Incidental Mutation 'R5361:Dnmt3a'
ID 422822
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 042940-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.404) question?
Stock # R5361 (G1)
Quality Score 199
Status Not validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 3945643 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 24 (V24A)
Ref Sequence ENSEMBL: ENSMUSP00000134689 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000111186] [ENSMUST00000172509] [ENSMUST00000172689] [ENSMUST00000172879] [ENSMUST00000174102] [ENSMUST00000174774] [ENSMUST00000174817] [ENSMUST00000174483]
AlphaFold O88508
Predicted Effect probably benign
Transcript: ENSMUST00000020991
AA Change: V243A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: V243A

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: V24A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000106817
Gene: ENSMUSG00000020661
AA Change: V24A

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
AA Change: V169A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000133869
Gene: ENSMUSG00000020661
AA Change: V169A

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: V24A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000133543
Gene: ENSMUSG00000020661
AA Change: V24A

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
AA Change: V17A

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000134567
Gene: ENSMUSG00000020661
AA Change: V17A

DomainStartEndE-ValueType
PWWP 61 119 7.62e-19 SMART
low complexity region 151 169 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000172879
AA Change: V24A

PolyPhen 2 Score 0.130 (Sensitivity: 0.93; Specificity: 0.86)
Predicted Effect probably benign
Transcript: ENSMUST00000174102
AA Change: V58A

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000134480
Gene: ENSMUSG00000020661
AA Change: V58A

DomainStartEndE-ValueType
Pfam:PWWP 101 140 2e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174774
AA Change: V24A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000134529
Gene: ENSMUSG00000020661
AA Change: V24A

DomainStartEndE-ValueType
PWWP 67 125 1.36e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000174817
AA Change: V243A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: V243A

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 noncoding transcript
Transcript: ENSMUST00000174272
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: ENSMUST00000174483
SMART Domains Protein: ENSMUSP00000133938
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 35 50 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.6%
  • 20x: 96.1%
Validation Efficiency
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017B05Rik T A 9: 57,164,468 (GRCm39) K635N probably damaging Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Ahnak T A 19: 8,992,705 (GRCm39) M4663K possibly damaging Het
C4b T A 17: 34,960,212 (GRCm39) T280S probably benign Het
Ccdc166 A G 15: 75,852,869 (GRCm39) V366A probably benign Het
Cdh23 A G 10: 60,493,044 (GRCm39) probably null Het
Col7a1 A G 9: 108,792,292 (GRCm39) T1281A unknown Het
Cul9 TTCCTCCTCCTCCTCCTCCTCCTC TTCCTCCTCCTCCTCCTCCTC 17: 46,811,775 (GRCm39) probably benign Het
Dbndd1 T A 8: 124,233,484 (GRCm39) D127V probably damaging Het
Ddx20 T A 3: 105,590,825 (GRCm39) E197V probably damaging Het
Dennd10 A G 19: 60,814,324 (GRCm39) M96V probably benign Het
Dnm3 A G 1: 161,838,471 (GRCm39) S826P probably damaging Het
Dop1b C A 16: 93,567,392 (GRCm39) A1273E probably damaging Het
Dsg1c T C 18: 20,416,703 (GRCm39) V868A possibly damaging Het
Dtx4 A G 19: 12,462,626 (GRCm39) probably null Het
Elovl4 A G 9: 83,672,154 (GRCm39) L55P possibly damaging Het
Fbxo40 T A 16: 36,789,914 (GRCm39) T399S possibly damaging Het
Fkbpl G A 17: 34,864,303 (GRCm39) A24T probably benign Het
Gm14399 T C 2: 174,973,371 (GRCm39) E96G probably damaging Het
Gm14496 T G 2: 181,642,147 (GRCm39) V606G probably benign Het
Gpr156 A G 16: 37,826,087 (GRCm39) E768G probably damaging Het
Grm5 A T 7: 87,723,704 (GRCm39) T665S probably damaging Het
Hsdl2 A G 4: 59,592,301 (GRCm39) probably benign Het
Htt T C 5: 35,064,928 (GRCm39) V3047A possibly damaging Het
Igkv3-2 A T 6: 70,676,011 (GRCm39) T107S probably benign Het
Insyn2b G A 11: 34,352,788 (GRCm39) E277K probably damaging Het
Itih2 T A 2: 10,101,272 (GRCm39) T899S probably benign Het
Lhcgr T A 17: 89,050,281 (GRCm39) Y415F probably damaging Het
Ltbr G A 6: 125,289,757 (GRCm39) R146W probably damaging Het
Med4 C A 14: 73,747,553 (GRCm39) S18* probably null Het
Nefl T C 14: 68,322,088 (GRCm39) V226A probably damaging Het
Nploc4 T A 11: 120,275,389 (GRCm39) N516Y probably damaging Het
Or1o4 A G 17: 37,590,501 (GRCm39) V270A probably benign Het
Or6c66 A T 10: 129,461,601 (GRCm39) F110I probably damaging Het
Otx1 C A 11: 21,947,037 (GRCm39) A91S probably damaging Het
Pcdha3 T G 18: 37,079,752 (GRCm39) L165V possibly damaging Het
Pcdhb12 T A 18: 37,570,099 (GRCm39) V415D probably damaging Het
Pcdhga10 T C 18: 37,880,503 (GRCm39) I88T probably damaging Het
Pigyl T A 9: 22,069,292 (GRCm39) M1K probably null Het
Prr27 T C 5: 87,991,203 (GRCm39) S272P probably damaging Het
Prss3 C T 6: 41,350,780 (GRCm39) D237N probably benign Het
Pstpip2 A G 18: 77,958,078 (GRCm39) D150G probably damaging Het
Robo4 T A 9: 37,324,674 (GRCm39) D909E probably benign Het
Serpinb3c A T 1: 107,204,661 (GRCm39) Y28* probably null Het
Slc26a3 T C 12: 31,500,980 (GRCm39) probably null Het
Slc6a1 A T 6: 114,279,493 (GRCm39) I91F probably benign Het
Smcr8 T G 11: 60,669,118 (GRCm39) Y89D probably damaging Het
Sspo T A 6: 48,443,247 (GRCm39) M1898K probably benign Het
Tbl1xr1 T A 3: 22,246,233 (GRCm39) I251K probably damaging Het
Thbs4 C T 13: 92,913,501 (GRCm39) D140N probably benign Het
Tmbim6 G A 15: 99,303,633 (GRCm39) A108T probably benign Het
Trim10 T G 17: 37,186,328 (GRCm39) L301R probably benign Het
Trpm7 A T 2: 126,671,161 (GRCm39) I607N possibly damaging Het
Vmn2r9 T A 5: 108,995,929 (GRCm39) I240F probably damaging Het
Xpot T A 10: 121,436,765 (GRCm39) I873F possibly damaging Het
Zfhx4 G A 3: 5,464,267 (GRCm39) S1475N probably damaging Het
Zfp712 A G 13: 67,189,079 (GRCm39) S483P possibly damaging Het
Zswim7 A T 11: 62,158,373 (GRCm39) H122Q 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
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'- AGATCCACTGAGTAGCCTTGC -3'
(R):5'- TGTGAACATCAGGTGACAAAGCC -3'

Sequencing Primer
(F):5'- GTAGCCTTGCTCACTCCTGGAG -3'
(R):5'- CAGATACTCTGGAAGCAGCC -3'
Posted On 2016-08-04