Incidental Mutation 'R4630:Dnmt3b'
ID 349096
Institutional Source Beutler Lab
Gene Symbol Dnmt3b
Ensembl Gene ENSMUSG00000027478
Gene Name DNA methyltransferase 3B
Synonyms
MMRRC Submission 041895-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4630 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 153491370-153529650 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 153512235 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Stop codon at position 319 (R319*)
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 null
Transcript: ENSMUST00000056495
AA Change: R319*
SMART Domains Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000072997
AA Change: R319*
SMART Domains Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000081628
AA Change: R319*
SMART Domains Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000088976
AA Change: R319*
SMART Domains Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000103150
AA Change: R319*
SMART Domains Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000103151
AA Change: R319*
SMART Domains Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000109771
AA Change: R319*
SMART Domains Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: R319*

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 noncoding transcript
Transcript: ENSMUST00000140811
Predicted Effect probably null
Transcript: ENSMUST00000109772
AA Change: R319*
SMART Domains Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000109773
AA Change: R319*
SMART Domains Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: R319*

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 null
Transcript: ENSMUST00000109774
AA Change: R319*
SMART Domains Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: R319*

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
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 97% (74/76)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3110070M22Rik A T 13: 119,624,622 (GRCm39) probably benign Het
Alkbh2 C T 5: 114,262,287 (GRCm39) E148K probably damaging Het
Aopep T C 13: 63,215,906 (GRCm39) S393P probably benign Het
BC024139 T G 15: 76,009,294 (GRCm39) Q240P probably benign Het
Bckdha A T 7: 25,330,884 (GRCm39) I44N probably damaging Het
Brpf1 T C 6: 113,286,867 (GRCm39) Y32H probably damaging Het
Catip A G 1: 74,408,072 (GRCm39) probably benign Het
Ccdc138 T C 10: 58,409,477 (GRCm39) L602P probably damaging Het
Cilp A T 9: 65,187,162 (GRCm39) T1086S probably benign Het
Comp A T 8: 70,827,032 (GRCm39) I58F possibly damaging Het
Crygs T C 16: 22,624,268 (GRCm39) E113G possibly damaging Het
Eif3a A G 19: 60,758,366 (GRCm39) I804T unknown Het
Eif3a A T 19: 60,766,424 (GRCm39) H301Q probably benign Het
Elf3 A T 1: 135,184,478 (GRCm39) probably benign Het
Fads2b C A 2: 85,348,990 (GRCm39) G41* probably null Het
Gm10384 A G 15: 36,872,017 (GRCm39) noncoding transcript Het
Gm11627 T A 11: 102,469,657 (GRCm39) probably benign Het
Gpr183 A T 14: 122,192,261 (GRCm39) Y87N probably damaging Het
Gpr183 G C 14: 122,192,262 (GRCm39) Y86* probably null Het
Gpr26 T C 7: 131,568,709 (GRCm39) V18A probably damaging Het
Herc1 T A 9: 66,340,996 (GRCm39) probably null Het
Hint2 C T 4: 43,656,396 (GRCm39) probably benign Het
Jag1 A T 2: 136,927,899 (GRCm39) D837E probably damaging Het
Jmjd1c C A 10: 66,993,753 (GRCm39) S78* probably null Het
Kcnd3 C T 3: 105,566,082 (GRCm39) A421V probably damaging Het
Krt1 C T 15: 101,754,622 (GRCm39) G543S unknown Het
Lalba T C 15: 98,380,549 (GRCm39) M2V probably benign Het
Lama1 T A 17: 68,101,295 (GRCm39) D1929E probably benign Het
Macf1 T C 4: 123,367,432 (GRCm39) K878R possibly damaging Het
Mboat4 T C 8: 34,591,108 (GRCm39) S182P probably damaging Het
Muc5b A T 7: 141,411,721 (GRCm39) T1556S unknown Het
Myo1g T C 11: 6,469,047 (GRCm39) Y85C probably damaging Het
Ncapd2 C A 6: 125,156,196 (GRCm39) probably null Het
Nox3 T C 17: 3,744,257 (GRCm39) D96G possibly damaging Het
Or10a48 T C 7: 108,424,802 (GRCm39) M135V probably damaging Het
Or1e17 T C 11: 73,831,822 (GRCm39) L250P probably damaging Het
Or6c212 A G 10: 129,559,350 (GRCm39) L21P probably damaging Het
Pacs1 C T 19: 5,206,384 (GRCm39) probably null Het
Pgap4 C G 4: 49,586,254 (GRCm39) V305L probably benign Het
Pgm5 C A 19: 24,812,110 (GRCm39) G141* probably null Het
Pik3r4 A G 9: 105,532,098 (GRCm39) M557V probably benign Het
Pld4 T A 12: 112,731,498 (GRCm39) V217D probably damaging Het
Pphln1-ps1 T C 16: 13,495,278 (GRCm39) S126P probably damaging Het
Ppp1r3c T C 19: 36,710,915 (GRCm39) E285G probably benign Het
Pradc1 T A 6: 85,424,275 (GRCm39) M24L possibly damaging Het
Prepl T C 17: 85,390,659 (GRCm39) T100A probably benign Het
Rmi2 C T 16: 10,704,073 (GRCm39) T138I probably benign Het
Rtkn A T 6: 83,129,163 (GRCm39) K540* probably null Het
Sag C A 1: 87,762,340 (GRCm39) T335K probably damaging Het
Setd4 A G 16: 93,388,114 (GRCm39) L124P probably benign Het
Sh3gl2 A G 4: 85,297,646 (GRCm39) D208G probably damaging Het
Sult4a1 T C 15: 83,989,779 (GRCm39) T8A possibly damaging Het
Tert A G 13: 73,797,110 (GRCm39) D1116G probably damaging Het
Tlr4 A G 4: 66,757,477 (GRCm39) E90G probably benign Het
Tmem123 T C 9: 7,791,393 (GRCm39) L164P probably damaging Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Trak1 G A 9: 121,283,491 (GRCm39) R419Q probably benign Het
Trp53bp1 G T 2: 121,038,368 (GRCm39) A1490D probably damaging Het
Ttc16 T C 2: 32,665,389 (GRCm39) probably benign Het
Tyw5 T A 1: 57,427,686 (GRCm39) Q306L probably damaging Het
Ube2j2 T A 4: 156,039,715 (GRCm39) I14N probably damaging Het
Vmn2r103 T C 17: 20,013,958 (GRCm39) I250T probably benign Het
Zar1 A G 5: 72,738,249 (GRCm39) V51A probably benign Het
Zbtb38 T G 9: 96,570,904 (GRCm39) N60T probably damaging Het
Zfp354a T C 11: 50,961,045 (GRCm39) S417P probably damaging Het
Zfp410 A T 12: 84,372,510 (GRCm39) D112V probably damaging Het
Zfp518a C T 19: 40,901,423 (GRCm39) Q451* probably null Het
Zfp64 T C 2: 168,768,463 (GRCm39) N383S possibly damaging Het
Zfp687 A T 3: 94,919,799 (GRCm39) probably null 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
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'- CATTGTCATACTACTAGAAAGGGCC -3'
(R):5'- GGGGCTATACCATCCACAAAGG -3'

Sequencing Primer
(F):5'- CTACTAGAAAGGGCCTTTTACAGAC -3'
(R):5'- AAGGCATAGGTTCATTCCCACCTG -3'
Posted On 2015-10-08