rs370451389 COSM2064554 COSM2064553 COSM3980719 COSM2064552 |
E>K | A:91 | (39.28, -10.99, 27.70) |
| 12:104712705 | D>H | A:99 | (46.80, -26.54, 40.48) | |
| 12:104712711 | M>L | A:101 | (50.76, -20.98, 40.52) | |
| 12:104712721 | A>V | A:104 | (55.82, -23.57, 38.45) | |
| 12:104712727 | rs553294226 | Q>R | A:106 | (57.13, -26.46, 43.85) |
| 12:104712728 | Q>H | A:106 | (57.13, -26.46, 43.85) | |
| 12:104712735 | I>V | A:109 | (61.50, -24.55, 44.75) | |
| 12:104712753 | rs199677400 | G>S | A:115 | (71.78, -26.57, 43.28) |
| 12:104712759 | R>G | A:117 | (71.55, -31.93, 46.36) | |
| 12:104712760 | rs189358801 | R>Q | A:117 | (71.55, -31.93, 46.36) |
| 12:104712762 | V>L | A:118 | (75.44, -29.49, 42.91) | |
| 12:104712771 | R>W | A:121 | (79.60, -31.23, 45.87) | |
| 12:104712772 | rs200501549 COSM3455358 COSM3455357 COSM3455356 |
R>Q | A:121 | (79.60, -31.23, 45.87) |
| 12:104712786 | rs539105473 | V>I | A:126 | (79.48, -33.21, 53.80) |
| 12:104712790 | Y>C | A:127 | (73.34, -32.67, 52.59) | |
| 12:104712802 | Y>F | A:131 | (67.40, -32.73, 64.22) | |
| 12:104712827 | R>S | A:139 | (80.28, -34.53, 70.63) | |
| 12:104712832 | K>T | A:141 | (72.65, -37.23, 68.15) | |
| 12:104713248 | A>T | A:142 | (72.70, -37.29, 63.59) | |
| 12:104713291 | R>I | A:156 | (85.53, -23.69, 65.11) | |
| 12:104713294 | F>S | A:157 | (79.92, -26.85, 66.05) | |
| 12:104713303 | COSM934251 COSM934250 |
A>G | A:160 | (71.62, -22.23, 61.25) |
| 12:104713305 | T>A | A:161 | (68.23, -23.49, 63.19) | |
| 12:104713320 | R>C | A:166 | (54.05, -18.06, 66.57) | |
| 12:104713321 | rs377062126 COSM3954087 COSM3954086 COSM3954085 COSM3954084 |
R>H | A:166 | (54.05, -18.06, 66.57) |
| 12:104713323 | Y>H | A:167 | (50.32, -23.33, 64.75) | |
| 12:104713342 | D>V | A:173 | (45.50, -25.14, 65.46) | |
| 12:104713345 | K>R | A:174 | (48.53, -27.98, 65.16) | |
| 12:104713351 | Y>C | A:176 | (40.97, -28.98, 61.20) | |
| 12:104713358 | rs369698058 | I>M | A:178 | (47.32, -23.39, 56.47) |
| 12:104713361 | rs371619524 | S>R | A:179 | (51.27, -22.29, 57.28) |
| 12:104714898 | P>L | A:190 | (42.52, -21.85, 48.82) | |
| 12:104714907 | rs368876895 | T>I | A:193 | (41.04, -17.29, 52.92) |
| 12:104714912 | V>I | A:195 | (44.78, -14.31, 56.98) | |
| 12:104714913 | V>A | A:195 | (44.78, -14.31, 56.98) | |
| 12:104714945 | rs375808643 | A>T | A:206 | (46.45, -11.58, 51.43) |
| 12:104714967 | G>V | A:213 | (40.46, -13.93, 43.13) | |
| 12:104714975 | rs568459445 | V>I | A:216 | (40.72, -12.48, 51.34) |
| 12:104714985 | M>T | A:219 | (41.44, -11.85, 62.24) | |
| 12:104714988 | V>D | A:220 | (43.93, -8.01, 63.26) | |
| 12:104715005 | R>G | A:226 | (53.91, -4.71, 66.45) | |
| 12:104715042 | E>G | A:238 | (44.00, 2.78, 53.78) | |
| 12:104715057 | H>R | A:243 | (42.26, -2.41, 45.94) | |
| 12:104715071 | rs376165844 | I>V | A:248 | (38.10, -8.81, 61.18) |
| 12:104715083 | rs199586854 | V>I | A:252 | (41.74, -13.59, 68.33) |
| 12:104719130 | rs377194082 | A>T | A:261 | (36.05, -32.35, 54.46) |
| 12:104719131 | A>V | A:261 | (36.05, -32.35, 54.46) | |
| 12:104719146 | rs370065005 | R>Q | A:266 | (32.14, -26.00, 54.65) |
| 12:104719152 | rs537451137 | R>K | A:268 | (32.14, -23.14, 62.16) |
| 12:104719154 | V>L | A:269 | (36.33, -19.32, 62.61) | |
| 12:104719163 | rs187437891 | Q>E | A:272 | (36.59, -13.41, 71.91) |
| 12:104719173 | rs367824614 | N>T | A:275 | (37.81, -4.78, 73.51) |
| 12:104719188 | I>T | A:280 | (32.58, -13.16, 65.34) | |
| 12:104719200 | Y>C | A:284 | (36.37, -18.42, 56.51) | |
| 12:104719206 | rs144671274 | T>M | A:286 | (41.45, -21.81, 53.91) |
| 12:104720130 | M>I | A:288 | (46.87, -18.48, 56.67) | |
| 12:104720149 | A>T | A:295 | (63.07, -20.53, 67.58) | |
| 12:104720156 | rs369434394 | T>I | A:297 | (66.81, -22.95, 69.91) |
| 12:104720164 | I>V | A:300 | (69.51, -28.16, 69.41) | |
| 12:104720176 | T>S | A:304 | (75.04, -30.74, 76.21) | |
| 12:104720179 | rs201533043 COSM934255 COSM934254 |
V>I | A:305 | (77.49, -27.32, 75.00) |
| 12:104720180 | V>A | A:305 | (77.49, -27.32, 75.00) | |
| 12:104720189 | K>R | A:308 | (74.15, -18.48, 77.68) | |
| 12:104720197 | E>K | A:311 | (64.84, -19.88, 78.03) | |
| 12:104721316 | D>G | A:320 | (80.40, -7.94, 67.17) | |
| 12:104721331 | rs376847283 | N>S | A:325 | (78.61, -18.57, 75.76) |
| 12:104721334 | V>A | A:326 | (80.64, -21.43, 73.84) | |
| 12:104721337 | P>R | A:327 | (84.18, -20.15, 72.50) | |
| 12:104721351 | rs574454350 | I>V | A:332 | (73.92, -17.29, 61.72) |
| 12:104721352 | I>T | A:332 | (73.92, -17.29, 61.72) | |
| 12:104721362 | I>M | A:335 | (68.22, -17.90, 65.92) | |
| 12:104721366 | rs375374294 | E>K | A:337 | (69.02, -11.54, 71.14) |
| 12:104721367 | E>A | A:337 | (69.02, -11.54, 71.14) | |
| 12:104721374 | rs377363341 | K>N | A:339 | (70.64, -8.68, 65.45) |
| 12:104721378 | E>K | A:341 | (64.53, -11.58, 61.56) | |
| 12:104721382 | L>P | A:342 | (66.23, -10.34, 56.50) | |
| 12:104721385 | T>I | A:343 | (68.06, -13.92, 53.56) | |
| 12:104721396 | rs370350536 | I>V | A:347 | (73.95, -14.58, 53.10) |
| 12:104721410 | rs375933357 | R>S | A:351 | (80.38, -13.61, 52.87) |
| 12:104721417 | rs576410327 | A>S | A:354 | (84.30, -17.43, 57.21) |
| 12:104721421 | Q>R | A:355 | (85.92, -13.94, 55.15) | |
| 12:104721435 | G>S | A:360 | (91.86, -12.66, 58.27) | |
| 12:104721441 | T>A | A:362 | (88.64, -7.61, 60.52) | |
| 12:104725325 | N>S | A:369 | (70.54, 1.42, 58.26) | |
| 12:104725333 | T>A | A:372 | (62.99, -3.96, 54.03) | |
| 12:104725348 | P>S | A:377 | (49.47, -5.30, 47.05) | |
| 12:104725366 | C>R | A:383 | (65.87, 2.33, 55.06) | |
| 12:104725391 | V>G | A:391 | (60.77, 11.38, 67.36) | |
| 12:104725397 | rs367604146 | K>R | A:393 | (67.37, 8.40, 68.27) |
| 12:104725400 | F>S | A:394 | (67.53, 12.05, 66.80) | |
| 12:104725402 | G>R | A:395 | (63.32, 14.76, 68.55) | |
| 12:104725415 | I>T | A:399 | (62.71, 15.25, 63.07) | |
| 12:104728015 | V>F | A:401 | (59.01, 14.68, 57.55) | |
| 12:104728069 | N>D | A:419 | (46.81, 10.77, 45.07) | |
| 12:104728099 | rs375723971 | T>A | A:429 | (67.98, 19.41, 61.91) |
| 12:104732920 | rs369684801 | R>C | A:434 | (72.72, 13.20, 57.98) |
| 12:104732921 | rs373593847 | R>H | A:434 | (72.72, 13.20, 57.98) |
| 12:104732930 | rs542935965 | G>A | A:437 | (64.79, 7.88, 56.61) |
| 12:104732957 | rs370121871 | G>E | A:446 | (63.05, -2.36, 46.02) |
| 12:104732961 | rs373217616 | E>D | A:447 | (64.21, -2.62, 42.45) |
| 12:104732984 | A>V | A:455 | (73.10, 6.50, 50.51) | |
| 12:104732996 | G>E | A:459 | (75.39, 10.00, 54.58) | |
| 12:104732998 | L>V | A:460 | (72.11, 10.99, 52.15) | |
| 12:104733028 | G>R | A:470 | (66.39, 12.86, 38.03) | |
| 12:104742131 | COSM1470510 COSM1470509 |
V>L | A:478 | (59.75, 11.65, 44.20) |
| 12:104742159 | R>H | A:487 | (57.09, 20.75, 61.61) | |
| 12:104742164 | G>R | A:489 | (50.77, 21.51, 56.52) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:104709645 | COSM1231464 | R>Q | A:84 | (41.87, -4.62, 28.84) |
| 12:104709665 | COSM2064554 | E>K | A:91 | (39.28, -10.99, 27.70) |
| 12:104714883 | COSM3455362 | S>F | A:185 | (52.55, -26.88, 48.44) |
| 12:104715041 | COSM3710656 | E>K | A:238 | (44.00, 2.78, 53.78) |
| 12:104725378 | COSM458284 | E>Q | A:387 | (57.93, 9.42, 61.68) |