Incidental Mutation 'R6818:Dnmt3b'
ID 537411
Institutional Source Beutler Lab
Gene Symbol Dnmt3b
Ensembl Gene ENSMUSG00000027478
Gene Name DNA methyltransferase 3B
Synonyms
MMRRC Submission 044930-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6818 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 153491370-153529650 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 153528204 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Methionine at position 822 (T822M)
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 damaging
Transcript: ENSMUST00000056495
AA Change: T823M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: T823M

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: T822M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: T822M

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 damaging
Transcript: ENSMUST00000081628
AA Change: T802M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: T802M

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: ENSMUST00000088976
AA Change: T759M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: T759M

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 damaging
Transcript: ENSMUST00000103150
AA Change: T739M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: T739M

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 damaging
Transcript: ENSMUST00000103151
AA Change: T739M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: T739M

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 damaging
Transcript: ENSMUST00000109771
AA Change: T823M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: T823M

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: ENSMUST00000109772
AA Change: T759M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: T759M

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 damaging
Transcript: ENSMUST00000109773
AA Change: T802M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: T802M

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: T822M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: T822M

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.6%
Validation Efficiency 97% (59/61)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 T A 12: 118,865,089 (GRCm39) probably null Het
Acot4 A C 12: 84,088,783 (GRCm39) E210D probably damaging Het
Adamts9 A C 6: 92,882,172 (GRCm39) S476A probably damaging Het
Ajm1 C CTCTA 2: 25,469,733 (GRCm39) probably null Het
Ak1 T A 2: 32,520,385 (GRCm39) M61K probably damaging Het
Ambp G T 4: 63,072,243 (GRCm39) S17* probably null Het
Anxa6 T A 11: 54,870,326 (GRCm39) M662L probably benign Het
Atp11b T C 3: 35,868,329 (GRCm39) I467T possibly damaging Het
B3gat1 G T 9: 26,662,998 (GRCm39) probably benign Het
Bccip T G 7: 133,319,488 (GRCm39) I193S probably damaging Het
Ccdc170 A G 10: 4,491,782 (GRCm39) E401G probably damaging Het
Cldn16 A G 16: 26,296,257 (GRCm39) T78A probably damaging Het
Cldn24 G T 8: 48,275,757 (GRCm39) A194S probably benign Het
Cltc A G 11: 86,595,054 (GRCm39) V1348A possibly damaging Het
Clvs1 T C 4: 9,282,014 (GRCm39) probably null Het
Csmd1 C T 8: 16,235,341 (GRCm39) D1161N probably damaging Het
Cuzd1 A G 7: 130,918,394 (GRCm39) V181A probably damaging Het
Dhx30 A G 9: 109,917,099 (GRCm39) I435T probably damaging Het
Dip2b T C 15: 100,091,835 (GRCm39) V858A probably benign Het
Dock10 A T 1: 80,593,082 (GRCm39) F97I possibly damaging Het
Dock8 T C 19: 25,146,865 (GRCm39) probably null Het
Dvl2 T C 11: 69,900,099 (GRCm39) L631P probably damaging Het
Faf2 T A 13: 54,789,419 (GRCm39) probably null Het
Fat2 T A 11: 55,200,167 (GRCm39) H969L probably benign Het
Fsip2 T A 2: 82,815,544 (GRCm39) V3759E probably benign Het
Gm10985 A C 3: 53,752,674 (GRCm39) Y19S probably damaging Het
Gm973 T C 1: 59,669,328 (GRCm39) L793P probably damaging Het
H2-M1 A G 17: 36,981,327 (GRCm39) I236T probably damaging Het
Hif1a A T 12: 73,992,337 (GRCm39) R765* probably null Het
Htt A G 5: 34,940,111 (GRCm39) K77E probably damaging Het
Ift172 G T 5: 31,423,304 (GRCm39) Q826K probably benign Het
Inafm1 C T 7: 16,007,086 (GRCm39) A44T probably damaging Het
Kctd4 A G 14: 76,200,748 (GRCm39) T240A probably damaging Het
Klk1 A T 7: 43,878,883 (GRCm39) I124F probably damaging Het
Krbox5 A G 13: 67,981,986 (GRCm39) Q66R possibly damaging Het
Kremen1 T C 11: 5,145,051 (GRCm39) T442A probably benign Het
Mei4 T A 9: 81,907,574 (GRCm39) D202E probably benign Het
Mest T A 6: 30,746,286 (GRCm39) D284E probably damaging Het
Nsfl1c T A 2: 151,344,940 (GRCm39) Y95* probably null Het
Or10al5 T A 17: 38,063,315 (GRCm39) V190D possibly damaging Het
Or10am5 T C 7: 6,517,550 (GRCm39) M293V probably damaging Het
Or2ak4 T A 11: 58,648,783 (GRCm39) C97* probably null Het
Or4k38 T G 2: 111,165,659 (GRCm39) I255L probably benign Het
Pgm1 T A 4: 99,820,763 (GRCm39) I220N probably damaging Het
Pirt T A 11: 66,816,719 (GRCm39) V10E possibly damaging Het
Prl7d1 C A 13: 27,898,454 (GRCm39) M19I probably benign Het
Samhd1 T C 2: 156,949,417 (GRCm39) N490D probably benign Het
Scn2a C A 2: 65,519,013 (GRCm39) S413* probably null Het
Serpinb6e A T 13: 34,016,337 (GRCm39) probably null Het
Slitrk5 A G 14: 111,917,726 (GRCm39) D450G probably benign Het
Tchh A G 3: 93,350,718 (GRCm39) T53A probably damaging Het
Tmem44 A T 16: 30,362,039 (GRCm39) probably null Het
Tpm3-rs7 A G 14: 113,552,448 (GRCm39) E114G possibly damaging Het
Treml2 A G 17: 48,609,925 (GRCm39) Y119C probably damaging Het
Ubxn1 T A 19: 8,851,245 (GRCm39) probably null Het
Vmn2r84 A T 10: 130,222,147 (GRCm39) M691K probably benign Het
Vmn2r97 A T 17: 19,168,193 (GRCm39) I816F possibly damaging Het
Was GCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC GCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC X: 7,952,450 (GRCm39) probably benign Het
Wfdc2 T C 2: 164,405,070 (GRCm39) probably null Het
Zscan4-ps3 T C 7: 11,346,986 (GRCm39) S341P 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
R6625:Dnmt3b UTSW 2 153,507,233 (GRCm39) missense probably benign
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'- AGTCCTGTCAGAAGGCATGG -3'
(R):5'- AGGTACAGTGATGTGAGGCC -3'

Sequencing Primer
(F):5'- CCTGTCAGAAGGCATGGGGAAG -3'
(R):5'- ACAGGTGAGGTGCCTTCAG -3'
Posted On 2018-10-18