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    HDAC4 histone deacetylase 4 [ Homo sapiens (human) ]

    Gene ID: 9759, updated on 24-Dec-2022

    Summary

    Official Symbol
    HDAC4provided by HGNC
    Official Full Name
    histone deacetylase 4provided by HGNC
    Primary source
    HGNC:HGNC:14063
    See related
    Ensembl:ENSG00000068024 MIM:605314; AllianceGenome:HGNC:14063
    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
    HD4; AHO3; BDMR; HDACA; HA6116; HDAC-4; HDAC-A; NEDCHF; NEDCHID
    Summary
    Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class II of the histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. This protein does not bind DNA directly, but through transcription factors MEF2C and MEF2D. It seems to interact in a multiprotein complex with RbAp48 and HDAC3. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 2.4), testis (RPKM 1.6) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HDAC4 in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (239048168..239401649, complement)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (239539541..239892233, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (239969864..240323343, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8511 Neighboring gene twist family bHLH transcription factor 2 Neighboring gene long intergenic non-protein coding RNA 1940 Neighboring gene microRNA 4440 Neighboring gene uncharacterized LOC124908009 Neighboring gene microRNA 4441 Neighboring gene uncharacterized LOC85009 Neighboring gene microRNA 4269 Neighboring gene microRNA 2467 Neighboring gene HDAC4 antisense RNA 1 Neighboring gene uncharacterized LOC124908011 Neighboring gene uncharacterized LOC124908012

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Chromosome 2q37 deletion syndrome
    MedGen: C2931817 OMIM: 600430 GeneReviews: Not available
    Compare labs
    Neurodevelopmental disorder with central hypotonia and dysmorphic facies
    MedGen: C5676944 OMIM: 619797 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2011-11-07)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2011-11-07)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
    EBI GWAS Catalog
    Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    reverse transcriptase gag-pol Amino acid starvation-dependent HDAC4 downregulation leads to HIV-1 transcriptional activation and RT activity production in T-lymphocytes PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0288

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in B cell activation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in B cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cardiac muscle hypertrophy in response to stress TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in histone H3 deacetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in histone H4 deacetylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in histone H4 deacetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in histone deacetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in histone deacetylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in inflammatory response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of glycolytic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of myotube differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in peptidyl-lysine deacetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein sumoylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein deacetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein sumoylation TAS
    Traceable Author Statement
    more info
     
    involved_in regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to denervation involved in regulation of muscle adaptation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to interleukin-1 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    part_of histone deacetylase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear speck 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
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription repressor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone deacetylase 4
    Names
    histone deacetylase A
    NP_001365343.1
    NP_001365344.1
    NP_001365345.1
    NP_001365346.1
    NP_006028.2
    XP_006712940.1
    XP_006712943.1
    XP_011510519.1
    XP_011510520.1
    XP_011510521.1
    XP_011510522.1
    XP_011510524.1
    XP_011510525.1
    XP_011510526.1
    XP_011510527.1
    XP_011510528.1
    XP_011510529.1
    XP_016860883.1
    XP_024309025.1
    XP_047302432.1
    XP_047302433.1
    XP_047302434.1
    XP_047302435.1
    XP_047302436.1
    XP_047302437.1
    XP_047302438.1
    XP_047302439.1
    XP_047302440.1
    XP_047302441.1
    XP_047302442.1
    XP_047302443.1
    XP_047302444.1
    XP_047302445.1
    XP_047302446.1
    XP_047302447.1
    XP_047302448.1
    XP_047302449.1
    XP_047302450.1
    XP_047302451.1
    XP_047302452.1
    XP_047302453.1
    XP_047302454.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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

    1. NG_009235.2 RefSeqGene

      Range
      5629..358481
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001378414.1NP_001365343.1  histone deacetylase 4 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC017028, AC062017
      Consensus CDS
      CCDS92981.1
      UniProtKB/TrEMBL
      A0A7I2SVS4
      Related
      ENSP00000440481.3, ENST00000543185.6
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6541062
      HDAC4; Histone deacetylase 4
    2. NM_001378415.1NP_001365344.1  histone deacetylase 4 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC017028, AC062017
      Consensus CDS
      CCDS92981.1
      UniProtKB/TrEMBL
      A0A7I2SVS4
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6541062
      HDAC4; Histone deacetylase 4
    3. NM_001378416.1NP_001365345.1  histone deacetylase 4 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC017028, AC062017
      Consensus CDS
      CCDS2529.1
      UniProtKB/Swiss-Prot
      Q9UND6
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6491057
      HDAC4; Histone deacetylase 4
    4. NM_001378417.1NP_001365346.1  histone deacetylase 4 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC017028, AC062017
      Consensus CDS
      CCDS2529.1
      UniProtKB/Swiss-Prot
      Q9UND6
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6491057
      HDAC4; Histone deacetylase 4
    5. NM_006037.4NP_006028.2  histone deacetylase 4 isoform 2

      See identical proteins and their annotated locations for NP_006028.2

      Status: REVIEWED

      Source sequence(s)
      AC017028, AC062017
      Consensus CDS
      CCDS2529.1
      UniProtKB/Swiss-Prot
      P56524, Q9UND6
      Related
      ENSP00000264606.3, ENST00000345617.7
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6491057
      HDAC4; Histone deacetylase 4

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      239048168..239401649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446489.1XP_047302445.1  histone deacetylase 4 isoform X20

    2. XM_047446486.1XP_047302442.1  histone deacetylase 4 isoform X17

    3. XM_047446483.1XP_047302439.1  histone deacetylase 4 isoform X14

    4. XM_047446498.1XP_047302454.1  histone deacetylase 4 isoform X29

    5. XM_047446491.1XP_047302447.1  histone deacetylase 4 isoform X21

    6. XM_047446490.1XP_047302446.1  histone deacetylase 4 isoform X20

    7. XM_011512226.3XP_011510528.1  histone deacetylase 4 isoform X17

      Conserved Domains (2) summary
      cd10162
      Location:67128
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6301038
      HDAC4; Histone deacetylase 4
    8. XM_047446496.1XP_047302452.1  histone deacetylase 4 isoform X27

    9. XM_047446493.1XP_047302449.1  histone deacetylase 4 isoform X24

    10. XM_047446494.1XP_047302450.1  histone deacetylase 4 isoform X25

    11. XM_047446492.1XP_047302448.1  histone deacetylase 4 isoform X22

    12. XM_047446482.1XP_047302438.1  histone deacetylase 4 isoform X14

    13. XM_047446480.1XP_047302436.1  histone deacetylase 4 isoform X10

    14. XM_047446479.1XP_047302435.1  histone deacetylase 4 isoform X9

      UniProtKB/Swiss-Prot
      Q9UND6
    15. XM_011512223.3XP_011510525.1  histone deacetylase 4 isoform X6

      See identical proteins and their annotated locations for XP_011510525.1

      UniProtKB/TrEMBL
      A0A7I2SVS4
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6541062
      HDAC4; Histone deacetylase 4
    16. XM_011512222.4XP_011510524.1  histone deacetylase 4 isoform X6

      See identical proteins and their annotated locations for XP_011510524.1

      UniProtKB/TrEMBL
      A0A7I2SVS4
      Conserved Domains (2) summary
      cd10162
      Location:91152
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6541062
      HDAC4; Histone deacetylase 4
    17. XM_047446484.1XP_047302440.1  histone deacetylase 4 isoform X14

    18. XM_047446476.1XP_047302432.1  histone deacetylase 4 isoform X6

      UniProtKB/TrEMBL
      A0A7I2SVS4
    19. XM_006712880.4XP_006712943.1  histone deacetylase 4 isoform X19

      See identical proteins and their annotated locations for XP_006712943.1

      Conserved Domains (2) summary
      cd10162
      Location:64125
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6271035
      HDAC4; Histone deacetylase 4
    20. XM_047446487.1XP_047302443.1  histone deacetylase 4 isoform X18

    21. XM_017005394.2XP_016860883.1  histone deacetylase 4 isoform X16

    22. XM_011512219.3XP_011510521.1  histone deacetylase 4 isoform X4

      Conserved Domains (2) summary
      cd10162
      Location:115176
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6731076
      HDAC4; Histone deacetylase 4
    23. XM_006712877.4XP_006712940.1  histone deacetylase 4 isoform X2

      Conserved Domains (2) summary
      cd10162
      Location:115176
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6731081
      HDAC4; Histone deacetylase 4
    24. XM_011512218.3XP_011510520.1  histone deacetylase 4 isoform X3

      Conserved Domains (2) summary
      cd10162
      Location:115176
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6781081
      HDAC4; Histone deacetylase 4
    25. XM_011512217.3XP_011510519.1  histone deacetylase 4 isoform X1

      Conserved Domains (2) summary
      cd10162
      Location:115176
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6781086
      HDAC4; Histone deacetylase 4
    26. XM_047446481.1XP_047302437.1  histone deacetylase 4 isoform X12

    27. XM_047446478.1XP_047302434.1  histone deacetylase 4 isoform X8

    28. XM_047446477.1XP_047302433.1  histone deacetylase 4 isoform X7

    29. XM_011512220.3XP_011510522.1  histone deacetylase 4 isoform X5

      Conserved Domains (2) summary
      cd10162
      Location:92153
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6551063
      HDAC4; Histone deacetylase 4
    30. XM_047446497.1XP_047302453.1  histone deacetylase 4 isoform X28

    31. XM_047446495.1XP_047302451.1  histone deacetylase 4 isoform X26

    32. XM_011512225.3XP_011510527.1  histone deacetylase 4 isoform X13

      Conserved Domains (2) summary
      cd10162
      Location:86147
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6441052
      HDAC4; Histone deacetylase 4
    33. XM_047446485.1XP_047302441.1  histone deacetylase 4 isoform X15

    34. XM_011512224.3XP_011510526.1  histone deacetylase 4 isoform X11

      Conserved Domains (2) summary
      cd10162
      Location:86147
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6491057
      HDAC4; Histone deacetylase 4
    35. XM_047446488.1XP_047302444.1  histone deacetylase 4 isoform X19

    36. XM_024453257.2XP_024309025.1  histone deacetylase 4 isoform X19

      Conserved Domains (2) summary
      cd10162
      Location:64125
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6271035
      HDAC4; Histone deacetylase 4
    37. XM_011512227.3XP_011510529.1  histone deacetylase 4 isoform X23

      Conserved Domains (2) summary
      cd10162
      Location:43104
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6061014
      HDAC4; Histone deacetylase 4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      239539541..239892233 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)