Incidental Mutation 'R2219:Dnmt3a'
ID 241355
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 040221-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.404) question?
Stock # R2219 (G1)
Quality Score 159
Status Not validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation utr 5 prime
DNA Base Change (assembly) A to G at 3899654 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000133938 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020991] [ENSMUST00000172509] [ENSMUST00000172719] [ENSMUST00000174483] [ENSMUST00000174817]
AlphaFold O88508
Predicted Effect unknown
Transcript: ENSMUST00000020991
AA Change: E28G
SMART Domains Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: E28G

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: ENSMUST00000085826
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 unknown
Transcript: ENSMUST00000172719
AA Change: E28G
SMART Domains Protein: ENSMUSP00000133501
Gene: ENSMUSG00000020661
AA Change: E28G

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: ENSMUST00000174483
SMART Domains Protein: ENSMUSP00000133938
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
low complexity region 35 50 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000174817
AA Change: E28G
SMART Domains Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: E28G

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: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.0%
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: 87 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933421I07Rik A G 7: 42,095,769 (GRCm39) Y160H probably damaging Het
Adamts16 G A 13: 70,927,637 (GRCm39) probably benign Het
Adgre1 T A 17: 57,708,912 (GRCm39) N34K possibly damaging Het
Ago2 T A 15: 73,018,260 (GRCm39) E59D probably benign Het
Akap8l G T 17: 32,553,605 (GRCm39) Q372K probably benign Het
Aox1 A G 1: 58,388,289 (GRCm39) probably null Het
Apc2 T C 10: 80,144,943 (GRCm39) V618A probably benign Het
Cacna1d A T 14: 29,764,047 (GRCm39) C2140S probably damaging Het
Cadps2 A G 6: 23,410,831 (GRCm39) L671P probably damaging Het
Capn9 C T 8: 125,335,898 (GRCm39) R529* probably null Het
Ccdc180 T A 4: 45,944,949 (GRCm39) N1452K probably damaging Het
Cdh5 A T 8: 104,869,538 (GRCm39) I755F possibly damaging Het
Cdkal1 T A 13: 29,538,741 (GRCm39) M473L probably benign Het
Cfap65 T C 1: 74,943,184 (GRCm39) I1614V probably damaging Het
Champ1 A G 8: 13,930,017 (GRCm39) H725R probably damaging Het
Cntnap5a A T 1: 116,508,369 (GRCm39) T1294S possibly damaging Het
Cops8 A C 1: 90,534,341 (GRCm39) N94T probably benign Het
Cpne7 G T 8: 123,851,177 (GRCm39) V155L probably benign Het
Dhx29 T C 13: 113,089,338 (GRCm39) V703A probably damaging Het
Dhx30 A G 9: 109,916,703 (GRCm39) L575P probably damaging Het
Dmc1 T A 15: 79,469,327 (GRCm39) H156L possibly damaging Het
Dst C G 1: 34,209,514 (GRCm39) L869V probably damaging Het
Eif3d A T 15: 77,849,142 (GRCm39) M180K probably benign Het
Erbb3 T C 10: 128,405,740 (GRCm39) T1173A probably damaging Het
Fat4 A T 3: 39,064,364 (GRCm39) K4773N probably damaging Het
Fbn2 G A 18: 58,186,035 (GRCm39) P1771L possibly damaging Het
Fer1l4 T G 2: 155,873,684 (GRCm39) Y1207S probably damaging Het
Fermt2 G A 14: 45,713,354 (GRCm39) T87I probably benign Het
Fpr3 T A 17: 18,191,644 (GRCm39) M305K possibly damaging Het
Fzd2 A G 11: 102,496,249 (GRCm39) E231G probably benign Het
Ggcx T C 6: 72,404,965 (GRCm39) Y458H probably benign Het
Ggt7 A G 2: 155,337,639 (GRCm39) S504P probably damaging Het
Gm4884 A G 7: 40,692,910 (GRCm39) H293R possibly damaging Het
Gm5475 A G 15: 100,322,094 (GRCm39) probably benign Het
Gm5930 A T 14: 44,573,993 (GRCm39) L115M probably damaging Het
Itln1 T A 1: 171,359,115 (GRCm39) T122S probably damaging Het
Itpr3 T A 17: 27,334,027 (GRCm39) L2033Q probably benign Het
Lama2 T C 10: 26,919,565 (GRCm39) D2222G probably damaging Het
Lars2 T C 9: 123,247,845 (GRCm39) L334P probably damaging Het
Ly9 T C 1: 171,425,249 (GRCm39) probably null Het
Man1a T C 10: 53,853,145 (GRCm39) I324M probably damaging Het
Mast3 T C 8: 71,233,607 (GRCm39) E994G probably damaging Het
Mettl21a A T 1: 64,655,442 (GRCm39) V46E probably damaging Het
Mmp15 A G 8: 96,096,801 (GRCm39) D398G probably benign Het
Mybpc1 T A 10: 88,391,540 (GRCm39) D319V probably damaging Het
Or10ad1c T A 15: 98,084,848 (GRCm39) K277* probably null Het
Or4a47 A T 2: 89,665,769 (GRCm39) D173E probably damaging Het
Or4a78 A T 2: 89,498,211 (GRCm39) N6K possibly damaging Het
Or4c35 G A 2: 89,808,256 (GRCm39) V45I possibly damaging Het
Or4f61 A T 2: 111,922,752 (GRCm39) I98N probably damaging Het
Or5b113 T A 19: 13,342,901 (GRCm39) I303N possibly damaging Het
Or5p5 G A 7: 107,414,429 (GRCm39) V213I probably benign Het
Or9m1 A C 2: 87,733,269 (GRCm39) Y250* probably null Het
Otogl C T 10: 107,692,838 (GRCm39) C882Y probably damaging Het
Parp10 A G 15: 76,117,783 (GRCm39) Y868H probably damaging Het
Pick1 T A 15: 79,123,899 (GRCm39) I90N probably damaging Het
Piezo1 C T 8: 123,218,227 (GRCm39) V1170I probably benign Het
Pim3 G A 15: 88,747,115 (GRCm39) V54I possibly damaging Het
Pinlyp T C 7: 24,245,433 (GRCm39) probably benign Het
Pira12 A T 7: 3,900,488 (GRCm39) N87K probably benign Het
Ppfia3 G A 7: 45,004,314 (GRCm39) Q473* probably null Het
Rab3gap2 G A 1: 185,008,113 (GRCm39) G1056E probably damaging Het
Ralgapa2 G A 2: 146,263,599 (GRCm39) T706I probably benign Het
Reln T C 5: 22,177,045 (GRCm39) T1874A possibly damaging Het
Rftn1 C A 17: 50,476,173 (GRCm39) M1I probably null Het
Ros1 T A 10: 52,042,175 (GRCm39) Q250L probably damaging Het
Slc11a1 T A 1: 74,419,824 (GRCm39) F166I probably damaging Het
Slc17a9 A G 2: 180,373,755 (GRCm39) T59A probably benign Het
Slc26a5 T C 5: 22,028,476 (GRCm39) K364R probably damaging Het
Slitrk2 T C X: 65,698,754 (GRCm39) I415T probably damaging Het
Stom A G 2: 35,211,613 (GRCm39) I136T possibly damaging Het
Strc G T 2: 121,195,004 (GRCm39) P1728T probably damaging Het
Telo2 C A 17: 25,322,673 (GRCm39) V640F probably benign Het
Tg T C 15: 66,553,782 (GRCm39) V399A probably benign Het
Tmem214 A G 5: 31,030,975 (GRCm39) K383E possibly damaging Het
Tomm40l A T 1: 171,049,550 (GRCm39) L13* probably null Het
Tonsl A T 15: 76,518,840 (GRCm39) N526K probably damaging Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Tymp T A 15: 89,258,965 (GRCm39) M240L probably benign Het
Ubr2 A T 17: 47,296,968 (GRCm39) S271T possibly damaging Het
Uggt2 A T 14: 119,312,749 (GRCm39) N353K probably damaging Het
Ugt2b35 T A 5: 87,151,191 (GRCm39) F266I possibly damaging Het
Vmn2r103 C T 17: 20,013,909 (GRCm39) R234W probably damaging Het
Zfp109 C A 7: 23,927,886 (GRCm39) D508Y probably damaging Het
Zfp623 T C 15: 75,819,379 (GRCm39) S112P possibly damaging Het
Zfp735 A G 11: 73,601,851 (GRCm39) N265S possibly damaging Het
Zfp879 A G 11: 50,724,094 (GRCm39) C321R 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
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'- TTTACCACACAGGAGGGTTGG -3'
(R):5'- CTGGCCTCTAGTCTAAAACTGG -3'

Sequencing Primer
(F):5'- TTGGGGACAGCATGACAC -3'
(R):5'- GGATGTAACAAAGCCCTACATCTGG -3'
Posted On 2014-10-15