Incidental Mutation 'R1585:Dnmt3a'
ID 177462
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 039622-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.460) question?
Stock # R1585 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 3951660 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 679 (Y679F)
Ref Sequence ENSEMBL: ENSMUSP00000134009 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000111186] [ENSMUST00000172509] [ENSMUST00000172689] [ENSMUST00000174483] [ENSMUST00000174817] [ENSMUST00000174774]
AlphaFold O88508
Predicted Effect probably damaging
Transcript: ENSMUST00000020991
AA Change: Y679F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: Y679F

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 damaging
Transcript: ENSMUST00000111186
AA Change: Y460F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000106817
Gene: ENSMUSG00000020661
AA Change: Y460F

DomainStartEndE-ValueType
PWWP 67 125 1.36e-24 SMART
low complexity region 193 211 N/A INTRINSIC
low complexity region 219 234 N/A INTRINSIC
PDB:3A1B|A 235 391 1e-101 PDB
Blast:RING 314 363 4e-16 BLAST
Pfam:DNA_methylase 411 554 9.5e-15 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 damaging
Transcript: ENSMUST00000172689
AA Change: Y460F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000133543
Gene: ENSMUSG00000020661
AA Change: Y460F

DomainStartEndE-ValueType
PWWP 67 125 1.36e-24 SMART
low complexity region 193 211 N/A INTRINSIC
low complexity region 219 234 N/A INTRINSIC
PDB:3A1B|A 235 391 1e-101 PDB
Blast:RING 314 363 4e-16 BLAST
Pfam:DNA_methylase 411 554 9.5e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000172749
SMART Domains Protein: ENSMUSP00000134567
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
PWWP 61 119 7.62e-19 SMART
low complexity region 151 169 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174272
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 damaging
Transcript: ENSMUST00000174817
AA Change: Y679F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: Y679F

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 unknown
Transcript: ENSMUST00000174733
AA Change: Y64F
SMART Domains Protein: ENSMUSP00000134492
Gene: ENSMUSG00000020661
AA Change: Y64F

DomainStartEndE-ValueType
Pfam:DNA_methylase 16 104 8.2e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174774
SMART Domains Protein: ENSMUSP00000134529
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
PWWP 67 125 1.36e-24 SMART
Meta Mutation Damage Score 0.3301 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.1%
  • 10x: 95.7%
  • 20x: 91.2%
Validation Efficiency 95% (81/85)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310057J18Rik T A 10: 28,858,518 (GRCm39) I50F possibly damaging Het
4930505A04Rik T C 11: 30,377,175 (GRCm39) probably benign Het
Aadat A T 8: 60,979,714 (GRCm39) D192V possibly damaging Het
Akap12 A G 10: 4,303,640 (GRCm39) D150G probably benign Het
Amigo3 A T 9: 107,931,231 (GRCm39) N218I probably damaging Het
Ankmy1 A G 1: 92,827,373 (GRCm39) S60P probably benign Het
Apol7e G A 15: 77,602,029 (GRCm39) S209N probably damaging Het
AW551984 A T 9: 39,510,632 (GRCm39) Y234* probably null Het
Bcam A T 7: 19,494,111 (GRCm39) D393E probably damaging Het
Card9 A G 2: 26,244,398 (GRCm39) L444P probably benign Het
Ccar1 T C 10: 62,586,780 (GRCm39) E886G unknown Het
Ccnb2 A T 9: 70,317,559 (GRCm39) probably null Het
Cd276 T C 9: 58,442,838 (GRCm39) S206G probably damaging Het
Cds1 T A 5: 101,965,828 (GRCm39) probably benign Het
Cfap96 G A 8: 46,409,515 (GRCm39) S268L probably benign Het
Chuk T C 19: 44,065,812 (GRCm39) S661G possibly damaging Het
Col17a1 T C 19: 47,639,276 (GRCm39) N1090D probably benign Het
Col3a1 A T 1: 45,367,026 (GRCm39) probably null Het
Crispld1 G T 1: 17,821,024 (GRCm39) V355F possibly damaging Het
Cspg4 A T 9: 56,806,151 (GRCm39) R2321W probably damaging Het
Dner T C 1: 84,563,177 (GRCm39) T61A probably benign Het
Dzip3 A T 16: 48,798,241 (GRCm39) probably benign Het
Eif3l T C 15: 78,968,381 (GRCm39) S217P possibly damaging Het
Fbxo42 T A 4: 140,925,417 (GRCm39) probably benign Het
Fhod1 A T 8: 106,063,957 (GRCm39) probably benign Het
Fzd1 T A 5: 4,806,278 (GRCm39) I435F probably damaging Het
Gapvd1 C T 2: 34,602,207 (GRCm39) V647I possibly damaging Het
Gm14496 T C 2: 181,638,002 (GRCm39) S359P possibly damaging Het
Gm5218 C A 15: 81,383,741 (GRCm39) noncoding transcript Het
Hnrnph3 A G 10: 62,851,579 (GRCm39) probably null Het
Hsd17b12 G T 2: 93,864,321 (GRCm39) T262K probably damaging Het
Igsf10 G C 3: 59,237,838 (GRCm39) P781R probably damaging Het
Il11ra1 T A 4: 41,768,207 (GRCm39) S373T probably damaging Het
Kdm3b A G 18: 34,942,345 (GRCm39) D612G probably damaging Het
Ldb1 T C 19: 46,022,903 (GRCm39) T261A probably damaging Het
Lep C A 6: 29,069,089 (GRCm39) H47N possibly damaging Het
Lrrtm2 A T 18: 35,346,428 (GRCm39) S291R possibly damaging Het
Ncor2 T C 5: 125,162,062 (GRCm39) Q404R unknown Het
Nlrp4d T C 7: 10,116,437 (GRCm39) H148R probably benign Het
Nlrp9a T A 7: 26,258,093 (GRCm39) D570E probably benign Het
Nphp3 G A 9: 103,886,413 (GRCm39) V202I probably damaging Het
Nptn T A 9: 58,548,073 (GRCm39) N159K probably benign Het
Or4a69 T A 2: 89,313,315 (GRCm39) T55S probably benign Het
Or4a72 A T 2: 89,405,746 (GRCm39) V108D possibly damaging Het
Or51f2 G A 7: 102,526,980 (GRCm39) V218I probably benign Het
Or52a24 A T 7: 103,381,585 (GRCm39) T151S possibly damaging Het
Or8b53 A T 9: 38,667,716 (GRCm39) H244L probably damaging Het
Pcolce T A 5: 137,608,769 (GRCm39) R13* probably null Het
Pdgfra A G 5: 75,353,264 (GRCm39) Y1018C probably damaging Het
Prima1 A G 12: 103,201,854 (GRCm39) S74P probably damaging Het
Prl7c1 A G 13: 27,962,838 (GRCm39) L55P probably damaging Het
Rasef A G 4: 73,658,574 (GRCm39) V513A probably damaging Het
Rgs1 T C 1: 144,121,227 (GRCm39) probably null Het
Rlf T C 4: 121,005,488 (GRCm39) E1164G probably benign Het
Rnf213 A T 11: 119,354,171 (GRCm39) N4016I probably damaging Het
Sae1 C T 7: 16,064,537 (GRCm39) probably null Het
Serping1 A T 2: 84,601,848 (GRCm39) D207E probably benign Het
Setd2 T A 9: 110,380,464 (GRCm39) D33E unknown Het
Simc1 T C 13: 54,673,071 (GRCm39) M473T probably benign Het
Slc30a6 T A 17: 74,725,610 (GRCm39) probably benign Het
Slc4a5 T C 6: 83,242,669 (GRCm39) L346P probably damaging Het
Spef2 T A 15: 9,596,660 (GRCm39) Q1473L probably damaging Het
St3gal3 G T 4: 117,817,204 (GRCm39) A44D possibly damaging Het
Sv2b G T 7: 74,797,425 (GRCm39) T323K probably damaging Het
Sycp2 T A 2: 177,993,461 (GRCm39) N1228I possibly damaging Het
Thbs2 T A 17: 14,910,030 (GRCm39) M190L probably benign Het
Tnrc6a G A 7: 122,776,098 (GRCm39) V1190I probably benign Het
Utrn A T 10: 12,312,029 (GRCm39) I673K possibly damaging Het
Vmn2r114 C T 17: 23,510,675 (GRCm39) V602M probably damaging Het
Wdr7 A T 18: 64,057,989 (GRCm39) I1273L probably benign Het
Zfp618 T C 4: 63,051,175 (GRCm39) L652P probably damaging Het
Zfp804a G A 2: 81,884,095 (GRCm39) 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
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'- AGCGCACATCTGTGCTGATCTGAC -3'
(R):5'- ATCTGCTCATCACCCTGAGATGCC -3'

Sequencing Primer
(F):5'- TGCATCTGGCAAGACAAGTC -3'
(R):5'- CCCTGAGATGCCACAGAAGTAAG -3'
Posted On 2014-04-24