Incidental Mutation 'R6625:Dnmt3b'
ID 524709
Institutional Source Beutler Lab
Gene Symbol Dnmt3b
Ensembl Gene ENSMUSG00000027478
Gene Name DNA methyltransferase 3B
Synonyms
MMRRC Submission 044747-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6625 (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 153507233 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 139 (I139T)
Ref Sequence ENSEMBL: ENSMUSP00000105396 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056495] [ENSMUST00000072997] [ENSMUST00000081628] [ENSMUST00000088976] [ENSMUST00000103150] [ENSMUST00000103151] [ENSMUST00000109771] [ENSMUST00000109772] [ENSMUST00000109773] [ENSMUST00000109774]
AlphaFold O88509
Predicted Effect probably benign
Transcript: ENSMUST00000056495
AA Change: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: I139T

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: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: I139T

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: ENSMUST00000109773
AA Change: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: I139T

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: ENSMUST00000109774
AA Change: I139T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: I139T

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 noncoding transcript
Transcript: ENSMUST00000132132
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140811
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.4%
  • 20x: 91.6%
Validation Efficiency 91% (30/33)
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap9 C G 5: 4,018,745 (GRCm39) H1109D probably benign Het
Apcdd1 C A 18: 63,084,929 (GRCm39) D375E probably damaging Het
Cacna2d1 A T 5: 16,567,391 (GRCm39) R984W probably null Het
Csmd3 T G 15: 47,470,471 (GRCm39) I3402L probably benign Het
Dnah7a T A 1: 53,604,916 (GRCm39) T1281S probably benign Het
Dtnbp1 T C 13: 45,145,507 (GRCm39) E40G possibly damaging Het
Fam162b C T 10: 51,466,391 (GRCm39) G43R probably damaging Het
G2e3 T G 12: 51,400,572 (GRCm39) probably null Het
Kiss1r G A 10: 79,755,368 (GRCm39) V118I possibly damaging Het
Mre11a T C 9: 14,716,687 (GRCm39) M294T possibly damaging Het
Muc16 A T 9: 18,571,574 (GRCm39) V315D unknown Het
Nelfe C T 17: 35,073,334 (GRCm39) P290S probably benign Het
Or2v2 T A 11: 49,003,896 (GRCm39) Y219F probably damaging Het
Or5a3 T G 19: 12,400,205 (GRCm39) H177Q probably damaging Het
Pcolce2 T A 9: 95,560,492 (GRCm39) C180* probably null Het
Piezo2 A T 18: 63,154,333 (GRCm39) V2482D probably damaging Het
Plagl1 T C 10: 13,003,806 (GRCm39) probably benign Het
Pramel31 T A 4: 144,090,369 (GRCm39) Y470N probably damaging Het
Pramel57 C T 5: 95,669,342 (GRCm39) H124Y possibly damaging Het
Prss48 G T 3: 85,905,373 (GRCm39) Q167K probably benign Het
Saxo4 G A 19: 10,459,100 (GRCm39) P65L probably damaging Het
Scyl1 C A 19: 5,810,854 (GRCm39) V488F probably damaging Het
Sh3pxd2b T A 11: 32,372,594 (GRCm39) L587Q possibly damaging Het
Sim1 A G 10: 50,860,082 (GRCm39) D648G probably benign Het
Snupn G A 9: 56,890,054 (GRCm39) V292I probably benign Het
St6galnac1 T C 11: 116,656,717 (GRCm39) H474R probably damaging Het
Thap12 G A 7: 98,365,277 (GRCm39) V482I probably benign Het
Usp13 T A 3: 32,949,025 (GRCm39) V454D probably damaging Het
Usp40 T C 1: 87,894,935 (GRCm39) I862V probably benign Het
Vmn2r59 A T 7: 41,693,177 (GRCm39) F474L probably benign Het
Zbtb38 T C 9: 96,569,366 (GRCm39) R573G probably damaging Het
Zfp493 C T 13: 67,934,514 (GRCm39) Q156* probably null Het
Zfp873 C A 10: 81,896,138 (GRCm39) P290T probably damaging 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
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'- ATGACATCCAGTGGTCTTCTTC -3'
(R):5'- AGCTCCAAGTAGGACGACTC -3'

Sequencing Primer
(F):5'- CACTTCAGGTTGATTTGAGGCC -3'
(R):5'- TCCAAGTAGGACGACTCAGAACAG -3'
Posted On 2018-06-22