Incidental Mutation 'R0387:Dnmt1'
ID 31354
Institutional Source Beutler Lab
Gene Symbol Dnmt1
Ensembl Gene ENSMUSG00000004099
Gene Name DNA methyltransferase 1
Synonyms MTase, Dnmt1o, Cxxc9, MommeD2
MMRRC Submission 038593-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0387 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 20818501-20871084 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 20829509 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 698 (L698P)
Ref Sequence ENSEMBL: ENSMUSP00000136669 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004202] [ENSMUST00000177754] [ENSMUST00000178110] [ENSMUST00000216540]
AlphaFold P13864
Predicted Effect probably damaging
Transcript: ENSMUST00000004202
AA Change: L817P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000004202
Gene: ENSMUSG00000004099
AA Change: L817P

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 damaging
Transcript: ENSMUST00000177754
AA Change: L698P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000136982
Gene: ENSMUSG00000004099
AA Change: L698P

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 damaging
Transcript: ENSMUST00000178110
AA Change: L698P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000136669
Gene: ENSMUSG00000004099
AA Change: L698P

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 noncoding transcript
Transcript: ENSMUST00000184490
Predicted Effect probably damaging
Transcript: ENSMUST00000216540
AA Change: L699P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Meta Mutation Damage Score 0.9362 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.7%
  • 10x: 94.2%
  • 20x: 85.0%
Validation Efficiency 99% (77/78)
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca15 T G 7: 119,932,075 (GRCm39) probably null Het
Abcc9 T A 6: 142,585,230 (GRCm39) K825* probably null Het
Afp T C 5: 90,645,150 (GRCm39) C189R probably damaging Het
Akap9 T C 5: 4,001,678 (GRCm39) probably benign Het
Alpk3 A T 7: 80,753,975 (GRCm39) T1652S possibly damaging Het
Atg4b C A 1: 93,714,278 (GRCm39) Q354K probably benign Het
Atxn2 T C 5: 121,940,206 (GRCm39) S388P possibly damaging Het
C2cd3 T A 7: 100,071,714 (GRCm39) probably benign Het
Cacna2d2 C A 9: 107,391,080 (GRCm39) T403K probably damaging Het
Cap2 C T 13: 46,713,992 (GRCm39) H79Y probably damaging Het
Car10 G T 11: 93,473,847 (GRCm39) probably null Het
Ccno T C 13: 113,126,401 (GRCm39) L290P probably damaging Het
Cfap69 T C 5: 5,639,303 (GRCm39) K624E probably damaging Het
Ctnna3 A G 10: 64,421,909 (GRCm39) M568V probably benign Het
Cyp1b1 C A 17: 80,021,203 (GRCm39) V180L probably benign Het
Cyp2u1 G T 3: 131,089,201 (GRCm39) probably null Het
Dcp1a T C 14: 30,241,636 (GRCm39) probably null Het
Dnm1 C T 2: 32,210,593 (GRCm39) G1S possibly damaging Het
Dock10 C A 1: 80,517,993 (GRCm39) C1327F probably damaging Het
Dph3b-ps A G 13: 106,683,363 (GRCm39) noncoding transcript Het
Dpyd G A 3: 119,220,875 (GRCm39) D949N probably benign Het
Dync2li1 A G 17: 84,962,768 (GRCm39) K345E possibly damaging Het
Eml2 T A 7: 18,916,184 (GRCm39) probably null Het
Exoc7 A G 11: 116,185,227 (GRCm39) probably benign Het
Faah A T 4: 115,862,889 (GRCm39) C113* probably null Het
Fcf1 T A 12: 85,019,776 (GRCm39) D16E probably benign Het
Fcgbp T C 7: 27,790,879 (GRCm39) probably benign Het
Ghr A G 15: 3,349,373 (GRCm39) S602P probably benign Het
Gm5114 T C 7: 39,058,233 (GRCm39) D462G probably benign Het
Gm8186 T A 17: 26,318,000 (GRCm39) S66C probably damaging Het
Gorab C T 1: 163,224,403 (GRCm39) V133M probably benign Het
Gria1 G A 11: 57,200,710 (GRCm39) probably null Het
Grik1 T A 16: 87,831,238 (GRCm39) probably benign Het
Gtf3c1 A G 7: 125,280,276 (GRCm39) L378P probably damaging Het
Htr5b A T 1: 121,455,275 (GRCm39) V215D probably damaging Het
Htra1 A G 7: 130,581,208 (GRCm39) T319A probably damaging Het
Idh2 C T 7: 79,748,005 (GRCm39) A232T probably damaging Het
Klrb1a A C 6: 128,586,697 (GRCm39) H189Q possibly damaging Het
Lhfpl6 A G 3: 52,950,749 (GRCm39) T8A probably benign Het
Ly75 T A 2: 60,136,748 (GRCm39) Y1493F probably benign Het
Mfsd5 T C 15: 102,189,531 (GRCm39) I301T possibly damaging Het
Mlkl C T 8: 112,059,982 (GRCm39) E135K probably damaging Het
Mrgprx2 A C 7: 48,148,908 (GRCm39) M1R probably null Het
Mroh2a G C 1: 88,173,764 (GRCm39) A871P probably damaging Het
Mtbp A G 15: 55,474,425 (GRCm39) I280V possibly damaging Het
Myo5c A T 9: 75,192,303 (GRCm39) probably benign Het
Nos3 A G 5: 24,572,583 (GRCm39) K174R probably damaging Het
Oas2 A T 5: 120,883,737 (GRCm39) probably benign Het
Or8b40 T A 9: 38,027,066 (GRCm39) probably null Het
Pi4kb G C 3: 94,892,051 (GRCm39) E256Q probably benign Het
Pik3c2a T A 7: 115,972,979 (GRCm39) I739F probably damaging Het
Pla2r1 T A 2: 60,262,945 (GRCm39) K1031N probably benign Het
Plk4 A T 3: 40,767,319 (GRCm39) probably benign Het
Polq T C 16: 36,849,792 (GRCm39) C349R probably damaging Het
Polq G T 16: 36,909,679 (GRCm39) E2354D probably damaging Het
Prss22 A G 17: 24,212,903 (GRCm39) L278P probably damaging Het
Prss3l A G 6: 41,420,303 (GRCm39) I141T possibly damaging Het
Ptprk G A 10: 28,230,625 (GRCm39) V239I possibly damaging Het
Raph1 T G 1: 60,549,655 (GRCm39) probably benign Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Ripor3 C T 2: 167,825,692 (GRCm39) W755* probably null Het
Rnd3 G T 2: 51,038,243 (GRCm39) D77E probably damaging Het
Ryr1 T C 7: 28,782,792 (GRCm39) probably benign Het
Serpinb1a C T 13: 33,032,721 (GRCm39) V63I probably benign Het
Six1 T G 12: 73,092,815 (GRCm39) Y129S probably damaging Het
Spata31d1a G A 13: 59,851,315 (GRCm39) T271I probably damaging Het
Stab1 T C 14: 30,870,058 (GRCm39) D1387G probably benign Het
Stra6 T A 9: 58,060,466 (GRCm39) M625K probably benign Het
Syne1 T C 10: 5,301,029 (GRCm39) S900G probably benign Het
Tdpoz4 A C 3: 93,704,007 (GRCm39) K101N probably benign Het
Tigd2 T C 6: 59,188,143 (GRCm39) Y337H probably benign Het
Tnxb A G 17: 34,902,548 (GRCm39) I1134V probably benign Het
Tspyl5 A G 15: 33,687,081 (GRCm39) I288T probably damaging Het
Ulk1 A G 5: 110,936,663 (GRCm39) V61A possibly damaging Het
Xxylt1 A G 16: 30,776,194 (GRCm39) Y381H probably benign Het
Zcchc9 T A 13: 91,949,066 (GRCm39) M12L probably benign Het
Zfp106 T C 2: 120,358,953 (GRCm39) probably null Het
Zfp74 T A 7: 29,634,179 (GRCm39) T510S probably benign Het
Zfp808 A G 13: 62,317,292 (GRCm39) T14A probably damaging 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
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
R8692:Dnmt1 UTSW 9 20,853,077 (GRCm39) missense probably damaging 1.00
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'- AGTAAGTCTTGCCATCCTCAGCCC -3'
(R):5'- GTCCAACTTTGTCAGAACAGACCCC -3'

Sequencing Primer
(F):5'- AGGGTCTGTGCCTCCCTATG -3'
(R):5'- GAACAGACCCCAGGTTCTGC -3'
Posted On 2013-04-24