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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 methyltransferase which is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is developmentally regulated. Mutations in this gene cause the immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined. [provided by RefSeq, May 2011]
DNMT3B (DNA Methyltransferase 3 Beta) is a Protein Coding gene. Diseases associated with DNMT3B include Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome 1 and Spermatogenic Failure 3. Among its related pathways are One carbon pool by folate and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity and unmethylated CpG binding. An important paralog of this gene is DNMT3A.
Protein arginine methyltransferases are enyzmes that catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the arginine residues on histones and other proteins. The dysregulation of this methylation is critical in the development of certain cancers.
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0003677 | DNA binding | IEA | -- |
GO:0003682 | chromatin binding | IEA | -- |
GO:0003714 | transcription corepressor activity | IMP | 18567530 |
GO:0003886 | DNA (cytosine-5-)-methyltransferase activity | IDA,TAS | 10433969 |
GO:0005515 | protein binding | IPI | 11735126 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0005634 | nucleus | TAS,IDA | 17303076 |
GO:0005654 | nucleoplasm | TAS | -- |
SuperPathway | Contained pathways | ||
---|---|---|---|
1 | Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 |
.88
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2 | One carbon pool by folate |
Methionine metabolism
.34
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3 | Mesodermal Commitment Pathway | ||
4 | Chromatin Regulation / Acetylation | ||
5 | Sulfur amino acid metabolism |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000122 | negative regulation of transcription by RNA polymerase II | IDA | 17303076 |
GO:0001666 | response to hypoxia | IEA | -- |
GO:0006306 | DNA methylation | TAS | 10433969 |
GO:0009636 | response to toxic substance | IEA | -- |
GO:0010212 | response to ionizing radiation | IEA | -- |
Name | Status | Disease Links | Group | Role | Mechanism of Action | Clinical Trials |
---|---|---|---|---|---|---|
Thioguanine | Approved | Pharma | Purine antimetabolite | 89 | ||
Decitabine | Approved, Investigational | Pharma | DNA methyltransferase inhibitor | 388 | ||
Zebularine | Experimental | Pharma | DNA methylation inhibitor, DNA methyltransferase and cytidine deaminase inhibitor | 0 | ||
s-adenosylhomocysteine | Experimental | Pharma | 0 | |||
5-Azacytidine | Pharma | DNA methyltransferase inhibitor., DNA methyltransferase inhibitor | 0 |
Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
---|---|---|---|---|---|---|
5-methylcytosine |
|
554-01-8 | ||||
s-adenosylmethionine |
|
485-80-3 |
|
Compound | Action | Cas Number |
---|---|---|
5-Azacytidine | DNA methyltransferase inhibitor | 320-67-2 |
Decitabine | DNA methyltransferase inhibitor | 2353-33-5 |
Lomeguatrib | MGMT inhibitor | 192441-08-0 |
RG 108 | Non-nucleoside DNA methyltransferase inhibitor | 48208-26-0 |
Zebularine | DNA methyltransferase and cytidine deaminase inhibitor | 3690-10-6 |
Compound | Action | Cas Number |
---|---|---|
5-Azacytidine | DNA methyltransferase inhibitor. | 320-67-2 |
Decitabine (NSC127716, 5AZA-CdR) | Deoxycytidine analog and cellular diifferentiation inducer | 2353-33-5 |
Lomeguatrib | MGMT inhibitor | 192441-08-0 |
Nanaomycin A | DNMT3B inhibitor | 52934-83-5 |
RG 108 | DNA methyltransferase inhibitor | 48208-26-0 |
SGI-1027 | DNMT inhibitor | 1020149-73-8 |
Thioguanine | Purine antimetabolite | 154-42-7 |
Zebularine | DNA methylation inhibitor | 3690-10-6 |
ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5a | · | 5b | ^ | 6 | ^ | 7a | · | 7b | · | 7c | · | 7d | ^ | 8 | ^ | 9a | · | 9b | · | 9c | ^ | 10a | · | 10b | ^ | 11a | · | 11b | ^ | 12a | · | 12b | ^ | 13 | ^ | 14 | ^ | 15 | ^ | 16a | · |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SP1: | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||||||
SP2: | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||||
SP3: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP4: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP5: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
SP6: | - | |||||||||||||||||||||||||||||||||||||||||||||||||||
SP7: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP8: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP9: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP10: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP11: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP12: | - | |||||||||||||||||||||||||||||||||||||||||||||||||||
SP13: | - | |||||||||||||||||||||||||||||||||||||||||||||||||||
SP14: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
SP15: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP16: | - | |||||||||||||||||||||||||||||||||||||||||||||||||||
SP17: |
ExUns: | 16b | · | 16c | ^ | 17 | ^ | 18a | · | 18b | · | 18c | ^ | 19a | · | 19b | ^ | 20a | · | 20b | ^ | 21 | ^ | 22 | ^ | 23a | · | 23b | ^ | 24a | · | 24b | · | 24c |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SP1: | |||||||||||||||||||||||||||||||||
SP2: | |||||||||||||||||||||||||||||||||
SP3: | |||||||||||||||||||||||||||||||||
SP4: | - | ||||||||||||||||||||||||||||||||
SP5: | |||||||||||||||||||||||||||||||||
SP6: | |||||||||||||||||||||||||||||||||
SP7: | |||||||||||||||||||||||||||||||||
SP8: | |||||||||||||||||||||||||||||||||
SP9: | - | - | - | ||||||||||||||||||||||||||||||
SP10: | |||||||||||||||||||||||||||||||||
SP11: | |||||||||||||||||||||||||||||||||
SP12: | |||||||||||||||||||||||||||||||||
SP13: | |||||||||||||||||||||||||||||||||
SP14: | |||||||||||||||||||||||||||||||||
SP15: | |||||||||||||||||||||||||||||||||
SP16: | |||||||||||||||||||||||||||||||||
SP17: |
This gene was present in the common ancestor of chordates.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | DNMT3B 30 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | DNMT3B 31 |
|
OneToOne | |
LOC100848415 30 |
|
||||
Dog (Canis familiaris) |
Mammalia | DNMT3B 30 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Dnmt3b 30 |
|
||
Mouse (Mus musculus) |
Mammalia | Dnmt3b 30 17 31 |
|
OneToOne | |
Oppossum (Monodelphis domestica) |
Mammalia | DNMT3B 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | DNMT3B 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | DNMT3B 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | DNMT3B 31 |
|
OneToOne | |
Zebrafish (Danio rerio) |
Actinopterygii | dnmt4 30 31 |
|
ManyToMany | |
-- 30 |
|
||||
Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
OneToMany |
SNP ID | Clinical significance and condition | Chr 20 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
638956 | Uncertain Significance: Immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 32,795,503(+) | C/T | SYNONYMOUS_VARIANT | |
639128 | Uncertain Significance: Immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 32,798,560(+) | C/T | MISSENSE_VARIANT | |
639732 | Uncertain Significance: Immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 32,787,273(+) | C/A | MISSENSE_VARIANT | |
640645 | Uncertain Significance: Immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 32,798,567(+) | A/G | MISSENSE_VARIANT | |
640978 | Uncertain Significance: Immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 32,801,353(+) | C/T | MISSENSE_VARIANT |
Variant ID | Type | Subtype | PubMed ID |
---|---|---|---|
nsv1056411 | CNV | loss | 25217958 |
nsv1072112 | CNV | deletion | 25765185 |
nsv833956 | CNV | loss | 17160897 |
nsv833957 | CNV | gain+loss | 17160897 |
nsv979490 | CNV | duplication | 23825009 |
Disorder | Aliases | PubMed IDs |
---|---|---|
immunodeficiency-centromeric instability-facial anomalies syndrome 1 |
|
|
spermatogenic failure 3 |
|
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facioscapulohumeral muscular dystrophy 2 |
|
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immunodeficiency-centromeric instability-facial anomalies syndrome |
|
|
kabuki syndrome 1 |
|
|