Incidental Mutation 'R5768:Dnmt3a'
ID 462737
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 043368-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.404) question?
Stock # R5768 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation splice site (5 bp from exon)
DNA Base Change (assembly) G to A at 3935660 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000134480 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000172509] [ENSMUST00000174102] [ENSMUST00000174483] [ENSMUST00000174817]
AlphaFold O88508
Predicted Effect probably benign
Transcript: ENSMUST00000020991
SMART Domains Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 15 37 N/A INTRINSIC
internal_repeat_1 55 101 6.44e-5 PROSPERO
low complexity region 109 124 N/A INTRINSIC
low complexity region 160 177 N/A INTRINSIC
low complexity region 204 215 N/A INTRINSIC
internal_repeat_1 241 283 6.44e-5 PROSPERO
PWWP 286 344 1.36e-24 SMART
low complexity region 412 430 N/A INTRINSIC
low complexity region 438 453 N/A INTRINSIC
PDB:3A1B|A 454 610 2e-99 PDB
Blast:RING 533 582 1e-17 BLAST
Pfam:DNA_methylase 630 772 2.1e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000172509
SMART Domains Protein: ENSMUSP00000133869
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 35 50 N/A INTRINSIC
low complexity region 86 103 N/A INTRINSIC
low complexity region 130 141 N/A INTRINSIC
PWWP 212 270 1.36e-24 SMART
Predicted Effect probably null
Transcript: ENSMUST00000174102
SMART Domains Protein: ENSMUSP00000134480
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
Pfam:PWWP 101 140 2e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174483
SMART Domains Protein: ENSMUSP00000133938
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 35 50 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000174817
SMART Domains Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 15 37 N/A INTRINSIC
internal_repeat_1 55 101 6.44e-5 PROSPERO
low complexity region 109 124 N/A INTRINSIC
low complexity region 160 177 N/A INTRINSIC
low complexity region 204 215 N/A INTRINSIC
internal_repeat_1 241 283 6.44e-5 PROSPERO
PWWP 286 344 1.36e-24 SMART
low complexity region 412 430 N/A INTRINSIC
low complexity region 438 453 N/A INTRINSIC
PDB:3A1B|A 454 610 2e-99 PDB
Blast:RING 533 582 1e-17 BLAST
Pfam:DNA_methylase 630 772 2.1e-14 PFAM
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.5%
Validation Efficiency 98% (59/60)
MGI Phenotype FUNCTION: This is one of two related genes encoding de novo DNA methyltransferases, which are responsible for the establishment of DNA methylation patterns in embryos. Loss of function of this gene causes developmental defects in multiple different organ systems. There is a pseudogene for this gene located on chromosome 3. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Nov 2012]
PHENOTYPE: Homozygotes for a targeted null mutation become runted and die around four weeks of age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam22 G A 5: 8,177,426 (GRCm39) T561I probably benign Het
Akp3 T C 1: 87,054,844 (GRCm39) I393T probably damaging Het
Atxn10 A T 15: 85,277,621 (GRCm39) I363F probably benign Het
BC004004 A T 17: 29,501,709 (GRCm39) S83C probably damaging Het
Bin1 T A 18: 32,559,264 (GRCm39) probably null Het
Cacna1c A G 6: 118,674,641 (GRCm39) I541T probably damaging Het
Cand1 A G 10: 119,046,910 (GRCm39) V860A probably benign Het
Ccdc69 T C 11: 54,945,856 (GRCm39) N50S possibly damaging Het
Cd209d T A 8: 3,921,968 (GRCm39) T235S probably benign Het
Cdhr3 G T 12: 33,096,685 (GRCm39) T591K possibly damaging Het
Cherp C T 8: 73,216,957 (GRCm39) D658N probably damaging Het
Clip4 T A 17: 72,113,494 (GRCm39) probably null Het
Cryzl1 C T 16: 91,492,242 (GRCm39) V195M probably damaging Het
Cst11 A T 2: 148,612,387 (GRCm39) Y83* probably null Het
Ddb2 T C 2: 91,042,337 (GRCm39) S419G possibly damaging Het
Ddi2 A T 4: 141,412,901 (GRCm39) L4M probably damaging Het
Dip2b C A 15: 100,055,826 (GRCm39) P393T probably benign Het
Elf5 C T 2: 103,279,367 (GRCm39) S196L probably damaging Het
Eps15 C G 4: 109,220,373 (GRCm39) probably null Het
Fra10ac1 T C 19: 38,195,734 (GRCm39) E163G probably benign Het
Gc T C 5: 89,589,125 (GRCm39) T213A probably damaging Het
Grpel1 A T 5: 36,622,503 (GRCm39) probably benign Het
Gsdme G A 6: 50,196,280 (GRCm39) Q377* probably null Het
Hira T C 16: 18,753,768 (GRCm39) probably benign Het
Hsd11b1 T A 1: 192,922,554 (GRCm39) I168F probably damaging Het
Htr6 G A 4: 138,789,015 (GRCm39) R347W probably damaging Het
Ipp A C 4: 116,367,967 (GRCm39) T67P probably damaging Het
Lrfn5 G A 12: 61,886,509 (GRCm39) R99Q probably benign Het
Madd T A 2: 90,998,174 (GRCm39) I649F probably damaging Het
Map2k7 T A 8: 4,295,757 (GRCm39) D368E probably benign Het
Mppe1 T G 18: 67,358,889 (GRCm39) T360P possibly damaging Het
Msi2 A G 11: 88,608,564 (GRCm39) F2L probably damaging Het
Nectin3 T C 16: 46,279,180 (GRCm39) Q266R probably damaging Het
Nfasc T C 1: 132,532,883 (GRCm39) H691R probably benign Het
Oprm1 G A 10: 6,739,026 (GRCm39) G51D probably damaging Het
Or4c117 T C 2: 88,955,793 (GRCm39) E94G probably benign Het
Or5ac15 TGAAGAAGAA TGAAGAA 16: 58,940,335 (GRCm39) probably benign Het
Papss2 G A 19: 32,638,119 (GRCm39) probably null Het
Pi4ka T C 16: 17,172,736 (GRCm39) K549E probably benign Het
Plekha6 A G 1: 133,208,116 (GRCm39) T596A probably benign Het
Polr2f A G 15: 79,035,845 (GRCm39) D117G probably damaging Het
Psd T C 19: 46,301,178 (GRCm39) E381G possibly damaging Het
Rfx6 G A 10: 51,602,976 (GRCm39) R831H probably damaging Het
Rpp25l A T 4: 41,712,649 (GRCm39) L42Q probably damaging Het
Ryr3 T C 2: 112,583,442 (GRCm39) M2810V probably benign Het
Sdk1 C A 5: 142,129,626 (GRCm39) L1616I probably benign Het
Spock2 T A 10: 59,962,029 (GRCm39) F215I probably damaging Het
Susd2 C T 10: 75,473,853 (GRCm39) A581T probably damaging Het
Tchh A T 3: 93,353,488 (GRCm39) E976V unknown Het
Tgfbr3 T C 5: 107,297,761 (GRCm39) E213G probably benign Het
Tmed1 T C 9: 21,420,619 (GRCm39) D71G probably benign Het
Tmtc4 T A 14: 123,170,565 (GRCm39) K527N possibly damaging Het
Zfhx2 T C 14: 55,311,822 (GRCm39) T291A probably benign Het
Other mutations in Dnmt3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00844:Dnmt3a APN 12 3,955,622 (GRCm39) missense probably damaging 1.00
IGL02255:Dnmt3a APN 12 3,922,886 (GRCm39) splice site probably benign
IGL02815:Dnmt3a APN 12 3,954,226 (GRCm39) critical splice donor site probably null
IGL03372:Dnmt3a APN 12 3,952,666 (GRCm39) missense probably damaging 1.00
Chromos UTSW 12 3,951,665 (GRCm39) missense probably damaging 1.00
Compaction UTSW 12 3,916,192 (GRCm39) nonsense probably null
R0028:Dnmt3a UTSW 12 3,950,337 (GRCm39) missense probably damaging 0.99
R0306:Dnmt3a UTSW 12 3,916,096 (GRCm39) missense possibly damaging 0.69
R0843:Dnmt3a UTSW 12 3,922,886 (GRCm39) splice site probably benign
R1055:Dnmt3a UTSW 12 3,922,864 (GRCm39) missense probably benign 0.05
R1465:Dnmt3a UTSW 12 3,916,088 (GRCm39) missense probably damaging 1.00
R1465:Dnmt3a UTSW 12 3,916,088 (GRCm39) missense probably damaging 1.00
R1585:Dnmt3a UTSW 12 3,951,660 (GRCm39) missense probably damaging 0.99
R1680:Dnmt3a UTSW 12 3,923,361 (GRCm39) missense probably damaging 0.97
R1753:Dnmt3a UTSW 12 3,923,342 (GRCm39) missense possibly damaging 0.54
R2055:Dnmt3a UTSW 12 3,922,859 (GRCm39) missense probably benign 0.44
R2219:Dnmt3a UTSW 12 3,899,654 (GRCm39) utr 5 prime probably benign
R2267:Dnmt3a UTSW 12 3,947,551 (GRCm39) splice site probably null
R2359:Dnmt3a UTSW 12 3,951,599 (GRCm39) missense probably damaging 1.00
R2384:Dnmt3a UTSW 12 3,951,591 (GRCm39) missense probably damaging 1.00
R2403:Dnmt3a UTSW 12 3,949,883 (GRCm39) missense probably damaging 1.00
R2884:Dnmt3a UTSW 12 3,946,132 (GRCm39) missense probably damaging 1.00
R3027:Dnmt3a UTSW 12 3,899,626 (GRCm39) splice site probably null
R4281:Dnmt3a UTSW 12 3,951,665 (GRCm39) missense probably damaging 1.00
R4282:Dnmt3a UTSW 12 3,951,665 (GRCm39) missense probably damaging 1.00
R4283:Dnmt3a UTSW 12 3,951,665 (GRCm39) missense probably damaging 1.00
R4809:Dnmt3a UTSW 12 3,950,352 (GRCm39) missense probably damaging 1.00
R5154:Dnmt3a UTSW 12 3,946,008 (GRCm39) missense probably damaging 1.00
R5361:Dnmt3a UTSW 12 3,945,643 (GRCm39) missense probably benign 0.13
R5483:Dnmt3a UTSW 12 3,949,615 (GRCm39) missense probably damaging 1.00
R5928:Dnmt3a UTSW 12 3,916,096 (GRCm39) missense possibly damaging 0.69
R6432:Dnmt3a UTSW 12 3,952,399 (GRCm39) missense probably damaging 0.99
R6552:Dnmt3a UTSW 12 3,957,623 (GRCm39) missense probably damaging 1.00
R6783:Dnmt3a UTSW 12 3,947,406 (GRCm39) missense probably damaging 0.99
R6850:Dnmt3a UTSW 12 3,947,600 (GRCm39) missense probably benign 0.40
R7106:Dnmt3a UTSW 12 3,947,591 (GRCm39) missense probably damaging 0.99
R7145:Dnmt3a UTSW 12 3,922,844 (GRCm39) missense probably benign 0.01
R7149:Dnmt3a UTSW 12 3,952,397 (GRCm39) missense probably damaging 1.00
R7239:Dnmt3a UTSW 12 3,922,850 (GRCm39) missense probably benign 0.01
R7490:Dnmt3a UTSW 12 3,954,204 (GRCm39) missense probably damaging 1.00
R7588:Dnmt3a UTSW 12 3,946,080 (GRCm39) missense possibly damaging 0.91
R7684:Dnmt3a UTSW 12 3,947,340 (GRCm39) missense probably benign 0.02
R8058:Dnmt3a UTSW 12 3,952,768 (GRCm39) missense possibly damaging 0.92
R8316:Dnmt3a UTSW 12 3,946,965 (GRCm39) missense probably benign 0.00
R8345:Dnmt3a UTSW 12 3,885,234 (GRCm39) missense unknown
R8464:Dnmt3a UTSW 12 3,949,635 (GRCm39) missense probably benign 0.03
R8914:Dnmt3a UTSW 12 3,916,192 (GRCm39) nonsense probably null
R9131:Dnmt3a UTSW 12 3,916,136 (GRCm39) missense probably benign 0.00
R9246:Dnmt3a UTSW 12 3,949,204 (GRCm39) missense probably damaging 1.00
R9476:Dnmt3a UTSW 12 3,957,707 (GRCm39) missense probably damaging 1.00
R9485:Dnmt3a UTSW 12 3,916,121 (GRCm39) missense probably benign 0.01
R9598:Dnmt3a UTSW 12 3,946,997 (GRCm39) missense probably benign 0.25
R9709:Dnmt3a UTSW 12 3,957,701 (GRCm39) missense probably damaging 1.00
Z1176:Dnmt3a UTSW 12 3,954,201 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCAGACTGAGGTTTCTCCAG -3'
(R):5'- CTGTGGGTTCCTGCTACATC -3'

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