Incidental Mutation 'R5719:Dnmt1'
ID 451354
Institutional Source Beutler Lab
Gene Symbol Dnmt1
Ensembl Gene ENSMUSG00000004099
Gene Name DNA methyltransferase 1
Synonyms MTase, Dnmt1o, Cxxc9, MommeD2
MMRRC Submission 043339-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5719 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 20818501-20871084 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 20823891 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 993 (N993S)
Ref Sequence ENSEMBL: ENSMUSP00000150433 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004202] [ENSMUST00000177754] [ENSMUST00000178110] [ENSMUST00000216540]
AlphaFold P13864
Predicted Effect possibly damaging
Transcript: ENSMUST00000004202
AA Change: N1111S

PolyPhen 2 Score 0.863 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000004202
Gene: ENSMUSG00000004099
AA Change: N1111S

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
AA Change: N992S

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000136982
Gene: ENSMUSG00000004099
AA Change: N992S

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
AA Change: N992S

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000136669
Gene: ENSMUSG00000004099
AA Change: N992S

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 noncoding transcript
Transcript: ENSMUST00000214964
Predicted Effect possibly damaging
Transcript: ENSMUST00000216540
AA Change: N993S

PolyPhen 2 Score 0.863 (Sensitivity: 0.83; Specificity: 0.93)
Meta Mutation Damage Score 0.0686 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency 98% (79/81)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A130051J06Rik C T 15: 95,688,641 (GRCm39) probably benign Het
A630001G21Rik T A 1: 85,651,106 (GRCm39) R110W probably benign Het
Abca4 T C 3: 121,928,915 (GRCm39) probably null Het
Abcc3 T C 11: 94,241,894 (GRCm39) N1379S probably damaging Het
Actrt3 A C 3: 30,652,276 (GRCm39) F273V probably benign Het
Adam22 T C 5: 8,417,217 (GRCm39) D75G probably benign Het
Ash1l C A 3: 88,961,805 (GRCm39) D2392E possibly damaging Het
Ash1l T C 3: 88,965,933 (GRCm39) I2445T probably damaging Het
Bltp2 T A 11: 78,164,071 (GRCm39) H1137Q probably damaging Het
Cacna2d2 A G 9: 107,401,851 (GRCm39) I762V probably benign Het
Ccdc127 T A 13: 74,505,187 (GRCm39) probably benign Het
Ccdc91 C G 6: 147,477,001 (GRCm39) L230V unknown Het
Cdk13 A G 13: 17,894,240 (GRCm39) I1129T probably damaging Het
Cnot1 C T 8: 96,470,924 (GRCm39) R1308H possibly damaging Het
Crhr2 T C 6: 55,080,207 (GRCm39) H144R probably damaging Het
Eif4g1 T A 16: 20,507,761 (GRCm39) V1182D probably damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Fam234a T A 17: 26,433,627 (GRCm39) Q399L possibly damaging Het
Fyb1 A T 15: 6,610,350 (GRCm39) K308* probably null Het
Gfral C T 9: 76,104,328 (GRCm39) R228Q probably benign Het
Gm10309 A T 17: 86,806,421 (GRCm39) probably benign Het
Gm11595 G A 11: 99,663,381 (GRCm39) R100C unknown Het
Gm5501 G A 18: 9,917,417 (GRCm39) noncoding transcript Het
Gm6309 A T 5: 146,104,992 (GRCm39) V307D probably benign Het
Gm9871 T A 6: 101,773,148 (GRCm39) noncoding transcript Het
Greb1l G A 18: 10,542,427 (GRCm39) E1341K probably damaging Het
Herc3 T A 6: 58,871,528 (GRCm39) V70E possibly damaging Het
Hes7 A G 11: 69,012,415 (GRCm39) E41G probably damaging Het
Ifi27l2b T C 12: 103,422,046 (GRCm39) D106G unknown Het
Igfbp6 A T 15: 102,056,616 (GRCm39) Y184F probably damaging Het
Isyna1 A G 8: 71,047,352 (GRCm39) Y25C probably damaging Het
Kcng3 G T 17: 83,938,563 (GRCm39) T162K possibly damaging Het
Krt36 T C 11: 99,994,987 (GRCm39) D195G possibly damaging Het
Lrwd1 A T 5: 136,161,093 (GRCm39) probably null Het
Lsg1 C T 16: 30,380,593 (GRCm39) A615T probably benign Het
Myo5a A T 9: 75,059,213 (GRCm39) E480D probably damaging Het
Myrf T A 19: 10,194,087 (GRCm39) D690V probably damaging Het
N4bp1 T C 8: 87,578,312 (GRCm39) I684M probably damaging Het
Nlrc3 C T 16: 3,781,589 (GRCm39) A607T probably damaging Het
Nuak1 A T 10: 84,245,584 (GRCm39) I87N probably damaging Het
Odad2 G T 18: 7,211,496 (GRCm39) Q793K probably benign Het
Or5p66 T G 7: 107,885,599 (GRCm39) T245P probably damaging Het
Or5w11 T C 2: 87,459,475 (GRCm39) probably null Het
Or8b4 A T 9: 37,830,647 (GRCm39) E236D probably damaging Het
Osbpl9 T A 4: 108,919,763 (GRCm39) R689* probably null Het
Ppargc1b T A 18: 61,440,639 (GRCm39) M744L probably benign Het
Prss40 A T 1: 34,591,598 (GRCm39) probably benign Het
Ptprd T A 4: 75,972,839 (GRCm39) probably null Het
Rft1 T C 14: 30,385,183 (GRCm39) probably benign Het
Rftn2 C T 1: 55,253,445 (GRCm39) V53I probably damaging Het
Rnaset2a T C 17: 8,350,879 (GRCm39) Y167C probably damaging Het
Schip1 T C 3: 68,315,560 (GRCm39) probably benign Het
Scn5a A C 9: 119,359,118 (GRCm39) L643R possibly damaging Het
Shroom3 T A 5: 93,090,877 (GRCm39) M1128K probably benign Het
Skint8 C A 4: 111,807,390 (GRCm39) L359M probably damaging Het
Slc14a2 A G 18: 78,252,257 (GRCm39) L18P probably benign Het
Slc22a3 C T 17: 12,642,691 (GRCm39) V509M probably damaging Het
Slc7a5 A C 8: 122,610,381 (GRCm39) F478V probably benign Het
Smc1b T A 15: 84,980,859 (GRCm39) N803I probably benign Het
Snf8 T A 11: 95,932,551 (GRCm39) N115K probably damaging Het
Stox2 T A 8: 47,866,172 (GRCm39) K57* probably null Het
Tmem248 T A 5: 130,258,429 (GRCm39) F41I probably damaging Het
Tmprss7 T C 16: 45,506,793 (GRCm39) S90G probably damaging Het
Top3b T C 16: 16,703,700 (GRCm39) V285A probably damaging Het
Tsen15 T C 1: 152,247,534 (GRCm39) T153A probably damaging Het
Usp34 T G 11: 23,304,846 (GRCm39) S360A probably benign Het
Wdr24 T C 17: 26,047,314 (GRCm39) probably null Het
Zbtb2 G A 10: 4,319,456 (GRCm39) T190I probably benign Het
Zranb3 T C 1: 127,891,613 (GRCm39) S788G 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
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'- TCTCTGCCATGCTATGTGAC -3'
(R):5'- ATTCCATTGGTGGCTAATTGGC -3'

Sequencing Primer
(F):5'- CTGCCATGCTATGTGACCTAGAG -3'
(R):5'- CTGTGGCTGAACTCCGATTAAGAG -3'
Posted On 2017-01-03