• Gene id: 1789

Gene Summary

• Gene Symbol: DNMT3B   Gene   UCSC   Ensembl
• Aliases: ICF, ICF1, M.HsaIIIB
• Gene name: DNA methyltransferase 3 beta
• Alternate names: DNA (cytosine-5)-methyltransferase 3B, DNA (cytosine-5-)-methyltransferase 3 beta, DNA MTase HsaIIIB, DNA cytosine-5--methyltransferase 3 beta, DNA methyltransferase HsaIIIB,
• Gene location: 20q11.21 (32762384: 32809355)     Exons: 24     NC_000020.11
• Gene summary(Entrez): CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA met
• OMIM: 602900

SNPs

rs2424909

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000020.11   g.32774055T>C
NC_000020.10   g.31361861T>C
NG_007290.1   g.16671T>C|SEQ=[T/C]|GENE=DNMT3B

Protein Summary

• Protein general information: Q9UBC3  
  • Name: DNA (cytosine 5) methyltransferase 3B (Dnmt3b) (EC 2.1.1.37) (DNA methyltransferase HsaIIIB) (DNA MTase HsaIIIB) (M.HsaIIIB)
  • Length: 853  
  • Mass: 95,751
• Sequence:

  MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGD
  GEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRA
  TASAGTPWPSPPSSYLTIDLTDDTEDTHGTPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGI
  GDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK
  AMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKSKVRRAGSRKLESRKY
  ENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLF
  EGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCY
  MCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK
  YVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEF
  YHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASK
  NDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGA
  RQKLLGRSWSVPVIRHLFAPLKDYFACE

• Structural information:
  • Protein Domains: PWWP. (225-283)
    ADD. (423-555)
    SAM-dependent (575-853)
  • Interpro: IPR025766  IPR018117  IPR001525  IPR030488  IPR000313   IPR029063  IPR011011  
  • Prosite: PS51533 PS00094 PS50812 PS51679
  • CDD: cd11728
  • PDB: 3FLG 3QKJ 5CIU
  • PDBsum: 3FLG 3QKJ 5CIU
  • DIP: 30000
  • STRING: ENSP00000328547
• Other Databases: GeneCards:  DNMT3B  Malacards:  DNMT3B

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IDA	biological process
GO:0001666	response to hypoxia	IEA	biological process
GO:0003682	chromatin binding	IEA	molecular function
GO:0003714	transcription corepressor activity	IDA	molecular function
GO:0003714	transcription corepressor activity	IMP	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	TAS	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	NAS	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	IDA	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005634	nucleus	IDA	cellular component
GO:0005654	nucleoplasm	IDA	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005737	cytoplasm	IEA	cellular component
GO:0006306	DNA methylation	TAS	biological process
GO:0006306	DNA methylation	NAS	biological process
GO:0006306	DNA methylation	NAS	biological process
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	TAS	molecular function
GO:0009636	response to toxic substance	IEA	biological process
GO:0010212	response to ionizing radiation	IEA	biological process
GO:0010424	DNA methylation on cytosine within a CG sequence	IEA	biological process
GO:0010628	positive regulation of gene expression	IMP	biological process
GO:0014823	response to activity	IEA	biological process
GO:0031000	response to caffeine	IEA	biological process
GO:0032355	response to estradiol	IEA	biological process
GO:0033189	response to vitamin A	IEA	biological process
GO:0042220	response to cocaine	IEA	biological process
GO:0042493	response to drug	IEA	biological process
GO:0042826	histone deacetylase binding	IEA	molecular function
GO:0043231	intracellular membrane-bounded organelle	IDA	cellular component
GO:0045322	unmethylated CpG binding	IEA	molecular function
GO:0045666	positive regulation of neuron differentiation	IEA	biological process
GO:0045814	negative regulation of gene expression, epigenetic	TAS	biological process
GO:0046498	S-adenosylhomocysteine metabolic process	IEA	biological process
GO:0046499	S-adenosylmethioninamine metabolic process	IEA	biological process
GO:0046872	metal ion binding	IEA	molecular function
GO:0051571	positive regulation of histone H3-K4 methylation	IMP	biological process
GO:0051573	negative regulation of histone H3-K9 methylation	IMP	biological process
GO:0051718	DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IEA	molecular function
GO:0071455	cellular response to hyperoxia	IEA	biological process
GO:0071549	cellular response to dexamethasone stimulus	IEA	biological process
GO:0090116	C-5 methylation of cytosine	IEA	biological process
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IDA	biological process
GO:0001666	response to hypoxia	IEA	biological process
GO:0003677	DNA binding	IEA	molecular function
GO:0003677	DNA binding	IEA	molecular function
GO:0003682	chromatin binding	IEA	molecular function
GO:0003714	transcription corepressor activity	IDA	molecular function
GO:0003714	transcription corepressor activity	IMP	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	IEA	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	TAS	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	NAS	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	IDA	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005634	nucleus	IEA	cellular component
GO:0005634	nucleus	IEA	cellular component
GO:0005634	nucleus	IEA	cellular component
GO:0005634	nucleus	TAS	cellular component
GO:0005634	nucleus	IDA	cellular component
GO:0005654	nucleoplasm	IDA	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005737	cytoplasm	IEA	cellular component
GO:0006306	DNA methylation	IEA	biological process
GO:0006306	DNA methylation	TAS	biological process
GO:0006306	DNA methylation	NAS	biological process
GO:0006306	DNA methylation	NAS	biological process
GO:0008168	methyltransferase activity	IEA	molecular function
GO:0008168	methyltransferase activity	IEA	molecular function
GO:0009008	DNA-methyltransferase activity	IEA	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	TAS	molecular function
GO:0009636	response to toxic substance	IEA	biological process
GO:0010212	response to ionizing radiation	IEA	biological process
GO:0010424	DNA methylation on cytosine within a CG sequence	IEA	biological process
GO:0010468	regulation of gene expression	IEA	biological process
GO:0010628	positive regulation of gene expression	IMP	biological process
GO:0014823	response to activity	IEA	biological process
GO:0016740	transferase activity	IEA	molecular function
GO:0031000	response to caffeine	IEA	biological process
GO:0032259	methylation	IEA	biological process
GO:0032355	response to estradiol	IEA	biological process
GO:0033189	response to vitamin A	IEA	biological process
GO:0042220	response to cocaine	IEA	biological process
GO:0042493	response to drug	IEA	biological process
GO:0042826	histone deacetylase binding	IEA	molecular function
GO:0043231	intracellular membrane-bounded organelle	IDA	cellular component
GO:0045322	unmethylated CpG binding	IEA	molecular function
GO:0045666	positive regulation of neuron differentiation	IEA	biological process
GO:0045814	negative regulation of gene expression, epigenetic	TAS	biological process
GO:0045892	negative regulation of transcription, DNA-templated	IEA	biological process
GO:0046498	S-adenosylhomocysteine metabolic process	IEA	biological process
GO:0046499	S-adenosylmethioninamine metabolic process	IEA	biological process
GO:0046872	metal ion binding	IEA	molecular function
GO:0051571	positive regulation of histone H3-K4 methylation	IMP	biological process
GO:0051573	negative regulation of histone H3-K9 methylation	IMP	biological process
GO:0051718	DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IEA	molecular function
GO:0071455	cellular response to hyperoxia	IEA	biological process
GO:0071549	cellular response to dexamethasone stimulus	IEA	biological process
GO:0090116	C-5 methylation of cytosine	IEA	biological process
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IDA	biological process
GO:0003714	transcription corepressor activity	IDA	molecular function
GO:0003714	transcription corepressor activity	IMP	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	TAS	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	NAS	molecular function
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	IDA	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005634	nucleus	TAS	cellular component
GO:0005634	nucleus	IDA	cellular component
GO:0005654	nucleoplasm	IDA	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0006306	DNA methylation	TAS	biological process
GO:0006306	DNA methylation	NAS	biological process
GO:0006306	DNA methylation	NAS	biological process
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	NAS	molecular function
GO:0009008	DNA-methyltransferase activity	TAS	molecular function
GO:0010628	positive regulation of gene expression	IMP	biological process
GO:0043231	intracellular membrane-bounded organelle	IDA	cellular component
GO:0045814	negative regulation of gene expression, epigenetic	TAS	biological process
GO:0051571	positive regulation of histone H3-K4 methylation	IMP	biological process
GO:0051573	negative regulation of histone H3-K9 methylation	IMP	biological process

KEGG pathways

Pathway id	Pathway name
hsa01100	Metabolic pathways
hsa05206	MicroRNAs in cancer

Diseases

Associated diseases	References
Cancer	GAD: 16211278
Cancer (colorectal)	GAD: 17318376
Cancer (gastric)	GAD: 19517237
Cancer (head and neck)	GAD: 20819778
Cancer (Hepatocellular)	GAD: 19465161
Cancer (leukemia)	GAD: 16194411
Cancer (lung)	GAD: 12208751
Cancer (Adenoma)	GAD: 18268116
Cancer (esophageal)	GAD: 18407600
Cancer (prostate)	GAD: 16012746
Cancer (Squamous cell)	GAD: 18455294
Cancer (stomach)	GAD: 16211278
Cancer (breast)	GAD: 15217506
Cancer (epithelial ovarian)	GAD: 19064572
Rheumatoid arthritis	GAD: 19777235
Other humoral immunodeficiencies	KEGG: H00087
Schizophrenia	GAD: 19576953
Non obstructive azoospermia	MIK: 25739334
Male factor infertility	MIK: 17277043
Spermatogenesis defects	MIK: 21482616
Male factor infertility	MIK: 21482616
Endometriosis	INFBASE: 23888948
Aberrant CpGs in Low Motility Sperm	MIK: 21674046
Associated with spermatogenesis and epigenetic regulation	MIK: 21674046
Cryptorchidism	MIK: 28606200
Non obstructive azoospermia	MIK: 31479588
Non-obstructive azoospermia	MIK: 25739334
Non-obstructive infertility	MIK: 17277043
Spermatogenic arrest	MIK: 21482616
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
25739334	Non-obstructive azoospermia			1466 (757 NOA patients, 709 fertile males)	Male infertility	BRWD1 DNMT1 DNMT3B RNF17 UBR2 USP1 USP26 BRDT and MTHFR
17277043	Non-obstructive infertility	MTHFR (C677T and A1298C) and DNMT3b (C46359T)	Indian	379 (179 oligoasthenoteratozoospermia patients, 200 fertile men)	Male infertility	MTHFR DNMT3b and GSTM1
21482616	Spermatogenic arrest			27 (16 fertile controls having normal spermatogenesis, 11 patients with bilateral spermatogenic arrest)	Male infertility
31479588	Non obstructive azoospermia	c.2452G>A p.(Val818Met)	Brazil, South America n	21 non-obstructive azoospermia	Male infertility	NGS
17327269	Teratozoospermia			13 (5 controls, 8 cases)	Male infertility	GSE6967 analyzed by GEO2R (cutoff 1.5 fold)
21674046	Aberrant CpGs in Low Motility Sperm			18	Male infertility	GSE26881
28606200	Cryptorchidism			Monozgotic twins (1 control, I cwith cryptorchidism)	Male infertility	MeDIP-Seq