General Structure Information
| PDB ID | 3pta |
| HGNC Gene Label(s) | DNMT1 |
| Structure Name | crystal structure of human dnmt1(646-1600) in complex with dna |
| Resolution | 3.6Å |
| Reference | AUTH J.SONG,O.RECHKOBLIT,T.H.BESTOR,D.J.PATELTITL STRUCTURE OF DNMT1-DNA COMPLEX REVEALS A ROLE FORTITL 2 AUTOINHIBITION IN MAINTENANCE DNA METHYLATION.REF SCIENCE V. 331 1036 2011REFN ISSN 0036-8075PMID 21163962DOI 10.1126/SCIENCE.1195380 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 904 |
| Number Of SNVs | 128 |
| Number Of Permutations | 44653 |
| Optimal Distance Threshold | 33.0 |
| K Statistic | 0.297 |
| p-value | 0.074 |
COSMIC
| Number Of Residues | 904 |
| Number Of SNVs | 7 |
| Number Of Permutations | 3845 |
| Optimal Distance Threshold | 5.0 |
| K Statistic | 0.048 |
| p-value | 0.69 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 128 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 39.0 |
| K Statistic | -0.316 |
| p-value | 0.467 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:10265001 | rs146467216 | A>T | A:647 | (9.73, -25.01, 25.05) |
| 19:10264996 | F>L | A:648 | (12.40, -25.24, 27.58) | |
| 19:10264991 | R>H | A:650 | (10.42, -19.30, 34.71) | |
| 19:10264992 | R>C | A:650 | (10.42, -19.30, 34.71) | |
| 19:10264989 | R>W | A:651 | (11.95, -23.72, 39.01) | |
| 19:10264980 | G>S | A:654 | (12.00, -24.80, 47.57) | |
| 19:10262492 | K>T | A:668 | (-7.70, -13.25, 43.67) | |
| 19:10262435 | Q>R | A:687 | (-1.25, -13.23, 46.99) | |
| 19:10262430 | R>W | A:689 | (2.66, -19.85, 47.29) | |
| 19:10262187 | rs368319266 | D>N | A:702 | (21.17, -32.22, 41.83) |
| 19:10262174 | D>G | A:706 | (28.11, -40.21, 40.99) | |
| 19:10262166 | I>F | A:709 | (31.94, -46.20, 45.13) | |
| 19:10262153 | P>L | A:713 | (40.62, -51.38, 38.47) | |
| 19:10262133 | Q>E | A:720 | (42.76, -60.42, 27.17) | |
| 19:10262079 | V>I | A:738 | (65.38, -57.85, 4.46) | |
| 19:10260640 | D>G | A:741 | (71.74, -58.25, 11.67) | |
| 19:10260635 | K>Q | A:743 | (70.09, -63.19, 17.00) | |
| 19:10260611 | C>G | A:751 | (53.29, -68.09, 2.80) | |
| 19:10260595 | rs142562681 | T>N | A:756 | (49.95, -63.24, 0.61) |
| 19:10260587 | V>L | A:759 | (55.26, -55.52, 5.86) | |
| 19:10260328 | rs148987580 | T>M | A:780 | (55.74, -54.28, 12.19) |
| 19:10260272 | rs373366822 | A>T | A:799 | (37.99, -51.80, 19.00) |
| 19:10260251 | rs183555527 | G>R | A:806 | (31.42, -48.44, 22.62) |
| 19:10260244 | rs140993011 | T>M | A:808 | (28.31, -44.89, 20.31) |
| 19:10260179 | S>G | A:830 | (42.72, -63.21, 8.36) | |
| 19:10260152 | P>T | A:839 | (41.94, -35.92, 7.17) | |
| 19:10260146 | E>K | A:841 | (43.86, -30.72, 2.25) | |
| 19:10260132 | M>I | A:845 | (34.76, -25.46, 4.38) | |
| 19:10259653 | G>E | A:860 | (31.22, -47.43, 5.47) | |
| 19:10259654 | rs62621087 | G>R | A:860 | (31.22, -47.43, 5.47) |
| 19:10259635 | Q>R | A:866 | (40.31, -41.35, 12.06) | |
| 19:10259614 | rs569867388 | Y>C | A:873 | (45.32, -40.65, 30.26) |
| 19:10259596 | P>L | A:879 | (48.06, -40.20, 13.72) | |
| 19:10259597 | P>S | A:879 | (48.06, -40.20, 13.72) | |
| 19:10259591 | K>E | A:881 | (55.34, -37.41, 12.39) | |
| 19:10259587 | rs201213597 | T>I | A:882 | (57.10, -41.49, 13.74) |
| 19:10257198 | F>C | A:892 | (58.93, -48.50, 12.42) | |
| 19:10257193 | rs150863675 | V>L | A:894 | (54.99, -46.57, 15.91) |
| 19:10257172 | E>K | A:901 | (61.06, -41.25, 24.14) | |
| 19:10257141 | L>P | A:911 | (74.87, -33.95, 32.25) | |
| 19:10257139 | E>K | A:912 | (78.37, -30.95, 32.71) | |
| 19:10257130 | E>K | A:915 | (84.46, -32.72, 41.52) | |
| 19:10257114 | R>Q | A:920 | (80.37, -37.46, 46.36) | |
| 19:10257115 | rs550380640 | R>W | A:920 | (80.37, -37.46, 46.36) |
| 19:10257112 | V>L | A:921 | (81.23, -37.71, 41.04) | |
| 19:10257108 | L>P | A:922 | (80.41, -33.35, 42.52) | |
| 19:10257109 | L>V | A:922 | (80.41, -33.35, 42.52) | |
| 19:10257100 | S>A | A:925 | (73.67, -31.10, 35.12) | |
| 19:10257058 | V>L | A:939 | (63.46, -28.04, 43.62) | |
| 19:10257037 | F>I | A:946 | (62.66, -31.54, 53.88) | |
| 19:10257033 | T>M | A:947 | (61.68, -32.06, 59.13) | |
| 19:10254620 | V>M | A:964 | (23.39, -28.81, 75.28) | |
| 19:10254616 | D>A | A:965 | (19.38, -27.59, 77.32) | |
| 19:10254609 | D>E | A:967 | (14.83, -29.66, 76.63) | |
| 19:10254608 | L>M | A:968 | (17.06, -24.93, 74.57) | |
| 19:10254602 | P>A | A:970 | (16.09, -29.69, 70.25) | |
| 19:10254584 | Y>H | A:976 | (25.76, -39.63, 64.77) | |
| 19:10254545 | E>K | A:989 | (51.85, -30.15, 53.78) | |
| 19:10254538 | Y>C | A:991 | (54.99, -29.57, 45.94) | |
| 19:10254522 | rs376854079 | I>M | A:996 | (69.96, -27.16, 43.31) |
| 19:10254521 | K>E | A:997 | (74.59, -25.68, 46.13) | |
| 19:10254516 | E>D | A:998 | (76.28, -30.13, 46.04) | |
| 19:10254481 | rs373940840 | N>I | A:1010 | (75.77, -44.61, 40.19) |
| 19:10254470 | I>V | A:1014 | (71.24, -39.26, 41.28) | |
| 19:10254460 | rs199827346 | R>Q | A:1017 | (73.87, -31.53, 49.44) |
| 19:10254453 | N>K | A:1019 | (69.42, -24.78, 50.62) | |
| 19:10252873 | T>I | A:1031 | (49.13, -20.94, 60.04) | |
| 19:10252874 | T>A | A:1031 | (49.13, -20.94, 60.04) | |
| 19:10252867 | A>V | A:1033 | (51.52, -16.04, 58.56) | |
| 19:10252856 | rs370786558 COSM4073747 |
A>T | A:1037 | (51.34, -13.66, 52.63) |
| 19:10252850 | I>V | A:1039 | (50.99, -17.56, 47.05) | |
| 19:10252846 | N>S | A:1040 | (55.30, -16.18, 45.95) | |
| 19:10252819 | A>V | A:1049 | (69.21, -31.67, 52.71) | |
| 19:10252817 | rs187394074 | V>M | A:1050 | (70.39, -35.24, 51.17) |
| 19:10252802 | A>P | A:1055 | (61.96, -37.22, 44.36) | |
| 19:10252789 | R>H | A:1059 | (62.56, -25.90, 36.79) | |
| 19:10252790 | rs140852137 | R>C | A:1059 | (62.56, -25.90, 36.79) |
| 19:10252784 | T>A | A:1061 | (62.00, -19.79, 39.93) | |
| 19:10252781 | rs560179619 | V>M | A:1062 | (63.89, -19.06, 43.95) |
| 19:10252736 | M>V | A:1077 | (51.91, -12.24, 37.17) | |
| 19:10252730 | G>S | A:1079 | (55.25, -16.78, 35.64) | |
| 19:10251831 | P>L | A:1099 | (69.55, -12.86, 53.48) | |
| 19:10251823 | rs374676749 | H>Y | A:1102 | (75.78, -17.50, 49.99) |
| 19:10251528 | COSM3736188 | K>R | A:1135 | (54.45, -12.22, 20.63) |
| 19:10251513 | COSM3148771 | R>Q | A:1140 | (39.86, -15.30, 14.88) |
| 19:10251502 | V>L | A:1144 | (27.94, -19.84, 22.94) | |
| 19:10251461 | rs151305495 | Q>H | A:1157 | (43.36, -13.36, 32.53) |
| 19:10250996 | D>H | A:1162 | (40.03, -12.03, 20.83) | |
| 19:10250992 | T>M | A:1163 | (35.81, -12.74, 22.53) | |
| 19:10250962 | A>V | A:1173 | (24.26, -11.19, 30.66) | |
| 19:10250933 | G>S | A:1183 | (35.07, -5.50, 20.94) | |
| 19:10250891 | L>M | A:1197 | (20.33, -17.26, 9.94) | |
| 19:10250873 | T>A | A:1203 | (25.22, -11.03, 6.19) | |
| 19:10250869 | rs142648642 | T>I | A:1204 | (22.74, -9.35, 8.99) |
| 19:10250860 | COSM990437 | R>H | A:1207 | (21.35, -4.45, 15.44) |
| 19:10250861 | R>C | A:1207 | (21.35, -4.45, 15.44) | |
| 19:10250858 | G>S | A:1208 | (22.68, -5.34, 12.45) | |
| 19:10250851 | R>Q | A:1210 | (28.64, -7.32, 12.50) | |
| 19:10250837 | G>R | A:1215 | (36.81, -18.95, 9.39) | |
| 19:10250767 | R>H | A:1238 | (9.78, -39.47, 26.73) | |
| 19:10250768 | R>C | A:1238 | (9.78, -39.47, 26.73) | |
| 19:10250470 | R>Q | A:1261 | (43.10, -23.65, 15.74) | |
| 19:10250425 | R>H | A:1276 | (23.12, -45.07, 32.93) | |
| 19:10250399 | R>C | A:1285 | (30.82, -41.12, 17.03) | |
| 19:10250386 | rs564106859 COSM180510 |
R>H | A:1289 | (30.93, -37.29, 13.37) |
| 19:10250387 | rs200312526 | R>C | A:1289 | (30.93, -37.29, 13.37) |
| 19:10250363 | G>S | A:1297 | (37.42, -34.23, 32.32) | |
| 19:10249229 | A>V | A:1318 | (41.40, -30.40, 18.12) | |
| 19:10249230 | A>S | A:1318 | (41.40, -30.40, 18.12) | |
| 19:10249226 | A>V | A:1319 | (42.16, -29.70, 14.84) | |
| 19:10249220 | G>E | A:1321 | (46.45, -29.86, 12.94) | |
| 19:10249213 | K>N | A:1323 | (48.69, -30.31, 20.75) | |
| 19:10249214 | K>R | A:1323 | (48.69, -30.31, 20.75) | |
| 19:10249178 | A>D | A:1335 | (40.39, -31.26, 50.09) | |
| 19:10249169 | rs141791913 | A>V | A:1338 | (36.75, -32.29, 46.59) |
| 19:10249155 | COSM3371126 | V>M | A:1343 | (35.44, -40.69, 35.57) |
| 19:10249115 | R>K | A:1356 | (50.59, -31.16, 40.39) | |
| 19:10248680 | S>I | A:1358 | (48.28, -34.32, 46.25) | |
| 19:10248678 | S>T | A:1359 | (50.54, -31.95, 46.65) | |
| 19:10248650 | COSM171794 | R>Q | A:1368 | (40.86, -15.68, 56.76) |
| 19:10248620 | R>Q | A:1378 | (24.28, -3.50, 58.09) | |
| 19:10248608 | rs375225009 COSM77600 |
S>L | A:1382 | (20.97, -2.12, 48.40) |
| 19:10248574 | Q>H | A:1393 | (43.73, -7.68, 55.37) | |
| 19:10248565 | F>L | A:1396 | (42.37, -14.19, 46.27) | |
| 19:10248546 | rs374047326 | A>T | A:1403 | (44.82, -1.03, 40.15) |
| 19:10247908 | P>S | A:1432 | (33.23, -23.45, 63.59) | |
| 19:10247868 | R>Q | A:1445 | (10.17, -8.98, 69.76) | |
| 19:10247835 | R>Q | A:1456 | (5.93, -28.73, 70.52) | |
| 19:10247830 | T>A | A:1458 | (3.21, -33.88, 68.76) | |
| 19:10247822 | rs142647321 | H>Q | A:1460 | (8.28, -41.71, 68.42) |
| 19:10247823 | H>R | A:1460 | (8.28, -41.71, 68.42) | |
| 19:10247811 | N>S | A:1464 | (15.41, -40.61, 66.25) | |
| 19:10247805 | R>H | A:1466 | (14.98, -40.15, 74.09) | |
| 19:10247806 | rs147984942 | R>C | A:1466 | (14.98, -40.15, 74.09) |
| 19:10247791 | rs536916632 | A>T | A:1471 | (11.59, -35.72, 74.51) |
| 19:10247787 | L>R | A:1472 | (8.57, -35.95, 71.90) | |
| 19:10247772 | S>F | A:1477 | (1.93, -38.02, 61.40) | |
| 19:10247767 | V>M | A:1479 | (7.83, -40.20, 61.83) | |
| 19:10246943 | A>T | A:1488 | (-2.66, -30.42, 60.69) | |
| 19:10246447 | R>W | A:1564 | (31.34, -3.34, 35.94) | |
| 19:10246431 | I>T | A:1569 | (20.21, -8.46, 43.80) | |
| 19:10246432 | I>V | A:1569 | (20.21, -8.46, 43.80) | |
| 19:10244935 | I>V | A:1592 | (45.48, -24.18, 24.72) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:10262102 | COSM1130019 | R>H | A:730 | (53.00, -73.67, 3.03) |
| 19:10257060 | COSM3712764 | G>V | A:938 | (64.67, -24.99, 41.71) |
| 19:10249143 | COSM239627 | D>N | A:1347 | (33.77, -51.73, 34.29) |
| 19:10248608 | COSM77600 | S>L | A:1382 | (20.97, -2.12, 48.40) |
| 19:10247929 | COSM1611470 | M>V | A:1425 | (20.37, -15.52, 60.21) |
| 19:10246816 | COSM26919 | P>L | A:1530 | (21.74, -17.24, 47.51) |
| 19:10246814 | COSM288125 | E>Q | A:1531 | (17.90, -19.13, 49.73) |