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HDAC8 histone deacetylase 8 [ Homo sapiens (human) ]

Gene ID: 55869, updated on 7-Jul-2024

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; AllianceGenome:HGNC:13315
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:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (72329516..72572843, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (70762405..71005758, complement)
105.20220307 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 ATAC-STARR-seq lymphoblastoid active region 29757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29758 Neighboring gene uncharacterized LOC105373250 Neighboring gene Sharpr-MPRA regulatory region 2135 Neighboring gene NANOG hESC enhancer GRCh37_chrX:71528736-71529237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:71532082-71532582 Neighboring gene ribosomal protein S4 X-linked Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29761 Neighboring gene RNA, U2 small nuclear 68, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:71773892-71775091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29762 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

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 histone deacetylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
enables histone decrotonylase activity IDA
Inferred from Direct Assay
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 
enables protein lysine deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
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 TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
histone deacetylase 8
Names
histone deacetylase-like 1
protein deacetylase HDAC8
protein decrotonylase HDAC8
NP_001159890.1
NP_001159891.1
NP_001159892.1
NP_001159894.1
NP_001159920.1
NP_001397654.1
NP_001397656.1
NP_001397657.1
NP_001397658.1
NP_001397659.1
NP_060956.1
XP_016885129.2
XP_016885132.2
XP_016885133.2
XP_016885134.2
XP_047298208.1
XP_047298211.1
XP_047298212.1
XP_047298213.1
XP_054183365.1
XP_054183366.1
XP_054183367.1
XP_054183368.1
XP_054183369.1
XP_054183370.1
XP_054183371.1
XP_054183372.1

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.

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/TrEMBL
    A0A3B3ISE4
    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/TrEMBL
    A0A3B3IRZ8
    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/TrEMBL
    A0A3B3IS93
    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/TrEMBL
    A0A3B3IS93
    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_001410725.1NP_001397654.1  histone deacetylase 8 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL133500, BX295542
    Consensus CDS
    CCDS94633.1
    UniProtKB/TrEMBL
    A0A3B3IS68, A0A3B3ISJ4
    Related
    ENSP00000497188.1, ENST00000647886.1
  7. NM_001410727.1NP_001397656.1  histone deacetylase 8 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL133500, BX295542
    Consensus CDS
    CCDS94631.1
    UniProtKB/TrEMBL
    A0A3B3ITZ3, A6NFW1
    Related
    ENSP00000362685.2, ENST00000373583.6
  8. NM_001410728.1NP_001397657.1  histone deacetylase 8 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AL133500, BX295542
    Consensus CDS
    CCDS94630.1
    UniProtKB/TrEMBL
    A0A3B3IT30
    Related
    ENSP00000497568.1, ENST00000647654.1
  9. NM_001410729.1NP_001397658.1  histone deacetylase 8 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AL133500, BX295542
    Consensus CDS
    CCDS94634.1
    UniProtKB/TrEMBL
    A0A3B3ISS7, A0A3B3IT95
    Related
    ENSP00000497764.1, ENST00000648834.1
  10. NM_001410730.1NP_001397659.1  histone deacetylase 8 isoform 11

    Status: REVIEWED

    Source sequence(s)
    AL133500, BX295542
    Consensus CDS
    CCDS94632.1
    UniProtKB/TrEMBL
    A0A3B3IRZ8, A0A3B3IU01
    Related
    ENSP00000498144.1, ENST00000650126.1
  11. 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
    A6ND12, A6ND61, A6NET3, A6NJR3, A8MQ62, B4DKN0, B4DV22, Q86VC8, Q9BY41, Q9NP76, Q9NYH4
    UniProtKB/TrEMBL
    A0A3B3ITZ3
    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: 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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    72329516..72572843 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442255.1XP_047298211.1  histone deacetylase 8 isoform X6

    UniProtKB/TrEMBL
    A0A3B3ISE4
  2. XM_017029644.3XP_016885133.2  histone deacetylase 8 isoform X4

  3. XM_017029645.3XP_016885134.2  histone deacetylase 8 isoform X5

    UniProtKB/TrEMBL
    A0A3B3IRJ3
    Related
    ENSP00000496818.1, ENST00000648139.1
  4. XM_017029643.3XP_016885132.2  histone deacetylase 8 isoform X3

    UniProtKB/TrEMBL
    A0A3B3IRJ3
  5. XM_017029640.3XP_016885129.2  histone deacetylase 8 isoform X1

    UniProtKB/TrEMBL
    A0A3B3ISJ4
    Conserved Domains (1) summary
    cd10000
    Location:16345
    HDAC8; Histone deacetylase 8 (HDAC8)
  6. XM_047442256.1XP_047298212.1  histone deacetylase 8 isoform X7

  7. XM_047442257.1XP_047298213.1  histone deacetylase 8 isoform X8

    UniProtKB/TrEMBL
    B4DQE7, E7ETC8
  8. XM_047442252.1XP_047298208.1  histone deacetylase 8 isoform X2

    UniProtKB/TrEMBL
    A0A3B3IT84
    Related
    ENSP00000396424.2, ENST00000415409.6

RNA

  1. XR_938402.4 RNA Sequence

    Related
    ENST00000647594.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    70762405..71005758 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327395.1XP_054183370.1  histone deacetylase 8 isoform X6

    UniProtKB/TrEMBL
    A0A3B3ISE4
  2. XM_054327393.1XP_054183368.1  histone deacetylase 8 isoform X4

  3. XM_054327394.1XP_054183369.1  histone deacetylase 8 isoform X5

    UniProtKB/TrEMBL
    A0A3B3IRJ3
  4. XM_054327392.1XP_054183367.1  histone deacetylase 8 isoform X3

    UniProtKB/TrEMBL
    A0A3B3IRJ3
  5. XM_054327390.1XP_054183365.1  histone deacetylase 8 isoform X1

    UniProtKB/TrEMBL
    A0A3B3ISJ4
  6. XM_054327396.1XP_054183371.1  histone deacetylase 8 isoform X7

  7. XM_054327397.1XP_054183372.1  histone deacetylase 8 isoform X8

    UniProtKB/TrEMBL
    B4DQE7, E7ETC8
  8. XM_054327391.1XP_054183366.1  histone deacetylase 8 isoform X2

    UniProtKB/TrEMBL
    A0A3B3IT84

RNA

  1. XR_008485495.1 RNA Sequence