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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
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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)