Incidental Mutation 'R7684:Dnmt3a'
ID 592954
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 067780-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.404) question?
Stock # R7684 (G1)
Quality Score 225.009
Status Validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 3947340 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 437 (V437A)
Ref Sequence ENSEMBL: ENSMUSP00000020991 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000111186] [ENSMUST00000172509] [ENSMUST00000172689] [ENSMUST00000172879] [ENSMUST00000174102] [ENSMUST00000174483] [ENSMUST00000174774] [ENSMUST00000174817]
AlphaFold O88508
Predicted Effect probably benign
Transcript: ENSMUST00000020991
AA Change: V437A

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: V437A

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: ENSMUST00000111186
AA Change: V218A

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000106817
Gene: ENSMUSG00000020661
AA Change: V218A

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 benign
Transcript: ENSMUST00000172689
AA Change: V218A

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000133543
Gene: ENSMUSG00000020661
AA Change: V218A

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
SMART Domains Protein: ENSMUSP00000134567
Gene: ENSMUSG00000020661
AA Change: V175A

DomainStartEndE-ValueType
PWWP 61 119 7.62e-19 SMART
low complexity region 151 169 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000172879
Predicted Effect probably benign
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: ENSMUST00000174733
SMART Domains Protein: ENSMUSP00000134492
Gene: ENSMUSG00000020661

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
Predicted Effect probably benign
Transcript: ENSMUST00000174817
AA Change: V437A

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: V437A

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (73/73)
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik A T 13: 77,760,659 (GRCm39) K1239* probably null Het
Abhd6 T C 14: 8,039,807 (GRCm38) F60S probably damaging Het
Adam6b G A 12: 113,455,196 (GRCm39) W671* probably null Het
Ankrd36 A G 11: 5,520,113 (GRCm39) T63A possibly damaging Het
Arhgef16 A G 4: 154,366,285 (GRCm39) V494A possibly damaging Het
Arhgef7 T A 8: 11,869,663 (GRCm39) M659K probably benign Het
Cacna1h A G 17: 25,608,346 (GRCm39) Y854H probably damaging Het
Chd3 A T 11: 69,248,692 (GRCm39) F780I possibly damaging Het
Cldn8 A G 16: 88,359,335 (GRCm39) Y197H probably damaging Het
Cpne8 A T 15: 90,533,450 (GRCm39) D58E probably damaging Het
Cul9 T G 17: 46,820,815 (GRCm39) Y1954S probably damaging Het
Cyp4a10 T A 4: 115,375,549 (GRCm39) F11I probably benign Het
Cysrt1 A T 2: 25,129,094 (GRCm39) C139* probably null Het
Dnajc16 A G 4: 141,501,879 (GRCm39) V317A probably benign Het
Dok5 T C 2: 170,683,344 (GRCm39) C202R probably damaging Het
Dusp11 T A 6: 85,927,542 (GRCm39) R164S probably damaging Het
Dysf T C 6: 84,077,117 (GRCm39) S648P probably benign Het
Egfem1 A T 3: 29,744,334 (GRCm39) R581S probably damaging Het
Enpep A G 3: 129,115,094 (GRCm39) F226S probably damaging Het
Ep400 A G 5: 110,845,218 (GRCm39) I1541T unknown Het
Exd1 A G 2: 119,350,684 (GRCm39) S526P probably damaging Het
Fam118a A G 15: 84,942,982 (GRCm39) E337G possibly damaging Het
Fam20b T C 1: 156,518,215 (GRCm39) N193S probably benign Het
Fat3 A G 9: 15,899,564 (GRCm39) probably null Het
Flg2 T C 3: 93,126,956 (GRCm39) V1956A unknown Het
Fzd10 A G 5: 128,678,480 (GRCm39) I67V possibly damaging Het
Gckr A T 5: 31,465,141 (GRCm39) D370V probably damaging Het
Gm8797 A T 3: 5,816,148 (GRCm39) Q62L probably benign Het
H6pd G T 4: 150,080,519 (GRCm39) Q109K probably benign Het
Higd1a T C 9: 121,679,322 (GRCm39) K55R possibly damaging Het
Il1b C T 2: 129,209,277 (GRCm39) V118I probably benign Het
Insr T C 8: 3,219,753 (GRCm39) N923S possibly damaging Het
Krit1 A G 5: 3,880,723 (GRCm39) I561V possibly damaging Het
Lamc2 T C 1: 153,002,771 (GRCm39) D1070G probably null Het
Lpcat2 T A 8: 93,635,823 (GRCm39) D408E possibly damaging Het
Mst1r T A 9: 107,788,762 (GRCm39) F427Y probably benign Het
Mtx1 A T 3: 89,117,739 (GRCm39) I258K possibly damaging Het
Nckap5 T C 1: 125,954,594 (GRCm39) T653A probably benign Het
Npas3 A T 12: 54,115,609 (GRCm39) N844Y probably damaging Het
Nrg3 A T 14: 39,194,522 (GRCm39) L79Q probably damaging Het
Nsmce1 C A 7: 125,070,348 (GRCm39) K154N probably damaging Het
Oard1 T C 17: 48,723,726 (GRCm39) L124P probably damaging Het
Or10ag57 T C 2: 87,218,372 (GRCm39) S108P probably damaging Het
Or10ak13 T C 4: 118,639,471 (GRCm39) M104V probably benign Het
Or51a10 G A 7: 103,698,667 (GRCm39) T298I probably damaging Het
Or51ah3 T C 7: 103,210,425 (GRCm39) F247S probably benign Het
Ovgp1 A T 3: 105,887,272 (GRCm39) T223S probably damaging Het
Pik3c2a A T 7: 115,987,312 (GRCm39) Y536* probably null Het
Plekho2 A T 9: 65,466,816 (GRCm39) probably null Het
Prelid3b T C 2: 174,310,210 (GRCm39) probably null Het
Rftn1 G T 17: 50,354,408 (GRCm39) A318D probably damaging Het
Rxfp1 T A 3: 79,578,214 (GRCm39) N159I possibly damaging Het
Sfmbt1 A G 14: 30,532,311 (GRCm39) Q557R probably damaging Het
Slc22a18 G T 7: 143,044,577 (GRCm39) V177L probably benign Het
Slc22a8 A G 19: 8,587,294 (GRCm39) I451M probably benign Het
Slc39a12 T C 2: 14,454,670 (GRCm39) S563P probably damaging Het
Snx20 T C 8: 89,353,863 (GRCm39) D289G probably benign Het
Sptb A G 12: 76,658,969 (GRCm39) Y1189H probably benign Het
Tbc1d1 T A 5: 64,473,829 (GRCm39) M784K probably benign Het
Tbkbp1 T C 11: 97,038,559 (GRCm39) probably benign Het
Tfap2b G C 1: 19,284,511 (GRCm39) D140H probably damaging Het
Thy1 G A 9: 43,957,855 (GRCm39) G13D unknown Het
Ticam1 A G 17: 56,576,984 (GRCm39) S704P unknown Het
Tmem151b A G 17: 45,857,929 (GRCm39) Y106H probably damaging Het
Trappc8 T C 18: 20,996,559 (GRCm39) N452S probably benign Het
Ttc9c A G 19: 8,789,128 (GRCm39) Y166H probably damaging Het
Txndc16 A G 14: 45,385,325 (GRCm39) V556A possibly damaging Het
Tyrp1 C A 4: 80,758,862 (GRCm39) S245Y probably damaging Het
Urb1 A T 16: 90,583,006 (GRCm39) L621* probably null Het
Wdr72 A T 9: 74,054,292 (GRCm39) T224S probably damaging Het
Zc3h18 T G 8: 123,134,165 (GRCm39) S544A unknown Het
Zfp462 T A 4: 55,008,908 (GRCm39) N291K probably benign Het
Zfp609 T C 9: 65,638,362 (GRCm39) N290S possibly damaging Het
Zfp979 A T 4: 147,697,799 (GRCm39) H303Q probably damaging 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
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
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'- TGTGAGGTCTGTTAGCCCAAG -3'
(R):5'- CATTAGGAGGTTGCCCAGATGG -3'

Sequencing Primer
(F):5'- GGCGTGTGCTACCATGTCATC -3'
(R):5'- CGCTCATCAATGATCTCC -3'
Posted On 2019-11-12