Incidental Mutation 'R0843:Dnmt3a'
ID 77260
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 039022-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.404) question?
Stock # R0843 (G1)
Quality Score 210
Status Validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to C at 3922886 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000134009 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000172509] [ENSMUST00000172719] [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 benign
Transcript: ENSMUST00000172719
SMART Domains Protein: ENSMUSP00000133501
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 15 37 N/A INTRINSIC
low complexity region 109 124 N/A INTRINSIC
low complexity region 160 177 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000173197
SMART Domains Protein: ENSMUSP00000133567
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 36 53 N/A INTRINSIC
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
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.5%
  • 10x: 96.5%
  • 20x: 92.6%
Validation Efficiency 98% (40/41)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adrb2 T C 18: 62,312,142 (GRCm39) R228G probably benign Het
Arrdc3 T C 13: 81,038,922 (GRCm39) probably benign Het
Cacna1d T C 14: 29,846,828 (GRCm39) Y526C probably damaging Het
Cenpn T C 8: 117,660,045 (GRCm39) V125A probably benign Het
Cyfip1 A T 7: 55,572,568 (GRCm39) H963L probably benign Het
Dnah8 T C 17: 31,032,069 (GRCm39) Y4130H probably damaging Het
Dync1h1 C T 12: 110,631,647 (GRCm39) T4448M possibly damaging Het
Efr3a T A 15: 65,709,272 (GRCm39) probably benign Het
Fgf11 T G 11: 69,689,602 (GRCm39) probably benign Het
Gabrr1 T A 4: 33,161,717 (GRCm39) I347N possibly damaging Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Hspa1b T A 17: 35,176,524 (GRCm39) N487I possibly damaging Het
Ifi207 A T 1: 173,555,143 (GRCm39) N853K probably damaging Het
Iqgap3 A G 3: 88,015,738 (GRCm39) D40G possibly damaging Het
Iyd T C 10: 3,495,663 (GRCm39) V107A possibly damaging Het
Kctd3 A T 1: 188,729,170 (GRCm39) L129* probably null Het
Myo7b A G 18: 32,107,137 (GRCm39) F1286S possibly damaging Het
Or4a47 C T 2: 89,665,960 (GRCm39) V110I probably benign Het
Or52s1b T A 7: 102,822,326 (GRCm39) T173S possibly damaging Het
Or8c15 T A 9: 38,120,579 (GRCm39) F77I possibly damaging Het
Pcsk5 T A 19: 17,632,182 (GRCm39) Y328F probably damaging Het
Plxnb1 T C 9: 108,942,769 (GRCm39) L1810P probably benign Het
Polr2h T A 16: 20,537,649 (GRCm39) V50E probably damaging Het
Ppm1g T C 5: 31,364,895 (GRCm39) probably benign Het
Ptpru T A 4: 131,525,259 (GRCm39) R741S probably benign Het
Pyroxd2 T C 19: 42,735,986 (GRCm39) E64G probably damaging Het
Rad54b T C 4: 11,609,471 (GRCm39) probably null Het
Rangap1 A T 15: 81,594,703 (GRCm39) D375E probably benign Het
Rhbdf1 G A 11: 32,165,053 (GRCm39) R107C probably damaging Het
Scaf11 T C 15: 96,329,706 (GRCm39) E140G probably damaging Het
Slitrk6 G T 14: 110,987,530 (GRCm39) H726N probably benign Het
Spry2 A G 14: 106,130,524 (GRCm39) C221R probably damaging Het
Stx2 C T 5: 129,076,612 (GRCm39) V24M probably damaging Het
Tent5b T C 4: 133,213,842 (GRCm39) S238P probably damaging Het
Tll2 T A 19: 41,116,902 (GRCm39) probably null Het
Ttyh3 C A 5: 140,612,201 (GRCm39) probably null Het
Vmn2r116 T C 17: 23,619,934 (GRCm39) V556A probably benign Het
Xpo5 T C 17: 46,533,576 (GRCm39) probably benign Het
Zc3h3 A G 15: 75,709,328 (GRCm39) S514P probably benign Het
Zfp277 A C 12: 40,370,599 (GRCm39) probably null 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
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
R5768:Dnmt3a UTSW 12 3,935,660 (GRCm39) splice site probably null
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'- TGTGGACGGCACATGAACAAGC -3'
(R):5'- TTGGCAGGGACTCATGAACAAGGC -3'

Sequencing Primer
(F):5'- GCAAACACTAGGAGGACCC -3'
(R):5'- TCTGGAGGGGGATGAGC -3'
Posted On 2013-10-16