DNMT3B DNA methyltransferase 3 beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: DNMT3Bprovided by HGNC
Official Full Name: DNA methyltransferase 3 betaprovided by HGNC
Primary source: HGNC:HGNC:2979
See related: Ensembl:ENSG00000088305 MIM:602900; AllianceGenome:HGNC:2979
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ICF; ICF1; FSHD4; M.HsaIIIB
Summary: 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]
Expression: Broad expression in testis (RPKM 3.4), skin (RPKM 1.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q11.21

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (32762385..32809356)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (34489113..34536082)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (31350191..31397162)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SOX7 inhibits the malignant progression of bladder cancer via the DNMT3B/CYGB axis.
Title: SOX7 inhibits the malignant progression of bladder cancer via the DNMT3B/CYGB axis.
Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B.
Title: Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B.
DNA methylation of miR-181a-5p mediated by DNMT3b drives renal interstitial fibrosis developed from acute kidney injury.
Title: DNA methylation of miR-181a-5p mediated by DNMT3b drives renal interstitial fibrosis developed from acute kidney injury.
DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis.
Title: DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis.
Inhibiting DNA methyltransferase DNMT3B confers protection against ferroptosis in nucleus pulposus and ameliorates intervertebral disc degeneration via upregulating SLC40A1.
Title: Inhibiting DNA methyltransferase DNMT3B confers protection against ferroptosis in nucleus pulposus and ameliorates intervertebral disc degeneration via upregulating SLC40A1.
An updated meta-analysis investigating the association between DNMTs gene polymorphism andgastric cancer risk.
Title: An updated meta-analysis investigating the association between DNMTs gene polymorphism andgastric cancer risk.
The interaction of RELN-DNMT genes involving in neurotrophin signaling pathway contributes to schizophrenia susceptibility.
Title: The interaction of RELN-DNMT genes involving in neurotrophin signaling pathway contributes to schizophrenia susceptibility.
Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization.
Title: Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization.
ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming.
Title: ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming.
Structural basis for the allosteric regulation and dynamic assembly of DNMT3B.
Title: Structural basis for the allosteric regulation and dynamic assembly of DNMT3B.

Submit: New GeneRIF Correction See all GeneRIFs (399)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Facioscapulohumeral muscular dystrophy 4, digenic MedGen: C5561960 OMIM: 619478 GeneReviews: Not available	not available
Immunodeficiency-centromeric instability-facial anomalies syndrome 1 MedGen: C4551557 OMIM: 242860 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association study of inattention and hyperactivity-impulsivity measured as quantitative traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat upregulates DNMT1, DNMT3A, and DNMT3B both at the mRNA and protein levels in primary tumors	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA (cytosine-5-)-methyltransferase activity	NAS Non-traceable Author Statement more info	PubMed
enables DNA (cytosine-5-)-methyltransferase activity	TAS Traceable Author Statement more info	PubMed
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-methyltransferase activity	NAS Non-traceable Author Statement more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of catalytic complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: DNA (cytosine-5)-methyltransferase 3B

Names: DNA (cytosine-5-)-methyltransferase 3 beta; DNA MTase HsaIIIB; DNA cytosine-5--methyltransferase 3 beta; DNA methyltransferase HsaIIIB

NP_001193984.1

EC 2.1.1.37

NP_001193985.1

EC 2.1.1.37

NP_001411280.1

EC 2.1.1.37

NP_001411281.1

EC 2.1.1.37

NP_001411282.1

EC 2.1.1.37

NP_001411283.1

EC 2.1.1.37

NP_001411284.1

EC 2.1.1.37

NP_001411285.1

EC 2.1.1.37

NP_001411286.1

EC 2.1.1.37

NP_001411287.1

EC 2.1.1.37

NP_001411288.1

EC 2.1.1.37

NP_001411289.1

EC 2.1.1.37

NP_008823.1

EC 2.1.1.37

NP_787044.1

EC 2.1.1.37

NP_787045.1

EC 2.1.1.37

NP_787046.1

EC 2.1.1.37

XP_047295902.1

EC 2.1.1.37

XP_047295905.1

EC 2.1.1.37

XP_047295906.1

EC 2.1.1.37

XP_047295911.1

EC 2.1.1.37

XP_047295912.1

EC 2.1.1.37

XP_047295915.1

EC 2.1.1.37

XP_047295916.1

EC 2.1.1.37

XP_054179091.1

EC 2.1.1.37

XP_054179094.1

EC 2.1.1.37

XP_054179095.1

EC 2.1.1.37

XP_054179101.1

EC 2.1.1.37

XP_054179102.1

EC 2.1.1.37

XP_054179106.1

EC 2.1.1.37

XP_054179107.1

EC 2.1.1.37

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007290.1 RefSeqGene

Range

5001..51972

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_56

mRNA and Protein(s)

NM_001207055.2 → NP_001193984.1 DNA (cytosine-5)-methyltransferase 3B isoform 7

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks several in-frame exons compared to variant 1. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AF156487, AF176228, AF331857, AK299915

Consensus CDS

CCDS56183.1

UniProtKB/TrEMBL

A0A2Z2CIT2

Related

ENSP00000403169.2, ENST00000443239.7

Conserved Domains (3) summary

cd05835
Location:181 → 267

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

COG0270
Location:512 → 674

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd11728
Location:369 → 488

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
NM_001207056.2 → NP_001193985.1 DNA (cytosine-5)-methyltransferase 3B isoform 8

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks several in-frame exons compared to variant 1. The resulting isoform (8) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AF156487, AF176228, AF331857, AK299821, AK299915

Consensus CDS

CCDS56184.1

UniProtKB/TrEMBL

A0A2Z2CIT2

Related

ENSP00000412305.1, ENST00000456297.6

Conserved Domains (3) summary

cd05835
Location:147 → 233

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

COG0270
Location:478 → 640

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd11728
Location:335 → 454

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
NM_001424351.1 → NP_001411280.1 DNA (cytosine-5)-methyltransferase 3B isoform 9

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424352.1 → NP_001411281.1 DNA (cytosine-5)-methyltransferase 3B isoform 10

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424353.1 → NP_001411282.1 DNA (cytosine-5)-methyltransferase 3B isoform 11

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424354.1 → NP_001411283.1 DNA (cytosine-5)-methyltransferase 3B isoform 12

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424355.1 → NP_001411284.1 DNA (cytosine-5)-methyltransferase 3B isoform 13

Status: REVIEWED

Source sequence(s)

AL035071

UniProtKB/TrEMBL

A0A8Q3SIG2

Related

ENSP00000512498.1, ENST00000696232.1
NM_001424356.1 → NP_001411285.1 DNA (cytosine-5)-methyltransferase 3B isoform 14

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424357.1 → NP_001411286.1 DNA (cytosine-5)-methyltransferase 3B isoform 15

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424358.1 → NP_001411287.1 DNA (cytosine-5)-methyltransferase 3B isoform 16

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424359.1 → NP_001411288.1 DNA (cytosine-5)-methyltransferase 3B isoform 17

Status: REVIEWED

Source sequence(s)

AL035071
NM_001424360.1 → NP_001411289.1 DNA (cytosine-5)-methyltransferase 3B isoform 18

Status: REVIEWED

Source sequence(s)

AL035071
NM_006892.4 → NP_008823.1 DNA (cytosine-5)-methyltransferase 3B isoform 1

See identical proteins and their annotated locations for NP_008823.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AF156487, AF331857

Consensus CDS

CCDS13205.1

UniProtKB/Swiss-Prot

A2A2E2, B4DSM8, B4DSU1, E1P5M6, E1P5M7, E7EN63, E9PBF2, Q9UBC3, Q9UBD4, Q9UJQ5, Q9UKA6, Q9UNE5, Q9Y5R9, Q9Y5S0

UniProtKB/TrEMBL

A0A2Z2CIT2

Related

ENSP00000328547.2, ENST00000328111.6

Conserved Domains (3) summary

cd05835
Location:223 → 309

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

COG0270
Location:574 → 756

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd11728
Location:431 → 550

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
NM_175848.2 → NP_787044.1 DNA (cytosine-5)-methyltransferase 3B isoform 2

See identical proteins and their annotated locations for NP_787044.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. Isoform 2 is shorter than isoform 1.

Source sequence(s)

AF156487, AF176228, AF331857

Consensus CDS

CCDS13206.1

UniProtKB/TrEMBL

A0A2Z2CIT2

Related

ENSP00000313397.4, ENST00000353855.6

Conserved Domains (3) summary

cd05835
Location:223 → 309

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

cd11728
Location:411 → 530

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

cl30459
Location:554 → 736

Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
NM_175849.2 → NP_787045.1 DNA (cytosine-5)-methyltransferase 3B isoform 3

See identical proteins and their annotated locations for NP_787045.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks three exons in the coding region but maintains the reading frame, compared to variant 1. Isoform 3 is shorter than isoform 1.

Source sequence(s)

AF156487, AF176228, AF331857

Consensus CDS

CCDS13207.1

UniProtKB/TrEMBL

A0A2Z2CIT2

Related

ENSP00000337764.2, ENST00000348286.6

Conserved Domains (3) summary

cd05835
Location:223 → 309

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

cd11728
Location:411 → 530

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

cl30459
Location:554 → 716

Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
NM_175850.3 → NP_787046.1 DNA (cytosine-5)-methyltransferase 3B isoform 6

See identical proteins and their annotated locations for NP_787046.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate exon in the 5' UTR and coding region that introduces an upstream start codon, compared to variant 1. Variant 6 also lacks an in-frame exon in the coding region, compared to variant 1. Isoform 6 is shorter and has a unique N-terminus, compared to isoform 1.

Source sequence(s)

AF156487, AF176228, AF331857

Consensus CDS

CCDS13204.1

UniProtKB/TrEMBL

A0A2Z2CIT2

Related

ENSP00000201963.3, ENST00000201963.3

Conserved Domains (3) summary

cd05835
Location:235 → 321

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

COG0270
Location:566 → 748

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd11728
Location:423 → 542

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

32762385..32809356

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439946.1 → XP_047295902.1 DNA (cytosine-5)-methyltransferase 3B isoform X1
XM_047439949.1 → XP_047295905.1 DNA (cytosine-5)-methyltransferase 3B isoform X4
XM_047439956.1 → XP_047295912.1 DNA (cytosine-5)-methyltransferase 3B isoform X12
XM_047439950.1 → XP_047295906.1 DNA (cytosine-5)-methyltransferase 3B isoform X5
XM_047439955.1 → XP_047295911.1 DNA (cytosine-5)-methyltransferase 3B isoform X11
XM_047439959.1 → XP_047295915.1 DNA (cytosine-5)-methyltransferase 3B isoform X16
XM_047439960.1 → XP_047295916.1 DNA (cytosine-5)-methyltransferase 3B isoform X17

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

34489113..34536082

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054323116.1 → XP_054179091.1 DNA (cytosine-5)-methyltransferase 3B isoform X1
XM_054323119.1 → XP_054179094.1 DNA (cytosine-5)-methyltransferase 3B isoform X4
XM_054323127.1 → XP_054179102.1 DNA (cytosine-5)-methyltransferase 3B isoform X12
XM_054323120.1 → XP_054179095.1 DNA (cytosine-5)-methyltransferase 3B isoform X5
XM_054323126.1 → XP_054179101.1 DNA (cytosine-5)-methyltransferase 3B isoform X11
XM_054323131.1 → XP_054179106.1 DNA (cytosine-5)-methyltransferase 3B isoform X16
XM_054323132.1 → XP_054179107.1 DNA (cytosine-5)-methyltransferase 3B isoform X17