MBD5 methyl-CpG binding domain protein 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: MBD5provided by HGNC
Official Full Name: methyl-CpG binding domain protein 5provided by HGNC
Primary source: HGNC:HGNC:20444
See related: Ensembl:ENSG00000204406 MIM:611472; AllianceGenome:HGNC:20444
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: MRD1; DEL2Q23.1; C2DELq23.1
Summary: This gene encodes a member of the methyl-CpG-binding domain (MBD) family. The MBD consists of about 70 residues and is the minimal region required for a methyl-CpG-binding protein binding specifically to methylated DNA. In addition to the MBD domain, this protein contains a PWWP domain (Pro-Trp-Trp-Pro motif), which consists of 100-150 amino acids and is found in numerous proteins that are involved in cell division, growth and differentiation. Mutations in this gene cause an autosomal dominant type of cognitive disability. The encoded protein interacts with the polycomb repressive complex PR-DUB which catalyzes the deubiquitination of a lysine residue of histone 2A. Haploinsufficiency of this gene is associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures. Alternatively spliced transcript variants have been found, but their full-length nature is not determined. [provided by RefSeq, Jul 2017]
Expression: Ubiquitous expression in brain (RPKM 2.6), gall bladder (RPKM 2.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q23.1

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (148020927..148516971)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (148471381..148967332)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (148778580..149274540)

Chromosome 2 - NC_000002.12 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
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?

Germline mosaicism in a family with MBD5 haploinsufficiency.
Title: Germline mosaicism in a family with MBD5 haploinsufficiency.
[Clinical phenotypes and genetic features of epilepsy children with MBD5 gene variants].
Title: [Clinical phenotypes and genetic features of epilepsy children with MBD5 gene variants].
Early-Onset Dementia Associated with a Heterozygous, Nonsense, and de novo Variant in the MBD5 Gene.
Title: Early-Onset Dementia Associated with a Heterozygous, Nonsense, and de novo Variant in the MBD5 Gene.
Long-read whole-genome sequencing identified a partial MBD5 deletion in an exome-negative patient with neurodevelopmental disorder.
Title: Long-read whole-genome sequencing identified a partial MBD5 deletion in an exome-negative patient with neurodevelopmental disorder.
MBD5-related intellectual disability in a Vietnamese child.
Title: MBD5-related intellectual disability in a Vietnamese child.
Based on segregation analysis of a patient (case 296491) with an intragenic deletion of the MBD5 gene, we classified deletions of exons 3 to 4 of the 5' untranslated region (UTR) of this gene as probably benign. The deletion of exon 3 was shared with the father and paternal uncle, both unaffected
Title: Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes.
A novel frameshift mutation c.254_255delGA (p.Arg85Asnfs*6) in the MBD5 gene was identified in a family with intellectual disability and epilepsy.
Title: Diagnostic exome sequencing identifies a heterozygous MBD5 frameshift mutation in a family with intellectual disability and epilepsy.
Circadian rhythm gene expression altered by haploinsufficiency of MBD5.
Title: MBD5 haploinsufficiency is associated with sleep disturbance and disrupts circadian pathways common to Smith-Magenis and fragile X syndromes.
Results show that when MBD5 and RAI1 are haploinsufficient, they perturb several common pathways that are linked to neuronal and behavioral development.
Title: Phenotypic and molecular convergence of 2q23.1 deletion syndrome with other neurodevelopmental syndromes associated with autism spectrum disorder.
Reduced MBD5 dosage leads to mRNA and microRNA expression patterns and DNA methylation patterns more characteristic of differentiating than proliferating neural stem cells. This balance change may underlie neurodevelopmental disorders.
Title: A molecular model for neurodevelopmental disorders.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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
Intellectual disability, autosomal dominant 1 MedGen: C1969562 OMIM: 156200 GeneReviews: MBD5 Haploinsufficiency	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AB055304 (e-PCR)
- UniSTS:480010

SHGC-58144 (e-PCR)
- UniSTS:59678

D2S2365 (e-PCR)
- UniSTS:76319

D2S1287 (e-PCR)
- UniSTS:13109

D2S2925 (e-PCR)
- UniSTS:12350

SHGC-31239 (e-PCR)
- UniSTS:63312

RH69599 (e-PCR)
- UniSTS:15192

SHGC-61983 (e-PCR)
- UniSTS:21601

MARC_16821-16822:1021560530:2 (e-PCR)
- UniSTS:268131

MARC_16821-16822:1033505180:1 (e-PCR)
- UniSTS:268131

SHGC-85194 (e-PCR)
- UniSTS:104037

D2S2335 (e-PCR), detects polymorphism
- UniSTS:44648

D2S2184 (e-PCR)
- UniSTS:13181

D2S222 (e-PCR), detects polymorphism
- UniSTS:148101

RH45661 (e-PCR)
- UniSTS:24453

G09491 (e-PCR)
- UniSTS:53662

A004M40 (e-PCR)
- UniSTS:35493

PMC149351P2 (e-PCR)
- UniSTS:271030

RH92574 (e-PCR)
- UniSTS:90810

RH119690 (e-PCR)
- UniSTS:133059

SHGC-132968 (e-PCR)
- UniSTS:170955

SHGC-152978 (e-PCR)
- UniSTS:177625

G16397 (e-PCR)
- UniSTS:54526

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in glucose homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of growth hormone receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of multicellular organism growth	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in chromocenter	IBA Inferred from Biological aspect of Ancestor more info
located_in chromocenter	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in midbody	IDA Inferred from Direct Assay more info
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

General protein information

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Preferred Names: methyl-CpG-binding domain protein 5

Names: methyl-CpG-binding protein MBD5

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_017003.3 RefSeqGene

Range

5166..501046

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001378120.1 → NP_001365049.1 methyl-CpG-binding domain protein 5 isoform 1

Status: REVIEWED

Source sequence(s)

AC016731, AC018465, AC019070, AC019226

Consensus CDS

CCDS92873.1

UniProtKB/TrEMBL

A0A2R8YDL9

Related

ENSP00000493871.2, ENST00000642680.2

Conserved Domains (2) summary

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

cl02554
Location:1616 → 1693

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_018328.5 → NP_060798.2 methyl-CpG-binding domain protein 5 isoform 2

See identical proteins and their annotated locations for NP_060798.2

Status: REVIEWED

Source sequence(s)

AC016731, BC150264, DA240785, DB214959

Consensus CDS

CCDS33302.1

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267

Related

ENSP00000386049.1, ENST00000407073.5

Conserved Domains (2) summary

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

cl02554
Location:1383 → 1460

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

148020927..148516971

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047445056.1 → XP_047301012.1 methyl-CpG-binding domain protein 5 isoform X1
XM_011511472.3 → XP_011509774.1 methyl-CpG-binding domain protein 5 isoform X1

See identical proteins and their annotated locations for XP_011509774.1

Conserved Domains (2) summary

cd05835
Location:1616 → 1706

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 ...

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
XM_047445068.1 → XP_047301024.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445088.1 → XP_047301044.1 methyl-CpG-binding domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A1B0GW10
XM_047445091.1 → XP_047301047.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_047445058.1 → XP_047301014.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445074.1 → XP_047301030.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445079.1 → XP_047301035.1 methyl-CpG-binding domain protein 5 isoform X1
XM_011511470.3 → XP_011509772.1 methyl-CpG-binding domain protein 5 isoform X1

See identical proteins and their annotated locations for XP_011509772.1

Conserved Domains (2) summary

cd05835
Location:1616 → 1706

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 ...

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
XM_047445083.1 → XP_047301039.1 methyl-CpG-binding domain protein 5 isoform X2

UniProtKB/TrEMBL

A0A2R8YDL9
XM_047445090.1 → XP_047301046.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_047445078.1 → XP_047301034.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445084.1 → XP_047301040.1 methyl-CpG-binding domain protein 5 isoform X2

UniProtKB/TrEMBL

A0A2R8YDL9
XM_047445055.1 → XP_047301011.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445087.1 → XP_047301043.1 methyl-CpG-binding domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A1B0GW10

Related

ENSP00000490728.2, ENST00000638043.2
XM_047445089.1 → XP_047301045.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_047445057.1 → XP_047301013.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445085.1 → XP_047301041.1 methyl-CpG-binding domain protein 5 isoform X2

UniProtKB/TrEMBL

A0A2R8YDL9
XM_024452990.2 → XP_024308758.1 methyl-CpG-binding domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A1B0GW10

Conserved Domains (2) summary

cd05835
Location:1383 → 1473

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 ...

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
XM_047445092.1 → XP_047301048.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_024452988.2 → XP_024308756.1 methyl-CpG-binding domain protein 5 isoform X3

Conserved Domains (2) summary

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

cl02554
Location:1616 → 1692

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
XM_024452989.2 → XP_024308757.1 methyl-CpG-binding domain protein 5 isoform X4

Conserved Domains (2) summary

cl00110
Location:21 → 79

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

cl02554
Location:1616 → 1679

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
XM_047445063.1 → XP_047301019.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445077.1 → XP_047301033.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445081.1 → XP_047301037.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445082.1 → XP_047301038.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445080.1 → XP_047301036.1 methyl-CpG-binding domain protein 5 isoform X1
XM_047445093.1 → XP_047301049.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_047445086.1 → XP_047301042.1 methyl-CpG-binding domain protein 5 isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

148471381..148967332

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054342945.1 → XP_054198920.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342954.1 → XP_054198929.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342949.1 → XP_054198924.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342965.1 → XP_054198940.1 methyl-CpG-binding domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A1B0GW10
XM_054342969.1 → XP_054198944.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_054342947.1 → XP_054198922.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342950.1 → XP_054198925.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342953.1 → XP_054198928.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342943.1 → XP_054198918.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342958.1 → XP_054198933.1 methyl-CpG-binding domain protein 5 isoform X2

UniProtKB/TrEMBL

A0A2R8YDL9
XM_054342968.1 → XP_054198943.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_054342952.1 → XP_054198927.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342959.1 → XP_054198934.1 methyl-CpG-binding domain protein 5 isoform X2

UniProtKB/TrEMBL

A0A2R8YDL9
XM_054342944.1 → XP_054198919.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342964.1 → XP_054198939.1 methyl-CpG-binding domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A1B0GW10
XM_054342967.1 → XP_054198942.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_054342946.1 → XP_054198921.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342960.1 → XP_054198935.1 methyl-CpG-binding domain protein 5 isoform X2

UniProtKB/TrEMBL

A0A2R8YDL9
XM_054342966.1 → XP_054198941.1 methyl-CpG-binding domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A1B0GW10
XM_054342970.1 → XP_054198945.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_054342961.1 → XP_054198936.1 methyl-CpG-binding domain protein 5 isoform X3
XM_054342962.1 → XP_054198937.1 methyl-CpG-binding domain protein 5 isoform X4
XM_054342948.1 → XP_054198923.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342951.1 → XP_054198926.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342956.1 → XP_054198931.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342957.1 → XP_054198932.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342955.1 → XP_054198930.1 methyl-CpG-binding domain protein 5 isoform X1
XM_054342971.1 → XP_054198946.1 methyl-CpG-binding domain protein 5 isoform X7

UniProtKB/Swiss-Prot

A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
XM_054342963.1 → XP_054198938.1 methyl-CpG-binding domain protein 5 isoform X5