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    PHF21A PHD finger protein 21A [ Homo sapiens (human) ]

    Gene ID: 51317, updated on 5-May-2013
    Official Symbol
    PHF21Aprovided by HGNC
    Official Full Name
    PHD finger protein 21Aprovided by HGNC
    Primary source
    HGNC:24156
    Locus tag
    BM-006
    See related
    Ensembl:ENSG00000135365; MIM:608325
    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
    Also known as
    BHC80; BM-006
    Summary
    The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]
    Location :
    11p11.2
    Sequence :
    Chromosome: 11; NC_000011.9 (45950870..46142985, complement)
    See PHF21A in Epigenomics, MapViewer

    Chromosome 11 - NC_000011.9Genomic Context describing neighboring genes Neighboring gene peroxisomal biogenesis factor 16 Neighboring gene glycosyltransferase-like 1B Neighboring gene filamin binding LIM protein 1 pseudogene Neighboring gene cAMP responsive element binding protein 3-like 1

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. Translocations disrupting PHF21A in the Potocki-Shaffer-syndrome region are associated with intellectual disability and craniofacial anomalies. Kim HG, et al. Am J Hum Genet, 2012 Jul 13. PMID 22770980.
    2. Purification and identification of endogenous polySUMO conjugates. Bruderer R, et al. EMBO Rep, 2011 Feb. PMID 21252943.
    3. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. Elks CE, et al. Nat Genet, 2010 Dec. PMID 21102462.
    4. A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes. Varier RA, et al. EMBO J, 2010 Dec 1. PMID 20953165.
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614.

    See all (21) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. we have uncovered evidence that the ID and CFA phenotypes are both caused by haploinsufficiency of a single gene, PHF21A, at 11p11.2.
      Title: Translocations disrupting PHF21A in the Potocki-Shaffer-syndrome region are associated with intellectual disability and craniofacial anomalies.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. the recovery of neurosecretion depends on the reciprocal level of BHC80 and REST, with BHC80 working as a negative modulator of REST repression
      Title: The rest repression of the neurosecretory phenotype is negatively modulated by BHC80, a protein of the BRAF/HDAC complex.
    4. Presumably serves as a scaffold protein in BHC in neuronal as well as non-neuronal cells. Possible role in spermatogenesis.
      Title: Characterization of BHC80 in BRAF-HDAC complex, involved in neuron-specific gene repression.
    Submit: New GeneRIF Correction

    Review eQTL and phenotype association data in this region using PheGenI

    Products Interactant Other Gene Complex Source Pubs Description
    BHC80 Q13547 HDAC1    HPRD  PubMed  
    BHC80 Q92769 HDAC2    HPRD  PubMed  
    BHC80 Q9P0W2 HMG20B    HPRD  PubMed  
    BHC80 O60341 KDM1A    HPRD  PubMed  
    BHC80 O60711 LPXN    HPRD  PubMed  
    BHC80 Q9UKL0 RCOR1    HPRD  PubMed  
    BioGRID:119468 BioGRID:108309 ELAVL1    BioGRID  PubMed Affinity Capture-RNA 
    BioGRID:119468 BioGRID:127605 ESCO2    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:119468 BioGRID:109224 GTF2I    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:119468 BioGRID:109315 HDAC1    BioGRID  PubMed Co-purification; Reconstituted Complex 
    BioGRID:119468 BioGRID:109316 HDAC2    BioGRID  PubMed Affinity Capture-MS; Co-purification; Reconstituted Complex 
    BioGRID:119468 BioGRID:126025 HIST2H3C    BioGRID  PubMed Co-crystal Structure; Reconstituted Complex 
    BioGRID:119468 BioGRID:113895 HIST3H3    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:119468 BioGRID:115642 HMG20B    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western; Co-purification; Reconstituted Complex 
    BioGRID:119468 BioGRID:116667 KDM1A    BioGRID  PubMed Affinity Capture-MS; Co-purification; Reconstituted Complex 
    BioGRID:119468 BioGRID:114801 LPXN    BioGRID  PubMed Two-hybrid 
    BioGRID:119468 BioGRID:116796 RCOR1    BioGRID  PubMed Co-purification; Reconstituted Complex 
    BioGRID:119468 BioGRID:112497 SUMO2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:119468 BioGRID:112744 TAF10    BioGRID  PubMed Affinity Capture-MS 
    • Factors involved in megakaryocyte development and platelet production, organism-specific biosystem (from REACTOME)
      Factors involved in megakaryocyte development and platelet production, organism-specific biosystemMegakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they underg...
    • Hemostasis, organism-specific biosystem (from REACTOME)
      Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...

    Markers

    Genotypes

    Homology

    Clone Names

    • KIAA1696

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    blood coagulation TAS
    Traceable Author Statement
    more info
    		  
    chromatin modification IEA
    Inferred from Electronic Annotation
    more info
    		  
    negative regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    regulation of transcription, DNA-dependent IEA
    Inferred from Electronic Annotation
    more info
    		  
    suckling behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    transcription, DNA-dependent IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    histone deacetylase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    Preferred Names
    PHD finger protein 21A
    Names
    PHD finger protein 21A
    BHC80a
    BRAF35/HDAC2 complex (80 kDa)
    BRAF35-HDAC complex protein BHC80

    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_001101802.1 → NP_001095272.1  PHD finger protein 21A isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AB051483, AC068385, AK023258, AL359608, BC015714, CB266669
      Consensus CDS
      CCDS44578.1
      UniProtKB/Swiss-Prot
      Q96BD5
      Related
      ENSP00000257821, ENST00000257821
      Conserved Domains (2) summary
      COG5034
      Location:374 – 536
      Blast Score: 107
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      pfam00628
      Location:490 – 533
      Blast Score: 180
      PHD; PHD-finger

    2. NM_016621.3 → NP_057705.3  PHD finger protein 21A isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the mid-coding region, and includes an alternate in-frame exon in the 3' coding region, but lacks a different alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform b) is shorter than isoform a.
      Source sequence(s)
      AB051483, AC068385, AK023258, AL359608, CB266669
      Consensus CDS
      CCDS31474.1
      UniProtKB/Swiss-Prot
      Q96BD5
      Conserved Domains (1) summary
      pfam00628
      Location:444 – 487
      Blast Score: 177
      PHD; PHD-finger

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000011.9 Reference GRCh37.p10 Primary Assembly

      Range
      45950870..46142985, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000143.1 Alternate HuRef

      Range
      45657507..45849706, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018922.1 Alternate CHM1_1.0

      Range
      45877401..46069065, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01060753.1 (73158..74149) None
    genomic ABBA01060754.1 None
    genomic ABBA01060755.1 None
    genomic ABBA01060756.1 None
    genomic AC024475.15 (113537..191960) None
    genomic AC068385.9 (104704..165493) None
    genomic AC129913.2 None
    genomic AMYH01003532.1 (29041..220705) None
    genomic CH471064.2 EAW68012.1
      EAW68013.1
      EAW68014.1
      EAW68015.1
      EAW68016.1
      EAW68017.1
      EAW68018.1
    mRNA AB051483.1 BAB21787.1
    mRNA AF208848.1 AAF64262.1
    mRNA AK021530.1 BAB13839.1
    mRNA AK023258.1 BAB14492.1
    mRNA AL359593.1 None
    mRNA AL359608.1 None
    mRNA AY090777.1 AAM09095.1
    mRNA BC015714.2 AAH15714.1
    mRNA BX648236.1 CAH10542.1
    mRNA CB266669.1 None
    other-genetic EU446805.1 ABZ92334.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96BD5.1 GenPept UniProtKB/Swiss-Prot:Q96BD5

    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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    Molecular Biology Databases
    Research Materials
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      Supplemental Content

      Table of contents

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      • Order cDNA clone
        Order cDNA clone
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        3D structure of a gene
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        BioAssays, RNAi Target,Active
      • BioProjects
        BioProjects related to a gene
      • BioSystems
        BioSystems
      • CCDS
        Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
      • Conserved Domains
        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • GAP
        GAP Links
      • Genome
        Genome records having the gene annotated on corresponding genomic reference sequence.
      • GEO Profiles
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      • HomoloGene
        Links between HomoloGene and Gene are provided by the HomoloGene group when a gene is included in a HomoloGene record.
      • Map Viewer
        These links are maintained by the Map Viewer group and are provided when a GeneID is annotated on a map for the same species.
      • Nucleotide
        Link to related Nucleotide entry
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      • Probe
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        Link to related protein entry
      • PubChem Compound
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        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
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        Link to Nucleotide RefSeq RNAs
      • SNP
        Related SNP records
      • SNP: GeneView
        SNPs linked from GeneView
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        Gene Genotype Report
      • Taxonomy
        Link to related taxonomy entry
      • UniGene
        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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