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MBD6 methyl-CpG binding domain protein 6 [ Homo sapiens (human) ]

Gene ID: 114785, updated on 3-Apr-2024

Summary

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Official Symbol
MBD6provided by HGNC
Official Full Name
methyl-CpG binding domain protein 6provided by HGNC
Primary source
HGNC:HGNC:20445
See related
Ensembl:ENSG00000166987 MIM:619458; AllianceGenome:HGNC:20445
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables chromatin binding activity. Located in chromocenter; fibrillar center; and nucleoplasm. Implicated in autism spectrum disorder. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 15.8), spleen (RPKM 15.7) and 25 other tissues See more
Orthologs
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Genomic context

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See MBD6 in Genome Data Viewer
Location:
12q13.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57520715..57531545)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57488889..57498388)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57916607..57923931)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene methionyl-tRNA synthetase 1 Neighboring gene uncharacterized LOC128125814 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57913133-57914094 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:57914069-57915268 Neighboring gene microRNA 6758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57916016-57916975 Neighboring gene DNA damage inducible transcript 3 Neighboring gene microRNA 616 Neighboring gene dynactin subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57944162-57944754 Neighboring gene kinesin family member 5A Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57955995-57956161 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57956855-57957072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6549 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57984713-57985214 Neighboring gene phosphatidylinositol-5-phosphate 4-kinase type 2 gamma

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The Expression of MBD6 Is Associated with Tumor Size in Uterine Leiomyomas. Liang MR, et al. Genet Test Mol Biomarkers, 2019 Aug. PMID 31313936
  2. Mutation and expression of a methyl-binding protein 6 (MBD6) in gastric and colorectal cancers. Choi YJ, et al. Pathol Oncol Res, 2015 Jul. PMID 25638327
  3. MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain. Baymaz HI, et al. Proteomics, 2014 Oct. PMID 24634419
  4. MBD6 is a direct target of Oct4 and controls the stemness and differentiation of adipose tissue-derived stem cells. Jung JS, et al. Cell Mol Life Sci, 2013 Feb. PMID 23052207
  5. Comparative study of methyl-CpG-binding domain proteins. Roloff TC, et al. BMC Genomics, 2003 Jan 16. PMID 12529184, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The decreased expression of the MBD6 protein was correlated with the tumor size of uterine leiomyomas
    Title: The Expression of MBD6 Is Associated with Tumor Size in Uterine Leiomyomas.
  2. Our findings imply that reduced stability and enhanced dynamics of MBD1 or MBD6 is the origin of ATP7B dysfunction in Wilson disease patients with the G85V or G591D mutation.
    Title: Disease-causing point-mutations in metal-binding domains of Wilson disease protein decrease stability and increase structural dynamics.
  3. Frameshift mutations of MBD6 gene is associated with stomach and colorectal cancers.
    Title: Mutation and expression of a methyl-binding protein 6 (MBD6) in gastric and colorectal cancers.
  4. We studied and showed that both MBD5 and MBD6 interact with the mammalian PR-DUB Polycomb protein complex in a mutually exclusive manner, and that the MBD of MBD5 and MBD6 is both necessary and sufficient to mediate this interaction.
    Title: MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain.
  5. This study demonstrates examples of autistic patients carrying alterations in MBD6.
    Title: The expanding role of MBD genes in autism: identification of a MECP2 duplication and novel alterations in MBD5, MBD6, and SETDB1.
  6. MBD6 is regulated by Ago2 via an interaction with Oct4, which alters self-renewal and gene expression in human adipose tissue-derived stem cells.
    Title: MBD6 is a direct target of Oct4 and controls the stemness and differentiation of adipose tissue-derived stem cells.
  7. MBD5 and MBD6 are unlikely to be methyl-binding proteins, yet they may contribute to the formation or function of heterochromatin.
    Title: The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1887

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 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 fibrillar center 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 6
Names
methyl-CpG-binding protein MBD6

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.

mRNA and Protein(s)

  1. NM_052897.4 → NP_443129.3  methyl-CpG-binding domain protein 6

    See identical proteins and their annotated locations for NP_443129.3

    Status: VALIDATED

    Source sequence(s)
    AB067474, AC022506, AK056399
    Consensus CDS
    CCDS8944.1
    UniProtKB/Swiss-Prot
    Q8N3M0, Q8NA81, Q96DN6, Q96Q00
    UniProtKB/TrEMBL
    Q6P0P0
    Related
    ENSP00000347896.3, ENST00000355673.8
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57520715..57531545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537851.4 → XP_011536153.1  methyl-CpG-binding domain protein 6 isoform X1

    See identical proteins and their annotated locations for XP_011536153.1

    UniProtKB/TrEMBL
    Q6P0P0
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

  2. XM_006719218.2 → XP_006719281.1  methyl-CpG-binding domain protein 6 isoform X1

    See identical proteins and their annotated locations for XP_006719281.1

    UniProtKB/TrEMBL
    Q6P0P0
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

  3. XM_006719217.2 → XP_006719280.1  methyl-CpG-binding domain protein 6 isoform X1

    See identical proteins and their annotated locations for XP_006719280.1

    UniProtKB/TrEMBL
    Q6P0P0
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

  4. XM_047428237.1 → XP_047284193.1  methyl-CpG-binding domain protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q8N3M0, Q8NA81, Q96DN6, Q96Q00

  5. XM_005268617.3 → XP_005268674.1  methyl-CpG-binding domain protein 6 isoform X1

    See identical proteins and their annotated locations for XP_005268674.1

    UniProtKB/TrEMBL
    Q6P0P0
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

  6. XM_005268620.4 → XP_005268677.1  methyl-CpG-binding domain protein 6 isoform X3

    UniProtKB/TrEMBL
    Q6P0P0
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

  7. XM_005268618.2 → XP_005268675.1  methyl-CpG-binding domain protein 6 isoform X1

    See identical proteins and their annotated locations for XP_005268675.1

    UniProtKB/TrEMBL
    Q6P0P0
    Conserved Domains (1) summary
    cl00110
    Location:16 → 84
    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 ...

  8. XM_047428238.1 → XP_047284194.1  methyl-CpG-binding domain protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q8N3M0, Q8NA81, Q96DN6, Q96Q00

RNA

  1. XR_007063031.1 RNA Sequence

  2. XR_007063034.1 RNA Sequence

  3. XR_007063033.1 RNA Sequence

  4. XR_007063029.1 RNA Sequence

  5. XR_007063035.1 RNA Sequence

  6. XR_007063032.1 RNA Sequence

  7. XR_429075.3 RNA Sequence

  8. XR_429073.3 RNA Sequence

  9. XR_429076.3 RNA Sequence

  10. XR_429078.3 RNA Sequence

  11. XR_007063030.1 RNA Sequence

  12. XR_429079.3 RNA Sequence

  13. XR_001748569.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57488889..57498388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370988.1 → XP_054226963.1  methyl-CpG-binding domain protein 6 isoform X1

  2. XM_054370992.1 → XP_054226967.1  methyl-CpG-binding domain protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q8N3M0, Q8NA81, Q96DN6, Q96Q00

  3. XM_054370989.1 → XP_054226964.1  methyl-CpG-binding domain protein 6 isoform X1

  4. XM_054370990.1 → XP_054226965.1  methyl-CpG-binding domain protein 6 isoform X1

  5. XM_054370987.1 → XP_054226962.1  methyl-CpG-binding domain protein 6 isoform X1

  6. XM_054370994.1 → XP_054226969.1  methyl-CpG-binding domain protein 6 isoform X3

  7. XM_054370993.1 → XP_054226968.1  methyl-CpG-binding domain protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q8N3M0, Q8NA81, Q96DN6, Q96Q00

  8. XM_054370991.1 → XP_054226966.1  methyl-CpG-binding domain protein 6 isoform X1

RNA

  1. XR_008488519.1 RNA Sequence

  2. XR_008488517.1 RNA Sequence

  3. XR_008488520.1 RNA Sequence

  4. XR_008488511.1 RNA Sequence

  5. XR_008488514.1 RNA Sequence

  6. XR_008488512.1 RNA Sequence

  7. XR_008488513.1 RNA Sequence

  8. XR_008488515.1 RNA Sequence

  9. XR_008488516.1 RNA Sequence

  10. XR_008488518.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96DN6.2 GenPept UniProtKB/Swiss-Prot:Q96DN6

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