HDAC10
protein-codinghistone deacetylase 10, the group of Histone deacetylases, class IIB
Gene summary
The protein encoded by this gene belongs to the histone deacetylase family, members of which deacetylate lysine residues on the N-terminal part of the core histones. Histone deacetylation modulates chromatin structure, and plays an important role in transcriptional regulation, cell cycle progression, and developmental events. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HDAC10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032019.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 121 | 6 | 127 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 129 | 6 | 0 | 135 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_114408.3 | 20 | MANE Select | |
| Ensembl | ENSP00000216271.5 | 20 | MANE Select | |
| RefSeq | NP_001152758.1 | 19 | Standard | |
| Ensembl | ENSP00000343540.4 | 19 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Viral carcinogenesis - Homo sapiens (human)
- Alcoholism - Homo sapiens (human)
- Human papillomavirus infection - Homo sapiens (human)
- Neural Crest Differentiation
- Ectoderm Differentiation
Biological Process
- negative regulation of transcription by RNA polymerase II
- chromatin organization
- regulation of transcription, DNA-templated
- protein deacetylation
- oligodendrocyte development
Molecular Function
- histone deacetylase activity
- protein binding
- enzyme binding
- NAD-dependent histone deacetylase activity (H3-K14 specific)
- protein deacetylase activity
Cellular Component
- histone deacetylase complex
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000216271
- Coding exons
- 20
- Length
- 6223
- Individuals with no LoFs
- 125324
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 363
- Defined
- 125687
- p
- 0.00145
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.451 | 423 | 398 | 1.06 | 0.0000231 | 4195 |
| Missense (PolyPhen) | 133 | 136.95 | 0.97113 | 1531 | ||
| Synonymous | -1.64 | 218 | 189 | 1.15 | 0.0000121 | 1495 |
| Loss of Function | -0.954 | 43 | 36.8 | 1.17 | 0.00000173 | 388 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0010 | 0.00098 | notable |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0.00031 | 0.00030 | rare |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.0020 | 0.0020 | notable |
| European (Non-Finnish) | 0.0014 | 0.0014 | notable |
| South Asian | 0.0015 | 0.0014 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.;
Recessive Scores
- pRec
- 0.154
Intolerance Scores
- LoFtool
- 0.849
- RVIS EVS
- -0.17
- RVIS percentile EVS
- 40.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.555
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |