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Gene Gene information from NCBI Gene database.
Entrez ID 8841
Gene name Histone deacetylase 3
Gene symbol HDAC3
Synonyms (NCBI Gene)
HD3KDAC3RPD3RPD3-2
Chromosome 5
Chromosome location 5q31.3
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 b
SNPs SNP information provided by dbSNP.
2
SNP ID Visualize variation Clinical significance Consequence
rs1554216303 C>T Likely-pathogenic Coding sequence variant, non coding transcript variant, missense variant
rs1554216308 T>C Likely-pathogenic Coding sequence variant, non coding transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
62 Show/Hide all (62)
miRTarBase ID miRNA Experiments Reference
MIRT732569 hsa-miR-4286 ImmunofluorescenceLuciferase reporter assayWestern blotting 33973278
MIRT734466 hsa-miR-132-3p MicroarrayRNA-seq 31669733
MIRT737020 hsa-miR-193b-3p Western blottingqRT-PCR 32098619
MIRT1042435 hsa-miR-1261 CLIP-seq
MIRT1042436 hsa-miR-1915 CLIP-seq
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
HDAC4 Unknown 11804585
YY1 Unknown 19279113
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
113 Show/Hide all (113)
GO ID Ontology Definition Evidence Reference
GO:0000118 Component Histone deacetylase complex IBA
GO:0000118 Component Histone deacetylase complex IDA 18326024
GO:0000118 Component Histone deacetylase complex TAS 12711221
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 16569215, 18417529, 18854353
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605166 4854 ENSG00000171720
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O15379
Protein name Histone deacetylase 3 (HD3) (EC 3.5.1.98) (Protein deacetylase HDAC3) (EC 3.5.1.-) (Protein deacylase HDAC3) (EC 3.5.1.-) (RPD3-2) (SMAP45)
Protein function Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4), and some other non-histone substrates (PubMed:21030595, PubMed:21444723, PubMed:23911289, PubMed:25301942,
PDB 4A69
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00850 Hist_deacetyl 22 → 314 Histone deacetylase domain Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:9464271}.
Sequence
Sequence length 428
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
KEGG Pathway Reactome Pathway
Neutrophil extracellular trap formation PPARA activates gene expression
Thyroid hormone signaling pathway Transcriptional activation of mitochondrial biogenesis
Alcoholism Constitutive Signaling by NOTCH1 PEST Domain Mutants
Viral carcinogenesis Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
  HDACs deacetylate histones
  Notch-HLH transcription pathway
  Transcriptional regulation of white adipocyte differentiation
  Regulation of lipid metabolism by PPARalpha
  Circadian Clock
  NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
  HCMV Early Events
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
9
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Show/Hide Unknown Diseases (9)
Phenotype Name Clinical Significance Source Reference Evidence Score
ATRIAL FIBRILLATION — GWAS catalog 40645996
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER — GenCC —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Ependymoma Uncertain significance ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
HEART DISEASES — CTD, Disgenet
CTD, Disgenet
18625706
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDER — GWAS catalog 39047730
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Show/Hide Text Mining Associations (198)
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 20636436
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 16533812
★★★★★
★☆☆☆☆
Found in Text Mining only
Adult Diffuse Large B-Cell Lymphoma B-cell Lymphoma BEFREE 22116549
★★★★★
★☆☆☆☆
Found in Text Mining only
Amyloidosis Amyloidosis BEFREE 28771976, 30397132
★★★★★
★☆☆☆☆
Found in Text Mining only
Ankylosing spondylitis Ankylosing Spondylitis BEFREE 26531724
★★★★★
★☆☆☆☆
Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA Syndromic microphthalmia BEFREE 30670333
★★★★★
★☆☆☆☆
Found in Text Mining only
Arteriosclerosis Arteriosclerosis BEFREE 20026773, 25007801
★★★★★
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 27457515 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 30402512 Inhibit
★★★★★
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma BEFREE 17007107
★★★★★
★☆☆☆☆
Found in Text Mining only