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HDAC8 histone deacetylase 8 [ Homo sapiens (human) ]

Gene ID: 55869, updated on 5-Jan-2022

Summary

Official Symbol
HDAC8provided by HGNC
Official Full Name
histone deacetylase 8provided by HGNC
Primary source
HGNC:HGNC:13315
See related
Ensembl:ENSG00000147099 MIM:300269
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
HD8; WTS; RPD3; CDA07; CDLS5; KDAC8; MRXS6; HDACL1
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 I of the histone deacetylase family. It catalyzes the deacetylation of lysine residues in the histone N-terminal tails and represses transcription in large multiprotein complexes with transcriptional co-repressors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
Expression
Ubiquitous expression in adrenal (RPKM 3.9), thyroid (RPKM 3.1) and 25 other tissues See more
Orthologs
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Genomic context

See HDAC8 in Genome Data Viewer
Location:
Xq13.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (72329516..72573099, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (71549366..71792693, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373250 Neighboring gene ribosomal protein S4 X-linked Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 Neighboring gene RNA, U2 small nuclear 68, pseudogene Neighboring gene phosphorylase kinase regulatory subunit alpha 1 Neighboring gene MATR3 pseudogene 1 Neighboring gene PHKA1 antisense RNA 1

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
Cornelia de Lange syndrome 5
MedGen: C3550903 OMIM: 300882 GeneReviews: Cornelia de Lange Syndrome
Compare labs
De Lange syndrome
MedGen: C0270972 GeneReviews: Cornelia de Lange Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-03-28)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2018-03-28)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr depletes HDAC1, 2, 3 and 8 to overcome HIV-1 proviral latency in macrophages 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding TAS
Traceable Author Statement
more info
PubMed 
enables Hsp70 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables Hsp90 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
enables histone deacetylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
more info
PubMed 
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of histone deacetylase complex TAS
Traceable Author Statement
more info
PubMed 
located_in nuclear chromosome TAS
Traceable Author Statement
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
histone deacetylase 8
Names
histone deacetylase-like 1
NP_001159890.1
NP_001159891.1
NP_001159892.1
NP_001159894.1
NP_001159920.1
NP_060956.1
XP_011529288.3
XP_016885129.2
XP_016885130.2
XP_016885131.1
XP_016885132.1
XP_016885133.1
XP_016885134.1
XP_016885135.1
XP_016885136.2
XP_024308173.1

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_015851.1 RefSeqGene

    Range
    5261..248588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166418.2NP_001159890.1  histone deacetylase 8 isoform 2

    See identical proteins and their annotated locations for NP_001159890.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate exons in the 5' coding region, compared to variant 1, resulting in a protein (isoform 2) that maintains the reading frame but is shorter, compared to isoform 1.
    Source sequence(s)
    AK296641, BC050433
    Consensus CDS
    CCDS55449.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362691.4, ENST00000373589.9
    Conserved Domains (1) summary
    cl17011
    Location:16286
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  2. NM_001166419.2NP_001159891.1  histone deacetylase 8 isoform 3

    See identical proteins and their annotated locations for NP_001159891.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several alternate 3' exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK074326
    Consensus CDS
    CCDS55451.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000414486.2, ENST00000439122.7
    Conserved Domains (1) summary
    cl17011
    Location:16246
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  3. NM_001166420.2NP_001159892.1  histone deacetylase 8 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks a large portion of the 3' coding region and has a distinct 3' UTR, compared to variant 1. The encoded isoform (5) has a shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AI651236, BF514915, BQ189619
    Consensus CDS
    CCDS55450.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362655.1, ENST00000373554.6
    Conserved Domains (1) summary
    cl17011
    Location:16146
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  4. NM_001166422.2NP_001159894.1  histone deacetylase 8 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks multiple alternate 3' exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (5) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI651236, AI916593, BP229332
    Consensus CDS
    CCDS55452.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362657.3, ENST00000373556.8
    Conserved Domains (1) summary
    cl17011
    Location:16147
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  5. NM_001166448.2NP_001159920.1  histone deacetylase 8 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks multiple alternate coding exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (3) maintains the reading frame, but is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK074326, BP229332, BQ632790
    Consensus CDS
    CCDS55448.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362660.4, ENST00000373559.8
    Conserved Domains (1) summary
    cl17011
    Location:16129
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  6. NM_018486.3NP_060956.1  histone deacetylase 8 isoform 1

    See identical proteins and their annotated locations for NP_060956.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AJ277724, BC050433, BP229332
    Consensus CDS
    CCDS14420.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362674.3, ENST00000373573.9
    Conserved Domains (1) summary
    cd10000
    Location:16377
    HDAC8; Histone deacetylase 8 (HDAC8)

RNA

  1. NR_051952.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK298767, BC050433, DC352390
    Related
    ENST00000650471.1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    72329516..72573099 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029644.2XP_016885133.1  histone deacetylase 8 isoform X6

  2. XM_017029642.1XP_016885131.1  histone deacetylase 8 isoform X4

    Related
    ENSP00000497568.1, ENST00000647654.1
  3. XM_017029643.2XP_016885132.1  histone deacetylase 8 isoform X5

  4. XM_017029641.2XP_016885130.2  histone deacetylase 8 isoform X3

    Related
    ENSP00000362685.2, ENST00000373583.6
    Conserved Domains (1) summary
    cd10000
    Location:16351
    HDAC8; Histone deacetylase 8 (HDAC8)
  5. XM_017029640.2XP_016885129.2  histone deacetylase 8 isoform X2

    Conserved Domains (1) summary
    cd10000
    Location:16345
    HDAC8; Histone deacetylase 8 (HDAC8)
  6. XM_011530986.3XP_011529288.3  histone deacetylase 8 isoform X1

    Related
    ENSP00000497188.1, ENST00000647886.1
    Conserved Domains (1) summary
    cd10000
    Location:16371
    HDAC8; Histone deacetylase 8 (HDAC8)
  7. XM_024452405.1XP_024308173.1  histone deacetylase 8 isoform X10

    Conserved Domains (1) summary
    cl17011
    Location:1176
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  8. XM_017029646.1XP_016885135.1  histone deacetylase 8 isoform X8

  9. XM_017029645.2XP_016885134.1  histone deacetylase 8 isoform X7

    Conserved Domains (1) summary
    cl17011
    Location:54315
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  10. XM_017029647.2XP_016885136.2  histone deacetylase 8 isoform X9

    Related
    ENSP00000498144.1, ENST00000650126.1
    Conserved Domains (1) summary
    cl17011
    Location:16220
    Arginase_HDAC; Arginase-like and histone-like hydrolases

RNA

  1. XR_938402.3 RNA Sequence

    Related
    ENST00000647594.1
  2. XR_001755711.2 RNA Sequence

    Related
    ENST00000648855.1
  3. XR_002958780.1 RNA Sequence

    Related
    ENST00000648939.1
  4. XR_002958781.1 RNA Sequence

    Related
    ENST00000648504.1
  5. XR_002958783.1 RNA Sequence

  6. XR_002958779.1 RNA Sequence

  7. XR_002958782.1 RNA Sequence

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