Incidental Mutation 'IGL02884:Dnmt3b'
ID362916
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Dnmt3b
Ensembl Gene ENSMUSG00000027478
Gene NameDNA methyltransferase 3B
Synonyms
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL02884
Quality Score
Status
Chromosome2
Chromosomal Location153649450-153687730 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to C at 153674377 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Serine at position 474 (Y474S)
Ref Sequence ENSEMBL: ENSMUSP00000105396 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056495] [ENSMUST00000072997] [ENSMUST00000081628] [ENSMUST00000088976] [ENSMUST00000103150] [ENSMUST00000103151] [ENSMUST00000109771] [ENSMUST00000109772] [ENSMUST00000109773] [ENSMUST00000109774]
Predicted Effect probably damaging
Transcript: ENSMUST00000056495
AA Change: Y474S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000051830
Gene: ENSMUSG00000027478
AA Change: Y474S

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: Y474S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000072761
Gene: ENSMUSG00000027478
AA Change: Y474S

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: Y454S

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000080334
Gene: ENSMUSG00000027478
AA Change: Y454S

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: Y474S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000086370
Gene: ENSMUSG00000027478
AA Change: Y474S

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: Y454S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099439
Gene: ENSMUSG00000027478
AA Change: Y454S

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: Y454S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099440
Gene: ENSMUSG00000027478
AA Change: Y454S

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: Y474S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000105393
Gene: ENSMUSG00000027478
AA Change: Y474S

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: Y474S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105394
Gene: ENSMUSG00000027478
AA Change: Y474S

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: Y454S

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000105395
Gene: ENSMUSG00000027478
AA Change: Y454S

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: Y474S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105396
Gene: ENSMUSG00000027478
AA Change: Y474S

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: ENSMUST00000140811
Coding Region Coverage
Validation Efficiency
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930438A08Rik A G 11: 58,287,476 I121V probably benign Het
Adprh C T 16: 38,446,034 V249I probably benign Het
Akap11 A T 14: 78,498,962 M1797K probably benign Het
Akap6 T A 12: 52,886,622 I299N probably benign Het
Akr1c12 A T 13: 4,272,212 M277K possibly damaging Het
Ankrd17 A T 5: 90,264,757 M1236K probably damaging Het
Arhgef11 A G 3: 87,728,006 D874G probably damaging Het
Atg4b T C 1: 93,787,715 probably benign Het
Bcl9 G A 3: 97,210,052 P442L probably damaging Het
Ccdc107 A T 4: 43,495,228 K98* probably null Het
Ccdc129 T C 6: 55,874,354 probably null Het
Cenpl A G 1: 161,086,049 Q343R probably benign Het
Cep104 T C 4: 153,989,862 C524R probably damaging Het
Clec3b C T 9: 123,156,762 T75I probably benign Het
Col13a1 A T 10: 61,905,285 probably benign Het
Crot C T 5: 8,978,197 probably null Het
Ddo G A 10: 40,637,364 V101I probably benign Het
Disp2 T C 2: 118,787,551 probably benign Het
Dpp6 T A 5: 27,634,556 N298K possibly damaging Het
Fbf1 C T 11: 116,146,513 E940K probably damaging Het
Fgd6 A G 10: 94,045,639 probably benign Het
H2-M10.2 T C 17: 36,284,676 R241G probably damaging Het
Haghl A T 17: 25,783,098 F207Y possibly damaging Het
Helt G A 8: 46,292,583 R88C probably damaging Het
Igf2bp2 T C 16: 22,162,885 K27E probably benign Het
Il1b T C 2: 129,365,102 H246R probably benign Het
Kcnu1 C T 8: 25,921,528 S167L probably damaging Het
Kif16b A T 2: 142,702,614 probably benign Het
Myh7 A T 14: 54,992,819 S19T probably benign Het
Ncaph2 T C 15: 89,364,244 probably null Het
Nlrp4c T C 7: 6,098,952 L879P probably damaging Het
Nqo2 T A 13: 33,972,361 N19K probably damaging Het
Olfr456 C T 6: 42,486,606 V196M probably damaging Het
Osbpl1a C A 18: 12,819,578 G93* probably null Het
Pdxdc1 A G 16: 13,843,795 F459L possibly damaging Het
Phc2 A T 4: 128,708,016 H88L probably damaging Het
Pkd1l2 G A 8: 117,065,745 T436I probably benign Het
Ptchd4 A T 17: 42,502,449 T414S possibly damaging Het
Rab7b A G 1: 131,698,542 R103G probably damaging Het
Retnla A G 16: 48,842,580 Y3C probably benign Het
Samd7 G A 3: 30,756,173 R113H probably damaging Het
Shisa9 G A 16: 11,997,043 probably benign Het
Soat1 A T 1: 156,441,356 I208N possibly damaging Het
Stab1 C A 14: 31,150,143 probably null Het
Tti2 C T 8: 31,151,477 L210F possibly damaging Het
Ube2v2 A G 16: 15,556,485 V77A probably benign Het
Ubr5 T C 15: 37,998,376 E1617G probably damaging Het
Vmn2r16 T A 5: 109,360,891 I495K possibly damaging Het
Vwce G T 19: 10,646,579 R278L possibly damaging Het
Wdr26 C T 1: 181,182,784 A551T probably damaging Het
Wee1 A G 7: 110,126,062 I304V probably benign Het
Xrcc5 C T 1: 72,346,237 H496Y possibly damaging Het
Zfp142 G T 1: 74,571,983 S884R probably damaging Het
Other mutations in Dnmt3b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00793:Dnmt3b APN 2 153672502 missense possibly damaging 0.88
IGL00931:Dnmt3b APN 2 153686250 splice site probably benign
IGL01073:Dnmt3b APN 2 153670842 splice site probably benign
IGL01138:Dnmt3b APN 2 153661441 missense probably benign 0.01
IGL01960:Dnmt3b APN 2 153676711 missense possibly damaging 0.83
IGL03382:Dnmt3b APN 2 153686359 missense probably damaging 1.00
PIT4151001:Dnmt3b UTSW 2 153684479 critical splice donor site probably null
R0062:Dnmt3b UTSW 2 153672272 missense probably benign 0.01
R0122:Dnmt3b UTSW 2 153676698 missense probably damaging 1.00
R0147:Dnmt3b UTSW 2 153661457 missense possibly damaging 0.68
R0178:Dnmt3b UTSW 2 153675018 missense probably benign 0.41
R0751:Dnmt3b UTSW 2 153674842 intron probably null
R1696:Dnmt3b UTSW 2 153676710 nonsense probably null
R1795:Dnmt3b UTSW 2 153683639 missense possibly damaging 0.92
R1889:Dnmt3b UTSW 2 153676759 missense probably benign
R2898:Dnmt3b UTSW 2 153667630 missense possibly damaging 0.85
R4201:Dnmt3b UTSW 2 153670417 nonsense probably null
R4630:Dnmt3b UTSW 2 153670315 nonsense probably null
R4870:Dnmt3b UTSW 2 153670364 missense probably benign 0.01
R5648:Dnmt3b UTSW 2 153677198 missense probably damaging 1.00
R5814:Dnmt3b UTSW 2 153672497 missense probably benign 0.00
R6311:Dnmt3b UTSW 2 153674005 missense probably damaging 1.00
R6625:Dnmt3b UTSW 2 153665313 missense probably benign
R6818:Dnmt3b UTSW 2 153686284 missense probably damaging 1.00
Posted On2015-12-18