Incidental Mutation 'R0062:Dnmt3b'
ID 46602
Institutional Source Beutler Lab
Gene Symbol Dnmt3b
Ensembl Gene ENSMUSG00000027478
Gene Name DNA methyltransferase 3B
Synonyms
MMRRC Submission 038354-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0062 (G1)
Quality Score 221
Status Validated
Chromosome 2
Chromosomal Location 153491370-153529650 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 153514192 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Serine at position 382 (P382S)
Ref Sequence ENSEMBL: ENSMUSP00000105395 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056495] [ENSMUST00000072997] [ENSMUST00000081628] [ENSMUST00000088976] [ENSMUST00000103150] [ENSMUST00000103151] [ENSMUST00000109771] [ENSMUST00000109772] [ENSMUST00000109774] [ENSMUST00000109773]
AlphaFold O88509
PDB Structure Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000056495
AA Change: P402S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: P402S

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 benign
Transcript: ENSMUST00000072997
AA Change: P402S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: P402S

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 probably benign
Transcript: ENSMUST00000081628
AA Change: P382S

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: P382S

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 benign
Transcript: ENSMUST00000088976
AA Change: P402S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: P402S

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 probably benign
Transcript: ENSMUST00000103150
AA Change: P382S

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: P382S

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 probably benign
Transcript: ENSMUST00000103151
AA Change: P382S

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: P382S

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 probably benign
Transcript: ENSMUST00000109771
AA Change: P402S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: P402S

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 benign
Transcript: ENSMUST00000109772
AA Change: P402S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: P402S

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 probably benign
Transcript: ENSMUST00000109774
AA Change: P402S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: P402S

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 probably benign
Transcript: ENSMUST00000109773
AA Change: P382S

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: P382S

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 noncoding transcript
Transcript: ENSMUST00000140811
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132132
Meta Mutation Damage Score 0.0777 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.4%
Validation Efficiency 100% (70/70)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921513I03Rik G T 10: 120,614,511 (GRCm39) probably benign Het
4930407I10Rik T A 15: 81,947,267 (GRCm39) I388K probably benign Het
4930407I10Rik T A 15: 81,950,504 (GRCm39) V1467D probably damaging Het
Abi2 T A 1: 60,492,884 (GRCm39) N182K probably benign Het
Adam25 A T 8: 41,207,829 (GRCm39) H365L probably damaging Het
Ankfy1 T A 11: 72,603,030 (GRCm39) Y20N probably damaging Het
Aqp11 C T 7: 97,387,068 (GRCm39) V43M probably benign Het
Arhgef10l A T 4: 140,279,843 (GRCm39) L503Q probably damaging Het
Arhgef28 A T 13: 98,093,150 (GRCm39) I977N possibly damaging Het
Cacna1b A G 2: 24,648,343 (GRCm39) Y161H probably damaging Het
Cacna1c T C 6: 118,579,198 (GRCm39) D1480G probably damaging Het
Clk3 A G 9: 57,659,449 (GRCm39) M533T probably damaging Het
Cnbd1 A G 4: 18,860,504 (GRCm39) I414T possibly damaging Het
Commd3 A T 2: 18,679,514 (GRCm39) probably null Het
Crybg1 G T 10: 43,873,902 (GRCm39) Q1069K probably damaging Het
Dnah8 T A 17: 30,984,685 (GRCm39) F3128I probably damaging Het
Dock1 A G 7: 134,379,224 (GRCm39) probably null Het
Dpysl3 C T 18: 43,466,941 (GRCm39) probably null Het
Ebf2 T A 14: 67,475,989 (GRCm39) probably benign Het
F830045P16Rik T C 2: 129,305,624 (GRCm39) E250G possibly damaging Het
Fbp2 A T 13: 63,001,862 (GRCm39) F118I probably damaging Het
Fetub T C 16: 22,747,836 (GRCm39) probably benign Het
Fmn2 A T 1: 174,436,015 (GRCm39) probably benign Het
Fryl T C 5: 73,179,621 (GRCm39) I2929V probably benign Het
Gm11232 T A 4: 71,675,112 (GRCm39) Q130L possibly damaging Het
Gm9637 G T 14: 19,402,570 (GRCm38) noncoding transcript Het
Gna15 A G 10: 81,348,239 (GRCm39) probably null Het
Gtf3c5 T C 2: 28,462,198 (GRCm39) probably benign Het
Irs2 G A 8: 11,055,723 (GRCm39) T903I possibly damaging Het
Itga2 G A 13: 115,007,032 (GRCm39) S432L possibly damaging Het
Izumo1 A G 7: 45,276,621 (GRCm39) T395A probably benign Het
Kcnd2 G A 6: 21,727,225 (GRCm39) V593M possibly damaging Het
Kprp T C 3: 92,731,989 (GRCm39) S354G probably damaging Het
Krt72 T C 15: 101,694,443 (GRCm39) K151E probably damaging Het
Letm2 A T 8: 26,077,464 (GRCm39) probably benign Het
Lipe A G 7: 25,097,874 (GRCm39) V23A possibly damaging Het
Mcc C G 18: 44,652,583 (GRCm39) probably benign Het
Mef2c A G 13: 83,800,992 (GRCm39) N231D possibly damaging Het
Mtdh T A 15: 34,134,426 (GRCm39) probably benign Het
Mthfd1 G A 12: 76,344,363 (GRCm39) probably benign Het
Nbeal1 C A 1: 60,286,876 (GRCm39) N899K probably benign Het
Noc3l T C 19: 38,803,253 (GRCm39) S129G probably benign Het
Odad2 T A 18: 7,129,593 (GRCm39) probably benign Het
Or10ak14 T C 4: 118,611,100 (GRCm39) I212V probably benign Het
Or2aj6 T C 16: 19,443,167 (GRCm39) M228V probably benign Het
Or4c118 T C 2: 88,974,966 (GRCm39) I134V possibly damaging Het
Or8b1c T A 9: 38,384,554 (GRCm39) D170E probably benign Het
Pik3r6 T A 11: 68,419,635 (GRCm39) Y149N probably damaging Het
Pja2 C A 17: 64,615,966 (GRCm39) V310L probably damaging Het
Plcd3 G A 11: 102,965,720 (GRCm39) A504V probably benign Het
Rint1 G A 5: 23,992,826 (GRCm39) probably benign Het
Ripor3 A G 2: 167,826,358 (GRCm39) probably benign Het
Rpa2 C A 4: 132,505,125 (GRCm39) N251K probably damaging Het
Rttn T C 18: 89,029,090 (GRCm39) probably null Het
Ryr2 C T 13: 11,884,002 (GRCm39) probably null Het
Scara3 T C 14: 66,168,417 (GRCm39) N400S probably damaging Het
Slc7a6 G T 8: 106,916,263 (GRCm39) V180L possibly damaging Het
Slc7a6 T A 8: 106,916,264 (GRCm39) V180E probably damaging Het
Slc8b1 T A 5: 120,659,928 (GRCm39) probably null Het
Slco1a4 G A 6: 141,765,205 (GRCm39) Q346* probably null Het
Stk32b A G 5: 37,618,792 (GRCm39) S229P probably damaging Het
Syde2 A G 3: 145,704,508 (GRCm39) R487G probably benign Het
Tbc1d2b T C 9: 90,104,355 (GRCm39) probably benign Het
Ticrr T C 7: 79,317,654 (GRCm39) V396A probably benign Het
Trrap T C 5: 144,719,003 (GRCm39) probably benign Het
Vmn1r124 A T 7: 20,993,743 (GRCm39) I267K probably benign Het
Vps13a A T 19: 16,646,054 (GRCm39) H1994Q probably damaging Het
Wdr36 T G 18: 32,997,802 (GRCm39) V820G possibly damaging Het
Wdr83 G A 8: 85,806,456 (GRCm39) T114I possibly damaging Het
Zc3h7a T C 16: 10,957,011 (GRCm39) N866S probably damaging Het
Zfc3h1 A G 10: 115,252,658 (GRCm39) K1324E 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
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
R9102:Dnmt3b UTSW 2 153,518,703 (GRCm39) missense probably damaging 0.98
R9228:Dnmt3b UTSW 2 153,507,980 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- ATGGTCCCCTGCTAAAGATGCAGC -3'
(R):5'- GACAACAGTACCTTCCAGATTGCCC -3'

Sequencing Primer
(F):5'- ATCTGCTTCCCTTGCAGAGAAC -3'
(R):5'- TGGTGACTTCAGAAGCCATCC -3'
Posted On 2013-06-11