HDAC9
histone deacetylase 9, the group of Histone deacetylases, class IIA
Basic information
Region (hg38): 7:18086949-19002416
Links
Phenotypes
GenCC
Source:
- auriculocondylar syndrome 4 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Auriculocondylar syndrome 4 | AD | Audiologic/Otolaryngologic | Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development | Audiologic/Otolaryngologic; Craniofacial | 34750192 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (86 variants)
- not_provided (16 variants)
- Syndromic_intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDAC9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178425.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 84 | 89 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 86 | 7 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HDAC9 | protein_coding | protein_coding | ENST00000441542 | 25 | 915468 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000268 | 124662 | 0 | 26 | 124688 | 0.000104 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.06 | 422 | 559 | 0.755 | 0.0000289 | 6906 |
| Missense in Polyphen | 121 | 239.67 | 0.50485 | 3034 | ||
| Synonymous | -0.0164 | 211 | 211 | 1.00 | 0.0000112 | 2057 |
| Loss of Function | 6.32 | 9 | 63.2 | 0.142 | 0.00000354 | 702 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000187 | 0.000187 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.000160 | 0.000159 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000981 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
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. Represses MEF2-dependent transcription.;
- Disease
- DISEASE: Note=A chromosomal aberration involving HDAC9 is found in a family with Peters anomaly. Translocation t(1;7)(q41;p21) with TGFB2 resulting in lack of HDAC9 protein. {ECO:0000269|PubMed:12706107}.;
- Pathway
- Viral carcinogenesis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Valproic Acid Pathway, Pharmacodynamics;Pathway_PA165964473;MicroRNAs in cardiomyocyte hypertrophy;Neural Crest Differentiation;Cardiac Hypertrophic Response;Initiation of transcription and translation elongation at the HIV-1 LTR;VEGFA-VEGFR2 Signaling Pathway;Ethanol effects on histone modifications;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Disease;Signal Transduction;sumoylation by ranbp2 regulates transcriptional repression;signal dependent regulation of myogenesis by corepressor mitr;nfat and hypertrophy of the heart ;Signaling by NOTCH1;Signaling by NOTCH;TGF-beta super family signaling pathway canonical;Signaling events mediated by HDAC Class II;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Diseases of signal transduction;NOTCH1 Intracellular Domain Regulates Transcription
(Consensus)
Recessive Scores
- pRec
- 0.715
Intolerance Scores
- loftool
- 0.306
- rvis_EVS
- -1.06
- rvis_percentile_EVS
- 7.52
Haploinsufficiency Scores
- pHI
- 0.933
- hipred
- Y
- hipred_score
- 0.603
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.555
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hdac9
- Phenotype
- muscle phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- hdac9b
- Affected structure
- vascular lymphangioblast
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;response to amphetamine;inflammatory response;heart development;histone deacetylation;neuron differentiation;B cell differentiation;cellular response to insulin stimulus;peptidyl-lysine deacetylation;B cell activation;negative regulation of transcription, DNA-templated;regulation of skeletal muscle fiber development;regulation of striated muscle cell differentiation;histone H3 deacetylation;histone H4 deacetylation;positive regulation of cell migration involved in sprouting angiogenesis
- Cellular component
- histone deacetylase complex;nucleus;nucleoplasm;transcription factor complex;cytoplasm;histone methyltransferase complex
- Molecular function
- transcription corepressor activity;histone deacetylase activity;protein kinase C binding;protein binding;transcription factor binding;NAD-dependent histone deacetylase activity (H3-K14 specific);protein deacetylase activity;histone deacetylase binding;metal ion binding;repressing transcription factor binding