Incidental Mutation 'R8692:Dnmt1'
ID 668441
Institutional Source Beutler Lab
Gene Symbol Dnmt1
Ensembl Gene ENSMUSG00000004099
Gene Name DNA methyltransferase 1
Synonyms MTase, Dnmt1o, Cxxc9, MommeD2
MMRRC Submission 068546-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8692 (G1)
Quality Score 225.009
Status Not validated
Chromosome 9
Chromosomal Location 20818501-20871084 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 20853077 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Serine at position 48 (L48S)
Ref Sequence ENSEMBL: ENSMUSP00000004202 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004202] [ENSMUST00000177754] [ENSMUST00000178110] [ENSMUST00000216540]
AlphaFold P13864
PDB Structure Crystal structure of mouse DNA methyltransferase 1 [X-RAY DIFFRACTION]
Crystal structure of mouse DNA methyltransferase 1 with AdoHcy [X-RAY DIFFRACTION]
Crystal structure of mouse DNA methyltransferase 1 with AdoMet [X-RAY DIFFRACTION]
Crystal structure of mouse DNMT1(650-1602) in complex with DNA [X-RAY DIFFRACTION]
Crystal structure of mouse DNMT1(731-1602) in the free state [X-RAY DIFFRACTION]
Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000004202
AA Change: L48S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000004202
Gene: ENSMUSG00000004099
AA Change: L48S

DomainStartEndE-ValueType
DMAP_binding 16 106 1.7e-13 SMART
low complexity region 121 143 N/A INTRINSIC
low complexity region 156 166 N/A INTRINSIC
low complexity region 180 194 N/A INTRINSIC
low complexity region 273 290 N/A INTRINSIC
low complexity region 306 328 N/A INTRINSIC
Pfam:DNMT1-RFD 405 540 4.8e-46 PFAM
low complexity region 610 625 N/A INTRINSIC
Pfam:zf-CXXC 648 694 2.7e-17 PFAM
low complexity region 701 711 N/A INTRINSIC
low complexity region 719 731 N/A INTRINSIC
BAH 758 884 4.62e-31 SMART
BAH 935 1103 1.79e-37 SMART
low complexity region 1110 1124 N/A INTRINSIC
Pfam:DNA_methylase 1142 1596 1.3e-49 PFAM
low complexity region 1600 1619 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000177754
SMART Domains Protein: ENSMUSP00000136982
Gene: ENSMUSG00000004099

DomainStartEndE-ValueType
low complexity region 3 25 N/A INTRINSIC
low complexity region 37 47 N/A INTRINSIC
low complexity region 61 75 N/A INTRINSIC
low complexity region 154 171 N/A INTRINSIC
low complexity region 187 209 N/A INTRINSIC
Pfam:DNMT1-RFD 286 421 3.4e-40 PFAM
low complexity region 491 506 N/A INTRINSIC
Pfam:zf-CXXC 529 575 2.3e-17 PFAM
low complexity region 582 592 N/A INTRINSIC
low complexity region 600 612 N/A INTRINSIC
BAH 639 765 4.62e-31 SMART
BAH 816 984 1.79e-37 SMART
low complexity region 991 1005 N/A INTRINSIC
Pfam:DNA_methylase 1023 1477 1.3e-49 PFAM
low complexity region 1481 1500 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000178110
SMART Domains Protein: ENSMUSP00000136669
Gene: ENSMUSG00000004099

DomainStartEndE-ValueType
low complexity region 3 25 N/A INTRINSIC
low complexity region 38 48 N/A INTRINSIC
low complexity region 62 76 N/A INTRINSIC
low complexity region 155 172 N/A INTRINSIC
low complexity region 188 210 N/A INTRINSIC
Pfam:DNMT1-RFD 287 422 2.6e-40 PFAM
low complexity region 492 507 N/A INTRINSIC
Pfam:zf-CXXC 530 576 4.7e-17 PFAM
low complexity region 583 593 N/A INTRINSIC
low complexity region 601 613 N/A INTRINSIC
BAH 640 766 4.62e-31 SMART
BAH 817 985 1.79e-37 SMART
low complexity region 992 1006 N/A INTRINSIC
Pfam:DNA_methylase 1024 1478 8e-50 PFAM
low complexity region 1482 1501 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000216540
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.1%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a methyltransferase that preferentially methylates cytosines of CpG residues in hemimethylated DNA to generate fully methylated CpG base pairs during DNA replication. This enzyme plays roles in diverse cellular processes including cell cycle regulation, DNA repair, and telomere maintenance. The encoded protein is composed of an N-terminal domain with a nuclear localization sequence and replication fork-targeting domain, a DNA-binding CXXC domain, two bromo-adjacent homology domains, and a C-terminal catalytic domain. Mouse embryonic stem cells mutant for this gene are viable, but when introduced into the germ line, cause a recessive lethal phenotype with mutant embryos displaying stunted growth and developmental defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mutations causing partial or severe loss of function were homozygous lethal by embryonic day 9.5, with lack of appropriate genomic imprinting observed at several loci. [provided by MGI curators]
Allele List at MGI

All alleles(109) : Targeted, knock-out(5) Targeted, other(11) Gene trapped(92) Chemically induced(1)

Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 A C 1: 71,327,874 (GRCm39) I1402S probably damaging Het
Abca9 T C 11: 110,032,409 (GRCm39) D736G probably benign Het
Acy1 T C 9: 106,310,377 (GRCm39) E377G probably damaging Het
Apob G A 12: 8,058,270 (GRCm39) V2251M probably damaging Het
Arhgap23 C A 11: 97,345,322 (GRCm39) T657K probably damaging Het
Cabin1 T C 10: 75,587,410 (GRCm39) K129R probably benign Het
Cdh24 A T 14: 54,875,793 (GRCm39) F259I probably benign Het
Cops6 A G 5: 138,162,083 (GRCm39) N307S probably benign Het
Cyp4a31 G A 4: 115,423,769 (GRCm39) V143M probably damaging Het
Deaf1 A T 7: 140,877,444 (GRCm39) I561K probably benign Het
Dnah7a A C 1: 53,472,175 (GRCm39) S3531A probably benign Het
Dnajc14 T A 10: 128,642,900 (GRCm39) I274N probably damaging Het
Efna4 A T 3: 89,242,549 (GRCm39) I115N probably damaging Het
Ermp1 T A 19: 29,594,093 (GRCm39) L692F probably benign Het
Fcho2 GT G 13: 98,882,382 (GRCm39) probably null Het
Fcsk A T 8: 111,615,722 (GRCm39) C536S probably benign Het
Fermt2 A T 14: 45,742,099 (GRCm39) C82* probably null Het
Gabra6 G T 11: 42,210,537 (GRCm39) D61E probably damaging Het
Gdpd4 T A 7: 97,690,140 (GRCm39) S611T probably benign Het
Gm10800 AAGAAAACTGAAAATCAT A 2: 98,497,379 (GRCm39) probably benign Het
Gm17430 G A 18: 9,726,336 (GRCm39) A112V probably benign Het
Gm2381 A T 7: 42,472,071 (GRCm39) L2Q probably damaging Het
Hif3a A T 7: 16,788,701 (GRCm39) L90Q probably benign Het
Irf3 C T 7: 44,649,889 (GRCm39) Q168* probably null Het
Krt82 T G 15: 101,456,828 (GRCm39) D184A possibly damaging Het
Lgals4 C T 7: 28,540,921 (GRCm39) R282C probably damaging Het
Lrrc49 A G 9: 60,594,445 (GRCm39) S28P probably damaging Het
Mfsd11 T A 11: 116,752,443 (GRCm39) N197K probably benign Het
Mindy1 A G 3: 95,199,587 (GRCm39) D243G probably damaging Het
Mphosph9 A T 5: 124,450,875 (GRCm39) W299R probably damaging Het
Mst1r G T 9: 107,792,050 (GRCm39) R862L possibly damaging Het
Nasp T A 4: 116,469,280 (GRCm39) probably null Het
Ncapg2 T C 12: 116,414,049 (GRCm39) I1073T probably damaging Het
Nek2 A T 1: 191,554,745 (GRCm39) K152N probably benign Het
Neurod2 T C 11: 98,218,960 (GRCm39) E68G probably benign Het
Or1j4 A T 2: 36,740,096 (GRCm39) I13F probably benign Het
Or2w3b T C 11: 58,623,595 (GRCm39) Y132C probably damaging Het
P4ha3 T A 7: 99,955,228 (GRCm39) I361N probably damaging Het
Pcdh15 T A 10: 74,289,805 (GRCm39) S875T possibly damaging Het
Pde7b G T 10: 20,423,639 (GRCm39) P79Q probably benign Het
Phb2 G A 6: 124,692,097 (GRCm39) A228T probably damaging Het
Piezo2 A T 18: 63,225,971 (GRCm39) C888* probably null Het
Pkhd1 A T 1: 20,462,374 (GRCm39) L2060Q probably damaging Het
Pms1 T C 1: 53,246,052 (GRCm39) M496V probably benign Het
Ppfibp1 C T 6: 146,892,013 (GRCm39) T91I probably benign Het
Ppp1r9b T C 11: 94,891,077 (GRCm39) L557P probably damaging Het
Ppp2r5c G T 12: 110,489,032 (GRCm39) V68L probably benign Het
Qrfp T A 2: 31,698,797 (GRCm39) H45L probably benign Het
Rasgrp1 G A 2: 117,115,353 (GRCm39) T745I probably damaging Het
Rnf144a G A 12: 26,370,972 (GRCm39) T163I probably benign Het
Sbsn A T 7: 30,451,522 (GRCm39) H179L unknown Het
Simc1 G A 13: 54,673,193 (GRCm39) V514I probably benign Het
Slc35d1 A G 4: 103,047,051 (GRCm39) M249T Het
Slfn4 T A 11: 83,079,709 (GRCm39) H466Q possibly damaging Het
Stab2 A T 10: 86,808,794 (GRCm39) C172S probably damaging Het
Tanc1 T C 2: 59,673,989 (GRCm39) I1698T probably benign Het
Tenm4 C T 7: 96,555,148 (GRCm39) P2618S probably benign Het
Tiam2 A C 17: 3,479,082 (GRCm39) D605A probably damaging Het
Tmed4 A T 11: 6,223,822 (GRCm39) D151E probably benign Het
Trim62 A T 4: 128,794,465 (GRCm39) I211F possibly damaging Het
Ttpa A G 4: 20,008,585 (GRCm39) D49G probably benign Het
Usf3 T C 16: 44,040,103 (GRCm39) S1528P probably benign Het
Usp34 C T 11: 23,379,325 (GRCm39) T1991I Het
Vash1 G A 12: 86,735,863 (GRCm39) V250M possibly damaging Het
Vmn1r199 T C 13: 22,567,809 (GRCm39) *368Q probably null Het
Vmn1r74 A G 7: 11,580,972 (GRCm39) T91A probably benign Het
Vmn1r8 T C 6: 57,013,557 (GRCm39) F203L probably benign Het
Vmn2r13 G T 5: 109,319,514 (GRCm39) Q489K probably benign Het
Vmn2r-ps158 G T 7: 42,697,108 (GRCm39) A722S probably benign Het
Zfp385b A T 2: 77,549,971 (GRCm39) V38E probably damaging Het
Zfp820 A G 17: 22,037,876 (GRCm39) I484T probably benign Het
Other mutations in Dnmt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00334:Dnmt1 APN 9 20,821,566 (GRCm39) missense possibly damaging 0.94
IGL01093:Dnmt1 APN 9 20,821,081 (GRCm39) missense possibly damaging 0.88
IGL01160:Dnmt1 APN 9 20,828,615 (GRCm39) missense possibly damaging 0.90
IGL01704:Dnmt1 APN 9 20,821,476 (GRCm39) missense probably damaging 1.00
IGL02105:Dnmt1 APN 9 20,819,178 (GRCm39) missense unknown
IGL02124:Dnmt1 APN 9 20,819,845 (GRCm39) missense probably damaging 1.00
IGL02188:Dnmt1 APN 9 20,853,034 (GRCm39) nonsense probably null
IGL02409:Dnmt1 APN 9 20,837,793 (GRCm39) missense probably benign 0.00
IGL02579:Dnmt1 APN 9 20,829,416 (GRCm39) missense possibly damaging 0.79
IGL02625:Dnmt1 APN 9 20,838,442 (GRCm39) missense probably benign 0.01
IGL02794:Dnmt1 APN 9 20,847,847 (GRCm39) missense probably benign
IGL02795:Dnmt1 APN 9 20,838,407 (GRCm39) missense probably benign 0.12
IGL02938:Dnmt1 APN 9 20,852,669 (GRCm39) missense probably benign 0.23
IGL03245:Dnmt1 APN 9 20,827,056 (GRCm39) missense probably damaging 0.99
IGL03303:Dnmt1 APN 9 20,838,006 (GRCm39) missense probably benign
Blankslate UTSW 9 20,823,521 (GRCm39) missense possibly damaging 0.86
Midrash UTSW 9 20,821,089 (GRCm39) nonsense probably null
Rashi UTSW 9 20,833,408 (GRCm39) missense possibly damaging 0.94
B5639:Dnmt1 UTSW 9 20,819,264 (GRCm39) splice site probably benign
BB003:Dnmt1 UTSW 9 20,818,855 (GRCm39) missense unknown
BB013:Dnmt1 UTSW 9 20,818,855 (GRCm39) missense unknown
PIT4576001:Dnmt1 UTSW 9 20,823,071 (GRCm39) missense probably benign 0.28
R0071:Dnmt1 UTSW 9 20,819,916 (GRCm39) missense probably damaging 0.99
R0180:Dnmt1 UTSW 9 20,819,916 (GRCm39) missense probably damaging 0.99
R0368:Dnmt1 UTSW 9 20,853,053 (GRCm39) missense probably damaging 0.99
R0387:Dnmt1 UTSW 9 20,829,509 (GRCm39) missense probably damaging 1.00
R0529:Dnmt1 UTSW 9 20,822,846 (GRCm39) missense probably damaging 1.00
R0532:Dnmt1 UTSW 9 20,829,852 (GRCm39) splice site probably benign
R0612:Dnmt1 UTSW 9 20,829,489 (GRCm39) missense probably damaging 0.98
R1109:Dnmt1 UTSW 9 20,833,684 (GRCm39) missense probably damaging 1.00
R1298:Dnmt1 UTSW 9 20,852,752 (GRCm39) missense probably benign
R1345:Dnmt1 UTSW 9 20,819,814 (GRCm39) missense probably damaging 1.00
R1472:Dnmt1 UTSW 9 20,843,472 (GRCm39) missense probably benign 0.28
R1654:Dnmt1 UTSW 9 20,847,870 (GRCm39) missense possibly damaging 0.75
R1817:Dnmt1 UTSW 9 20,838,422 (GRCm39) missense probably benign
R1836:Dnmt1 UTSW 9 20,829,542 (GRCm39) missense probably damaging 1.00
R1957:Dnmt1 UTSW 9 20,838,442 (GRCm39) missense probably benign 0.01
R1958:Dnmt1 UTSW 9 20,838,442 (GRCm39) missense probably benign 0.01
R2097:Dnmt1 UTSW 9 20,821,084 (GRCm39) missense probably benign 0.00
R2145:Dnmt1 UTSW 9 20,848,451 (GRCm39) splice site probably benign
R2326:Dnmt1 UTSW 9 20,835,442 (GRCm39) splice site probably benign
R4199:Dnmt1 UTSW 9 20,849,414 (GRCm39) missense probably benign 0.00
R4456:Dnmt1 UTSW 9 20,821,138 (GRCm39) missense probably damaging 1.00
R4518:Dnmt1 UTSW 9 20,823,274 (GRCm39) missense probably benign 0.00
R4586:Dnmt1 UTSW 9 20,837,989 (GRCm39) missense probably benign 0.05
R4836:Dnmt1 UTSW 9 20,819,854 (GRCm39) missense probably damaging 1.00
R5014:Dnmt1 UTSW 9 20,823,550 (GRCm39) missense probably benign 0.07
R5338:Dnmt1 UTSW 9 20,864,015 (GRCm39) missense probably benign 0.44
R5385:Dnmt1 UTSW 9 20,829,776 (GRCm39) missense probably damaging 1.00
R5579:Dnmt1 UTSW 9 20,831,501 (GRCm39) missense probably damaging 1.00
R5645:Dnmt1 UTSW 9 20,833,443 (GRCm39) missense probably damaging 1.00
R5719:Dnmt1 UTSW 9 20,823,891 (GRCm39) missense possibly damaging 0.86
R5881:Dnmt1 UTSW 9 20,864,013 (GRCm39) missense probably damaging 0.97
R6039:Dnmt1 UTSW 9 20,837,716 (GRCm39) intron probably benign
R6039:Dnmt1 UTSW 9 20,837,716 (GRCm39) intron probably benign
R6143:Dnmt1 UTSW 9 20,838,430 (GRCm39) missense probably benign 0.30
R6342:Dnmt1 UTSW 9 20,821,089 (GRCm39) nonsense probably null
R6374:Dnmt1 UTSW 9 20,835,341 (GRCm39) missense possibly damaging 0.73
R6953:Dnmt1 UTSW 9 20,829,822 (GRCm39) missense probably benign
R6990:Dnmt1 UTSW 9 20,827,110 (GRCm39) nonsense probably null
R7089:Dnmt1 UTSW 9 20,819,785 (GRCm39) missense probably damaging 0.99
R7463:Dnmt1 UTSW 9 20,823,521 (GRCm39) missense possibly damaging 0.86
R7522:Dnmt1 UTSW 9 20,831,498 (GRCm39) missense probably damaging 0.99
R7695:Dnmt1 UTSW 9 20,825,281 (GRCm39) missense probably null 1.00
R7785:Dnmt1 UTSW 9 20,833,345 (GRCm39) missense probably damaging 0.98
R7926:Dnmt1 UTSW 9 20,818,855 (GRCm39) missense unknown
R8037:Dnmt1 UTSW 9 20,852,860 (GRCm39) missense probably damaging 0.99
R8038:Dnmt1 UTSW 9 20,852,860 (GRCm39) missense probably damaging 0.99
R8424:Dnmt1 UTSW 9 20,829,836 (GRCm39) missense probably benign 0.07
R9016:Dnmt1 UTSW 9 20,847,855 (GRCm39) missense possibly damaging 0.67
R9101:Dnmt1 UTSW 9 20,852,839 (GRCm39) missense probably damaging 1.00
R9200:Dnmt1 UTSW 9 20,819,896 (GRCm39) missense probably benign 0.00
R9248:Dnmt1 UTSW 9 20,833,408 (GRCm39) missense possibly damaging 0.94
R9317:Dnmt1 UTSW 9 20,829,575 (GRCm39) missense probably damaging 0.99
R9352:Dnmt1 UTSW 9 20,840,384 (GRCm39) missense probably benign 0.00
R9438:Dnmt1 UTSW 9 20,827,190 (GRCm39) missense probably benign
RF003:Dnmt1 UTSW 9 20,821,427 (GRCm39) nonsense probably null
RF004:Dnmt1 UTSW 9 20,821,423 (GRCm39) nonsense probably null
RF011:Dnmt1 UTSW 9 20,821,440 (GRCm39) nonsense probably null
RF011:Dnmt1 UTSW 9 20,821,424 (GRCm39) nonsense probably null
RF015:Dnmt1 UTSW 9 20,821,425 (GRCm39) nonsense probably null
RF015:Dnmt1 UTSW 9 20,821,420 (GRCm39) nonsense probably null
RF017:Dnmt1 UTSW 9 20,821,422 (GRCm39) nonsense probably null
RF023:Dnmt1 UTSW 9 20,821,427 (GRCm39) nonsense probably null
RF024:Dnmt1 UTSW 9 20,821,434 (GRCm39) small insertion probably benign
RF024:Dnmt1 UTSW 9 20,821,426 (GRCm39) nonsense probably null
RF025:Dnmt1 UTSW 9 20,821,431 (GRCm39) nonsense probably null
RF025:Dnmt1 UTSW 9 20,821,416 (GRCm39) nonsense probably null
RF029:Dnmt1 UTSW 9 20,821,419 (GRCm39) nonsense probably null
RF034:Dnmt1 UTSW 9 20,821,416 (GRCm39) nonsense probably null
RF037:Dnmt1 UTSW 9 20,821,437 (GRCm39) nonsense probably null
RF037:Dnmt1 UTSW 9 20,821,429 (GRCm39) nonsense probably null
RF037:Dnmt1 UTSW 9 20,821,415 (GRCm39) critical splice donor site probably benign
RF042:Dnmt1 UTSW 9 20,821,415 (GRCm39) nonsense probably null
RF045:Dnmt1 UTSW 9 20,821,433 (GRCm39) small insertion probably benign
RF045:Dnmt1 UTSW 9 20,821,425 (GRCm39) nonsense probably null
RF047:Dnmt1 UTSW 9 20,821,421 (GRCm39) nonsense probably null
RF048:Dnmt1 UTSW 9 20,821,422 (GRCm39) nonsense probably null
RF054:Dnmt1 UTSW 9 20,821,435 (GRCm39) nonsense probably null
RF055:Dnmt1 UTSW 9 20,821,432 (GRCm39) small insertion probably benign
RF055:Dnmt1 UTSW 9 20,821,431 (GRCm39) nonsense probably null
RF055:Dnmt1 UTSW 9 20,821,424 (GRCm39) nonsense probably null
RF059:Dnmt1 UTSW 9 20,821,434 (GRCm39) small insertion probably benign
RF059:Dnmt1 UTSW 9 20,821,435 (GRCm39) nonsense probably null
RF060:Dnmt1 UTSW 9 20,821,438 (GRCm39) nonsense probably null
RF061:Dnmt1 UTSW 9 20,821,426 (GRCm39) nonsense probably null
X0026:Dnmt1 UTSW 9 20,825,210 (GRCm39) missense probably damaging 1.00
Z1176:Dnmt1 UTSW 9 20,837,850 (GRCm39) missense probably benign 0.00
Z1176:Dnmt1 UTSW 9 20,827,159 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- AGGTAGCCTTCCTACAACAGG -3'
(R):5'- ACAGCACGTGTCTGAGTGTC -3'

Sequencing Primer
(F):5'- ACAACAGGAAAGGATATCTTAGTAGG -3'
(R):5'- GAGATCTCGGGCATCCTACACTATG -3'
Posted On 2021-04-30