Incidental Mutation 'R4283:Dnmt3a'
ID 321961
Institutional Source Beutler Lab
Gene Symbol Dnmt3a
Ensembl Gene ENSMUSG00000020661
Gene Name DNA methyltransferase 3A
Synonyms
MMRRC Submission 041651-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.404) question?
Stock # R4283 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 3856007-3964443 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 3951665 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Arginine at position 681 (G681R)
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: G681R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000020991
Gene: ENSMUSG00000020661
AA Change: G681R

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: G462R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000106817
Gene: ENSMUSG00000020661
AA Change: G462R

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: G462R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000133543
Gene: ENSMUSG00000020661
AA Change: G462R

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 unknown
Transcript: ENSMUST00000174733
AA Change: G66R
SMART Domains Protein: ENSMUSP00000134492
Gene: ENSMUSG00000020661
AA Change: G66R

DomainStartEndE-ValueType
Pfam:DNA_methylase 16 104 8.2e-10 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000174817
AA Change: G681R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000134009
Gene: ENSMUSG00000020661
AA Change: G681R

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: ENSMUST00000174774
SMART Domains Protein: ENSMUSP00000134529
Gene: ENSMUSG00000020661

DomainStartEndE-ValueType
PWWP 67 125 1.36e-24 SMART
Meta Mutation Damage Score 0.5284 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency 100% (41/41)
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: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6030468B19Rik A G 11: 117,697,087 (GRCm39) T229A probably benign Het
Adgrg5 T G 8: 95,664,326 (GRCm39) V312G probably benign Het
Arl6ip1 AAAATAAATAAATAAATAAATAAATA AAAATAAATAAATAAATAAATAAATAAATA 7: 117,721,122 (GRCm39) probably benign Het
Camk2b A C 11: 5,937,099 (GRCm39) S327A probably benign Het
Card9 A G 2: 26,247,309 (GRCm39) I280T possibly damaging Het
Cd274 A T 19: 29,357,871 (GRCm39) M188L probably benign Het
Cga T C 4: 34,905,264 (GRCm39) probably null Het
Copg1 C T 6: 87,885,527 (GRCm39) T723M probably damaging Het
Cplx2 A G 13: 54,527,377 (GRCm39) E87G probably damaging Het
Crtc2 A G 3: 90,166,543 (GRCm39) probably benign Het
Defa27 A G 8: 21,805,632 (GRCm39) N24S probably benign Het
Defb40 A G 8: 19,028,093 (GRCm39) S14P probably damaging Het
Ghr C A 15: 3,362,930 (GRCm39) V181L possibly damaging Het
Gm10750 A G 2: 148,857,916 (GRCm39) F112L unknown Het
Gm17541 A G 12: 4,739,656 (GRCm39) probably benign Het
Gmip T A 8: 70,266,251 (GRCm39) probably benign Het
Hdac10 A G 15: 89,009,826 (GRCm39) L402P possibly damaging Het
Hsd17b12 G C 2: 93,863,931 (GRCm39) R304G unknown Het
Iqgap3 T C 3: 88,006,167 (GRCm39) V526A probably benign Het
Ncaph A G 2: 126,963,005 (GRCm39) probably benign Het
Ninl T C 2: 150,795,336 (GRCm39) probably benign Het
Pcgf1 T A 6: 83,056,714 (GRCm39) L90Q probably damaging Het
Pcsk4 C A 10: 80,165,287 (GRCm39) probably benign Het
Ptpn21 T C 12: 98,699,734 (GRCm39) E60G probably damaging Het
Rec8 A G 14: 55,856,091 (GRCm39) H11R probably damaging Het
Ric1 A G 19: 29,563,950 (GRCm39) Y568C probably damaging Het
Slc17a6 A G 7: 51,294,824 (GRCm39) Y177C probably damaging Het
Tas2r104 C T 6: 131,662,374 (GRCm39) A112T probably damaging Het
Tas2r123 G A 6: 132,825,008 (GRCm39) V302I possibly damaging Het
Tas2r143 T A 6: 42,378,007 (GRCm39) probably null Het
Tfeb A G 17: 48,100,699 (GRCm39) E305G probably damaging Het
Ttn T A 2: 76,585,168 (GRCm39) I22042F probably damaging Het
Upf2 A G 2: 5,978,369 (GRCm39) N411S unknown Het
Vmn2r52 C T 7: 9,904,565 (GRCm39) G425R possibly damaging Het
Zfp28 A T 7: 6,396,700 (GRCm39) Q378H probably benign Het
Zfp429 A C 13: 67,538,914 (GRCm39) C177G 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
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'- CACAGTCATAGCGCACATCTG -3'
(R):5'- ATCACCCTGAGATGCCACAG -3'

Sequencing Primer
(F):5'- CTGACTTGATTTGGGAAAGGATAC -3'
(R):5'- CCCTGAGATGCCACAGAAGTAAG -3'
Posted On 2015-06-20