Incidental Mutation 'R9102:Dnmt3b'
ID 691737
Institutional Source Beutler Lab
Gene Symbol Dnmt3b
Ensembl Gene ENSMUSG00000027478
Gene Name DNA methyltransferase 3B
Synonyms
MMRRC Submission 068916-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9102 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 153491370-153529650 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 153518703 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 622 (V622A)
Ref Sequence ENSEMBL: ENSMUSP00000072761 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056495] [ENSMUST00000072997] [ENSMUST00000081628] [ENSMUST00000088976] [ENSMUST00000103150] [ENSMUST00000103151] [ENSMUST00000109771] [ENSMUST00000109772] [ENSMUST00000109773] [ENSMUST00000109774]
AlphaFold O88509
Predicted Effect possibly damaging
Transcript: ENSMUST00000056495
AA Change: V623A

PolyPhen 2 Score 0.782 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: V623A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
low complexity region 380 389 N/A INTRINSIC
PDB:3A1A|A 421 560 8e-55 PDB
Blast:RING 483 532 6e-28 BLAST
Pfam:DNA_methylase 582 732 3.1e-15 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000072997
AA Change: V622A

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: V622A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
low complexity region 380 389 N/A INTRINSIC
PDB:3A1A|A 421 560 8e-55 PDB
Blast:RING 483 532 6e-28 BLAST
Pfam:DNA_methylase 581 731 4.5e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000081628
AA Change: V602A

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: V602A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
PDB:3A1A|A 401 540 1e-54 PDB
Blast:RING 463 512 7e-28 BLAST
Pfam:DNA_methylase 561 711 4.4e-15 PFAM
Predicted Effect
SMART Domains Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: V622A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
low complexity region 380 389 N/A INTRINSIC
PDB:3A1A|A 421 560 7e-55 PDB
Blast:RING 483 532 5e-28 BLAST
Pfam:DNA_methylase 581 727 2.9e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000103150
AA Change: V602A

PolyPhen 2 Score 0.766 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: V602A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
PDB:3A1A|A 401 540 8e-55 PDB
Blast:RING 463 512 6e-28 BLAST
Pfam:DNA_methylase 561 707 4.2e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000103151
AA Change: V602A

PolyPhen 2 Score 0.766 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: V602A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
PDB:3A1A|A 401 540 8e-55 PDB
Blast:RING 463 512 6e-28 BLAST
Pfam:DNA_methylase 561 707 4.2e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000109771
AA Change: V623A

PolyPhen 2 Score 0.782 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: V623A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
low complexity region 380 389 N/A INTRINSIC
PDB:3A1A|A 421 560 8e-55 PDB
Blast:RING 483 532 6e-28 BLAST
Pfam:DNA_methylase 582 732 3.1e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000109772
AA Change: V622A

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: V622A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
low complexity region 380 389 N/A INTRINSIC
PDB:3A1A|A 421 560 7e-55 PDB
Blast:RING 483 532 5e-28 BLAST
Pfam:DNA_methylase 581 727 2.9e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000109773
AA Change: V602A

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: V602A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
PDB:3A1A|A 401 540 1e-54 PDB
Blast:RING 463 512 7e-28 BLAST
Pfam:DNA_methylase 561 711 4.4e-15 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000109774
AA Change: V622A

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: V622A

DomainStartEndE-ValueType
low complexity region 57 74 N/A INTRINSIC
low complexity region 79 97 N/A INTRINSIC
low complexity region 157 179 N/A INTRINSIC
PWWP 230 288 2.43e-26 SMART
low complexity region 380 389 N/A INTRINSIC
PDB:3A1A|A 421 560 8e-55 PDB
Blast:RING 483 532 6e-28 BLAST
Pfam:DNA_methylase 581 731 4.5e-15 PFAM
Meta Mutation Damage Score 0.1116 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 97% (62/64)
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 results in severe developmental defects and loss of viability. Mutation of the related gene in humans causes immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. There is a pseudogene for this gene located adjacent to this gene in the same region of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Nov 2012]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit growth retardation and rostral neural tube defects, and die prenatally. Mutants exhibit slight under-methylation of endogenous viral DNA and substantial demethylation of minor satellite DNA. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb9 T C 5: 124,228,176 (GRCm39) T22A possibly damaging Het
Adam33 T C 2: 130,897,737 (GRCm39) Q227R probably benign Het
Adgrb2 G A 4: 129,912,802 (GRCm39) G1276D probably benign Het
Adra1b A G 11: 43,667,056 (GRCm39) S394P possibly damaging Het
Arap2 T A 5: 62,906,341 (GRCm39) H226L probably benign Het
Bckdk A G 7: 127,506,658 (GRCm39) D297G probably null Het
Brwd1 T C 16: 95,869,725 (GRCm39) T101A probably benign Het
Ciita A G 16: 10,324,565 (GRCm39) R166G probably benign Het
Cnksr1 A G 4: 133,956,323 (GRCm39) F587S probably damaging Het
Col4a1 A T 8: 11,253,007 (GRCm39) C1548S possibly damaging Het
Cxcl15 G T 5: 90,949,154 (GRCm39) M106I Het
Dennd6a T C 14: 26,350,689 (GRCm39) I598T probably damaging Het
Dlg5 G A 14: 24,199,567 (GRCm39) P1446S probably damaging Het
Dnah6 A T 6: 73,044,469 (GRCm39) I3214N probably benign Het
Fam170b T A 14: 32,557,404 (GRCm39) S80T probably damaging Het
Fbxl13 G T 5: 21,837,801 (GRCm39) H45Q probably benign Het
Fbxo39 T C 11: 72,208,316 (GRCm39) F223L possibly damaging Het
Fndc3b C A 3: 27,523,014 (GRCm39) probably null Het
Gbp3 G C 3: 142,273,586 (GRCm39) V378L probably benign Het
Gc C T 5: 89,591,444 (GRCm39) S98N probably benign Het
Gck A G 11: 5,856,516 (GRCm39) Y214H probably damaging Het
Gpr158 A T 2: 21,830,078 (GRCm39) S708C probably damaging Het
Hmcn1 A T 1: 150,573,331 (GRCm39) M2106K probably benign Het
Hoxd11 T A 2: 74,513,274 (GRCm39) Y180N possibly damaging Het
Hydin A G 8: 111,235,546 (GRCm39) I1844V probably benign Het
Knl1 T C 2: 118,917,973 (GRCm39) I1777T probably benign Het
Krt33b A C 11: 99,915,846 (GRCm39) L300R probably damaging Het
Madd C T 2: 90,988,404 (GRCm39) A1208T probably benign Het
Meis2 T A 2: 115,694,760 (GRCm39) N461I probably benign Het
Mgat1 T A 11: 49,152,165 (GRCm39) V216E probably damaging Het
Nox4 G A 7: 87,025,448 (GRCm39) R525Q probably benign Het
Npc1l1 C T 11: 6,164,684 (GRCm39) V1122M possibly damaging Het
Nrsn1 A G 13: 25,437,517 (GRCm39) M137T probably benign Het
Nrxn3 T C 12: 90,298,924 (GRCm39) S1015P probably benign Het
Nudt22 T A 19: 6,972,119 (GRCm39) I166F probably benign Het
Or10d1b A C 9: 39,613,984 (GRCm39) V27G probably benign Het
Or5j1 C T 2: 86,879,171 (GRCm39) M136I possibly damaging Het
Or6k4 A T 1: 173,964,322 (GRCm39) N4I Het
Or6n2 T A 1: 173,897,176 (GRCm39) F104Y probably damaging Het
Or8b4 T A 9: 37,829,992 (GRCm39) I13N probably damaging Het
Or8g31-ps1 C T 9: 39,276,388 (GRCm39) P178S unknown Het
Pcdha4 T A 18: 37,087,630 (GRCm39) N604K probably damaging Het
Plxnc1 C T 10: 94,663,107 (GRCm39) V1181M probably damaging Het
Pms1 G C 1: 53,307,021 (GRCm39) H128Q probably benign Het
Prkar2b G A 12: 32,013,025 (GRCm39) H364Y probably benign Het
Pus7 A T 5: 23,957,380 (GRCm39) I357K possibly damaging Het
Rsf1 GCGGC GCGGCGGCGCCGGC 7: 97,229,138 (GRCm39) probably benign Het
Ryr3 T C 2: 112,508,906 (GRCm39) probably benign Het
Siglec1 T C 2: 130,915,389 (GRCm39) I1401V probably benign Het
Slc6a6 G T 6: 91,731,940 (GRCm39) V590L probably benign Het
Slc9b1 C T 3: 135,100,725 (GRCm39) P490L probably damaging Het
Sprn T C 7: 139,733,278 (GRCm39) D98G possibly damaging Het
Srrm4 T C 5: 116,620,563 (GRCm39) D55G unknown Het
Sugct A G 13: 17,497,833 (GRCm39) V280A probably benign Het
Tbx6 A G 7: 126,381,014 (GRCm39) E83G possibly damaging Het
Tmem120a T C 5: 135,765,455 (GRCm39) T209A probably benign Het
Top3a T C 11: 60,647,155 (GRCm39) R255G probably damaging Het
Trav6-1 T A 14: 52,876,008 (GRCm39) F13I probably benign Het
Tsnaxip1 A G 8: 106,568,622 (GRCm39) E410G probably benign Het
Ubr5 A G 15: 38,018,596 (GRCm39) V842A Het
Ubtf A G 11: 102,201,015 (GRCm39) probably null Het
Vwa3b G A 1: 37,174,593 (GRCm39) M1I probably null Het
Zfp518b T C 5: 38,831,181 (GRCm39) T275A probably benign Het
Other mutations in Dnmt3b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00793:Dnmt3b APN 2 153,514,422 (GRCm39) missense possibly damaging 0.88
IGL00931:Dnmt3b APN 2 153,528,170 (GRCm39) splice site probably benign
IGL01073:Dnmt3b APN 2 153,512,762 (GRCm39) splice site probably benign
IGL01138:Dnmt3b APN 2 153,503,361 (GRCm39) missense probably benign 0.01
IGL01960:Dnmt3b APN 2 153,518,631 (GRCm39) missense possibly damaging 0.83
IGL02884:Dnmt3b APN 2 153,516,297 (GRCm39) missense probably damaging 1.00
IGL03382:Dnmt3b APN 2 153,528,279 (GRCm39) missense probably damaging 1.00
PIT4151001:Dnmt3b UTSW 2 153,526,399 (GRCm39) critical splice donor site probably null
R0062:Dnmt3b UTSW 2 153,514,192 (GRCm39) missense probably benign 0.01
R0122:Dnmt3b UTSW 2 153,518,618 (GRCm39) missense probably damaging 1.00
R0147:Dnmt3b UTSW 2 153,503,377 (GRCm39) missense possibly damaging 0.68
R0178:Dnmt3b UTSW 2 153,516,938 (GRCm39) missense probably benign 0.41
R0751:Dnmt3b UTSW 2 153,516,762 (GRCm39) splice site probably null
R1696:Dnmt3b UTSW 2 153,518,630 (GRCm39) nonsense probably null
R1795:Dnmt3b UTSW 2 153,525,559 (GRCm39) missense possibly damaging 0.92
R1889:Dnmt3b UTSW 2 153,518,679 (GRCm39) missense probably benign
R2898:Dnmt3b UTSW 2 153,509,550 (GRCm39) missense possibly damaging 0.85
R4201:Dnmt3b UTSW 2 153,512,337 (GRCm39) nonsense probably null
R4630:Dnmt3b UTSW 2 153,512,235 (GRCm39) nonsense probably null
R4870:Dnmt3b UTSW 2 153,512,284 (GRCm39) missense probably benign 0.01
R5648:Dnmt3b UTSW 2 153,519,118 (GRCm39) missense probably damaging 1.00
R5814:Dnmt3b UTSW 2 153,514,417 (GRCm39) missense probably benign 0.00
R6311:Dnmt3b UTSW 2 153,515,925 (GRCm39) missense probably damaging 1.00
R6625:Dnmt3b UTSW 2 153,507,233 (GRCm39) missense probably benign
R6818:Dnmt3b UTSW 2 153,528,204 (GRCm39) missense probably damaging 1.00
R7258:Dnmt3b UTSW 2 153,525,519 (GRCm39) splice site probably null
R7473:Dnmt3b UTSW 2 153,526,370 (GRCm39) missense probably damaging 1.00
R7570:Dnmt3b UTSW 2 153,518,619 (GRCm39) missense probably damaging 1.00
R7627:Dnmt3b UTSW 2 153,519,500 (GRCm39) missense probably benign 0.03
R7709:Dnmt3b UTSW 2 153,514,140 (GRCm39) missense probably benign 0.10
R8483:Dnmt3b UTSW 2 153,516,306 (GRCm39) missense probably damaging 1.00
R8771:Dnmt3b UTSW 2 153,504,734 (GRCm39) missense possibly damaging 0.94
R8775:Dnmt3b UTSW 2 153,511,711 (GRCm39) missense possibly damaging 0.83
R8775-TAIL:Dnmt3b UTSW 2 153,511,711 (GRCm39) missense possibly damaging 0.83
R8821:Dnmt3b UTSW 2 153,518,734 (GRCm39) missense probably benign 0.15
R8850:Dnmt3b UTSW 2 153,515,933 (GRCm39) missense probably benign 0.16
R9228:Dnmt3b UTSW 2 153,507,980 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- TCCTCATTGTGCTGCAGGAG -3'
(R):5'- GTAAACCTGAATTATACCTCCAACTGC -3'

Sequencing Primer
(F):5'- TGCAGGAGGACACCGTG -3'
(R):5'- GCACTTTTTCTAAGGTGTCTACAG -3'
Posted On 2021-12-30