General Structure Information
| PDB ID | 2qtl |
| HGNC Gene Label(s) | MTRR |
| Structure Name | crystal structure of the fad-containing fnr-like module of human methionine synthase reductase |
| Resolution | 1.9Å |
| Reference | AUTH K.R.WOLTHERS,X.LOU,H.S.TOOGOOD,D.LEYS,N.S.SCRUTTONTITL MECHANISM OF COENZYME BINDING TO HUMAN METHIONINE SYNTHASETITL 2 REDUCTASE REVEALED THROUGH THE CRYSTAL STRUCTURE OF THETITL 3 FNR-LIKE MODULE AND ISOTHERMAL TITRATION CALORIMETRYREF BIOCHEMISTRY V. 46 11833 2007REFN ISSN 0006-2960PMID 17892308DOI 10.1021/BI701209P |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 445 |
| Number Of SNVs | 143 |
| Number Of Permutations | 33449 |
| Optimal Distance Threshold | 26.0 |
| K Statistic | 0.358 |
| p-value | 0.674 |
COSMIC
| Number Of Residues | 445 |
| Number Of SNVs | 6 |
| Number Of Permutations | 2882 |
| Optimal Distance Threshold | 24.0 |
| K Statistic | 0.067 |
| p-value | 0.185 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 143 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 24.0 |
| K Statistic | -0.241 |
| p-value | 0.176 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:7878304 | rs115741769 | S>P | A:217 | (32.49, -1.80, 66.34) |
| 5:7878305 | S>C | A:217 | (32.49, -1.80, 66.34) | |
| 5:7878308 | rs541734980 | N>S | A:218 | (34.59, -0.13, 69.25) |
| 5:7878309 | N>K | A:218 | (34.59, -0.13, 69.25) | |
| 5:7878316 | rs372359132 | I>V | A:221 | (42.26, 5.96, 67.66) |
| 5:7878344 | COSM1438841 | R>H | A:230 | (46.01, 12.86, 69.76) |
| 5:7878347 | rs201557658 | S>L | A:231 | (48.71, 16.28, 69.67) |
| 5:7878352 | P>T | A:233 | (55.08, 14.33, 69.19) | |
| 5:7878356 | P>Q | A:234 | (56.61, 18.12, 68.62) | |
| 5:7878371 | rs371860776 | S>F | A:239 | (56.65, 25.30, 75.41) |
| 5:7878394 | rs114053717 | P>S | A:247 | (39.43, 42.49, 75.81) |
| 5:7878407 | Q>R | A:251 | (25.87, 43.58, 79.42) | |
| 5:7878409 | V>L | A:252 | (24.06, 39.68, 77.41) | |
| 5:7878424 | rs2303080 | S>T | A:257 | (8.50, 38.78, 75.53) |
| 5:7883302 | P>Q | A:272 | (17.15, 49.56, 50.02) | |
| 5:7883344 | rs79430644 | T>M | A:286 | (22.99, 15.89, 34.59) |
| 5:7883350 | D>G | A:288 | (25.73, 12.53, 36.51) | |
| 5:7883352 | A>T | A:289 | (26.81, 16.20, 38.03) | |
| 5:7883356 | rs144899305 | I>T | A:290 | (30.47, 16.54, 40.35) |
| 5:7883357 | I>M | A:290 | (30.47, 16.54, 40.35) | |
| 5:7883361 | rs376109940 | T>A | A:292 | (24.09, 21.01, 41.14) |
| 5:7883376 | E>K | A:297 | (12.27, 33.19, 37.40) | |
| 5:7883389 | S>L | A:301 | (6.60, 42.85, 38.96) | |
| 5:7885818 | T>I | A:303 | (9.37, 45.97, 42.17) | |
| 5:7885821 | D>G | A:304 | (11.17, 50.05, 42.13) | |
| 5:7885830 | rs112125408 | Y>C | A:307 | (17.80, 43.64, 35.36) |
| 5:7885832 | Q>E | A:308 | (20.92, 46.43, 32.37) | |
| 5:7885833 | Q>L | A:308 | (20.92, 46.43, 32.37) | |
| 5:7885839 | G>A | A:310 | (25.87, 42.20, 34.59) | |
| 5:7885845 | A>G | A:312 | (24.82, 42.49, 40.70) | |
| 5:7885853 | V>M | A:315 | (20.85, 37.20, 48.39) | |
| 5:7885856 | I>F | A:316 | (19.22, 38.63, 52.49) | |
| 5:7885860 | C>F | A:317 | (20.99, 34.41, 53.68) | |
| 5:7885862 | rs375421492 | P>S | A:318 | (19.37, 32.03, 56.02) |
| 5:7885868 | rs199762141 | S>G | A:320 | (20.62, 26.09, 59.10) |
| 5:7885883 | rs138098668 | Q>K | A:325 | (18.18, 23.33, 67.06) |
| 5:7885902 | rs148544221 | L>P | A:331 | (25.38, 27.51, 73.86) |
| 5:7885926 | H>R | A:339 | (14.12, 35.10, 75.73) | |
| 5:7885931 | rs74790259 | V>I | A:341 | (19.41, 40.13, 72.72) |
| 5:7885945 | rs140944718 | I>M | A:345 | (29.44, 48.23, 76.86) |
| 5:7885955 | T>S | A:349 | (35.74, 47.05, 79.81) | |
| 5:7885959 | rs162036 | K>R | A:350 | (39.73, 46.88, 79.21) |
| 5:7885966 | K>N | A:352 | (39.74, 50.76, 74.21) | |
| 5:7886730 | A>T | A:354 | (33.99, 49.79, 72.96) | |
| 5:7886733 | rs375332745 | T>A | A:355 | (31.59, 49.55, 69.96) |
| 5:7886739 | P>T | A:357 | (28.00, 44.90, 67.59) | |
| 5:7886743 | Q>R | A:358 | (26.58, 47.16, 63.85) | |
| 5:7886746 | H>R | A:359 | (26.63, 42.41, 63.34) | |
| 5:7886758 | COSM325865 | G>E | A:363 | (16.22, 43.25, 70.60) |
| 5:7886775 | I>V | A:369 | (20.59, 37.26, 66.22) | |
| 5:7886787 | C>R | A:373 | (22.79, 38.33, 62.07) | |
| 5:7886790 | rs372106115 | L>F | A:374 | (25.54, 35.74, 63.62) |
| 5:7886797 | I>T | A:376 | (27.21, 30.19, 62.51) | |
| 5:7886800 | rs559714440 | R>Q | A:377 | (28.96, 27.60, 58.15) |
| 5:7886805 | I>V | A:379 | (37.03, 29.75, 60.27) | |
| 5:7889218 | rs368943570 COSM483079 |
R>Q | A:386 | (43.42, 32.68, 74.87) |
| 5:7889223 | L>F | A:388 | (37.17, 29.28, 73.82) | |
| 5:7889226 | V>M | A:389 | (41.24, 28.42, 76.89) | |
| 5:7889236 | T>S | A:392 | (37.91, 24.72, 78.69) | |
| 5:7889243 | rs149678769 | D>E | A:394 | (39.41, 18.80, 80.15) |
| 5:7889244 | COSM3856472 | S>C | A:395 | (43.12, 19.43, 81.21) |
| 5:7889245 | S>N | A:395 | (43.12, 19.43, 81.21) | |
| 5:7889256 | rs531325011 | R>C | A:399 | (48.17, 21.79, 75.78) |
| 5:7889304 | rs2287780 | R>C | A:415 | (46.23, 18.95, 59.44) |
| 5:7889305 | R>H | A:415 | (46.23, 18.95, 59.44) | |
| 5:7889307 | F>L | A:416 | (43.79, 19.48, 62.17) | |
| 5:7889314 | R>Q | A:418 | (43.28, 27.02, 57.05) | |
| 5:7889316 | D>N | A:419 | (42.71, 23.44, 55.60) | |
| 5:7889326 | A>G | A:422 | (36.07, 24.72, 61.25) | |
| 5:7889330 | C>W | A:423 | (32.69, 25.72, 62.84) | |
| 5:7889335 | L>S | A:425 | (28.88, 23.50, 66.33) | |
| 5:7889340 | L>I | A:427 | (35.49, 23.74, 67.69) | |
| 5:7889349 | rs564953226 | A>T | A:430 | (35.31, 18.53, 69.93) |
| 5:7889356 | P>L | A:432 | (33.02, 18.62, 75.21) | |
| 5:7889376 | S>G | A:439 | (29.22, 37.46, 75.52) | |
| 5:7889383 | L>Q | A:441 | (29.72, 33.76, 70.88) | |
| 5:7891491 | L>H | A:445 | (30.39, 35.28, 65.71) | |
| 5:7891498 | K>N | A:447 | (27.51, 40.73, 58.90) | |
| 5:7891505 | P>S | A:450 | (25.04, 39.50, 51.88) | |
| 5:7891506 | rs16879334 | P>R | A:450 | (25.04, 39.50, 51.88) |
| 5:7891514 | Y>H | A:453 | (24.26, 35.32, 43.60) | |
| 5:7891520 | C>S | A:455 | (22.22, 39.38, 36.15) | |
| 5:7891521 | C>S | A:455 | (22.22, 39.38, 36.15) | |
| 5:7891523 | A>T | A:456 | (21.17, 35.81, 33.68) | |
| 5:7891524 | A>V | A:456 | (21.17, 35.81, 33.68) | |
| 5:7892862 | K>E | A:465 | (10.61, 37.87, 35.31) | |
| 5:7892868 | H>Y | A:467 | (16.56, 34.68, 35.07) | |
| 5:7892869 | H>R | A:467 | (16.56, 34.68, 35.07) | |
| 5:7892884 | I>T | A:472 | (24.70, 23.63, 44.92) | |
| 5:7892887 | V>A | A:473 | (28.64, 25.04, 47.41) | |
| 5:7892893 | F>S | A:475 | (32.08, 22.45, 52.35) | |
| 5:7892911 | T>I | A:481 | (27.45, 13.15, 61.31) | |
| 5:7892914 | E>V | A:482 | (28.57, 14.88, 57.75) | |
| 5:7892923 | rs146475928 | R>Q | A:485 | (29.20, 21.45, 56.03) |
| 5:7892931 | V>L | A:488 | (24.82, 29.32, 53.61) | |
| 5:7892934 | C>R | A:489 | (22.98, 30.80, 49.97) | |
| 5:7892937 | rs41283145 | T>A | A:490 | (23.65, 27.67, 47.65) |
| 5:7892941 | rs148284479 | G>D | A:491 | (21.35, 25.55, 50.25) |
| 5:7892967 | V>I | A:500 | (9.51, 25.25, 42.40) | |
| 5:7893018 | rs149581788 | A>P | A:517 | (5.88, 31.37, 46.57) |
| 5:7893021 | P>S | A:518 | (9.13, 30.85, 47.48) | |
| 5:7895847 | I>V | A:520 | (14.21, 35.98, 48.12) | |
| 5:7895851 | S>F | A:521 | (15.39, 39.40, 50.39) | |
| 5:7895853 | rs374903302 | I>V | A:522 | (16.78, 41.31, 46.60) |
| 5:7895865 | T>A | A:526 | (25.17, 50.96, 43.79) | |
| 5:7895871 | rs375420169 | N>D | A:528 | (26.98, 47.66, 38.39) |
| 5:7895872 | rs543608145 COSM1070443 |
N>T | A:528 | (26.98, 47.66, 38.39) |
| 5:7895886 | P>S | A:533 | (29.04, 47.93, 24.76) | |
| 5:7895892 | D>N | A:535 | (28.46, 51.22, 20.19) | |
| 5:7895904 | P>S | A:539 | (33.35, 44.23, 18.66) | |
| 5:7895905 | P>L | A:539 | (33.35, 44.23, 18.66) | |
| 5:7895910 | I>L | A:541 | (35.53, 38.67, 23.33) | |
| 5:7895913 | M>L | A:542 | (31.72, 36.63, 25.64) | |
| 5:7895917 | V>G | A:543 | (35.50, 34.34, 28.66) | |
| 5:7895919 | G>C | A:544 | (32.65, 31.52, 30.43) | |
| 5:7895943 | F>L | A:552 | (28.49, 36.34, 29.17) | |
| 5:7895959 | Q>R | A:557 | (18.53, 37.34, 26.65) | |
| 5:7895961 | rs115297357 | H>N | A:558 | (19.85, 43.44, 25.77) |
| 5:7895964 | R>G | A:559 | (23.05, 42.38, 20.91) | |
| 5:7897020 | M>V | A:574 | (28.47, 38.61, 20.11) | |
| 5:7897027 | L>W | A:576 | (30.96, 32.45, 24.03) | |
| 5:7897042 | R>K | A:581 | (33.64, 19.06, 33.32) | |
| 5:7897045 | H>R | A:582 | (31.78, 15.86, 31.19) | |
| 5:7897054 | R>K | A:585 | (28.11, 14.79, 33.37) | |
| 5:7897058 | rs148424643 | D>E | A:586 | (28.52, 20.42, 32.50) |
| 5:7897060 | Y>F | A:587 | (26.91, 22.45, 26.56) | |
| 5:7897179 | rs368741550 | K>E | A:591 | (19.59, 24.74, 23.52) |
| 5:7897191 | rs10380 | H>Y | A:595 | (18.05, 30.82, 19.63) |
| 5:7897192 | H>R | A:595 | (18.05, 30.82, 19.63) | |
| 5:7897195 | F>C | A:596 | (21.31, 33.12, 21.33) | |
| 5:7897197 | L>I | A:597 | (24.50, 30.46, 16.90) | |
| 5:7897201 | K>R | A:598 | (18.79, 29.80, 14.31) | |
| 5:7897203 | H>Y | A:599 | (18.02, 33.33, 15.25) | |
| 5:7897204 | H>L | A:599 | (18.02, 33.33, 15.25) | |
| 5:7897222 | L>R | A:605 | (30.13, 28.82, 20.35) | |
| 5:7897227 | rs114259126 | V>I | A:607 | (32.88, 24.65, 23.54) |
| 5:7897237 | S>L | A:610 | (37.82, 19.26, 30.76) | |
| 5:7897244 | D>E | A:612 | (35.19, 14.79, 27.51) | |
| 5:7897246 | A>V | A:613 | (37.72, 11.76, 25.66) | |
| 5:7897281 | rs201802094 | V>M | A:625 | (38.64, 28.77, 27.74) |
| 5:7897284 | rs62342555 | Q>E | A:626 | (42.77, 28.75, 28.44) |
| 5:7897317 | A>S | A:637 | (43.75, 40.74, 18.17) | |
| 5:7897335 | E>Q | A:643 | (37.70, 45.66, 15.23) | |
| 5:7897341 | rs141002013 | G>S | A:645 | (37.02, 45.94, 21.58) |
| 5:7897345 | H>R | A:646 | (34.84, 45.87, 24.71) | |
| 5:7900032 | A>E | A:653 | (38.31, 31.15, 39.01) | |
| 5:7900038 | rs562405817 | N>S | A:655 | (43.00, 30.78, 37.83) |
| 5:7900051 | D>E | A:659 | (45.05, 30.89, 32.97) | |
| 5:7900056 | rs148909799 | H>R | A:661 | (46.46, 38.00, 31.52) |
| 5:7900073 | I>V | A:667 | (47.40, 36.15, 21.59) | |
| 5:7900080 | rs201686214 | S>N | A:669 | (53.22, 38.66, 21.37) |
| 5:7900088 | V>I | A:672 | (51.71, 42.35, 16.90) | |
| 5:7900109 | A>T | A:679 | (51.68, 42.64, 25.80) | |
| 5:7900127 | T>A | A:685 | (45.97, 50.03, 28.55) | |
| 5:7900145 | rs148414435 | R>C | A:691 | (38.73, 48.10, 25.22) |
| 5:7900158 | D>G | A:695 | (32.63, 39.09, 37.30) | |
| 5:7900161 | COSM179990 | I>T | A:696 | (36.20, 37.09, 39.25) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:7885907 | COSM4985425 | L>V | A:333 | (20.75, 29.31, 74.89) |
| 5:7885959 | COSM4985051 | K>R | A:350 | (39.73, 46.88, 79.21) |
| 5:7889295 | COSM245800 | D>N | A:412 | (48.03, 21.46, 64.02) |
| 5:7891518 | COSM3429677 | S>L | A:454 | (25.04, 37.53, 38.35) |
| 5:7891527 | COSM1671501 | S>I | A:457 | (18.74, 38.24, 32.42) |
| 5:7900136 | COSM1258056 | E>K | A:688 | (43.89, 51.48, 32.42) |