HDAC7
histone deacetylase 7, the group of Histone deacetylases, class IIA
Basic information
Region (hg38): 12:47782722-47833132
Previous symbols: [ "HDAC7A" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (142 variants)
- not_provided (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDAC7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015401.5. 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 | 5 | |||||
| missense | 137 | 144 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 137 | 11 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HDAC7 | protein_coding | protein_coding | ENST00000080059 | 26 | 50411 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000310 | 125711 | 0 | 6 | 125717 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.83 | 403 | 597 | 0.675 | 0.0000383 | 6286 |
| Missense in Polyphen | 124 | 268.73 | 0.46143 | 2959 | ||
| Synonymous | -0.176 | 254 | 250 | 1.01 | 0.0000165 | 2125 |
| Loss of Function | 5.74 | 6 | 49.6 | 0.121 | 0.00000261 | 548 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000584 | 0.0000584 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000934 | 0.0000924 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| 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. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation by repressing transcription of myocyte enhancer factors such as MEF2A, MEF2B and MEF2C. During muscle differentiation, it shuttles into the cytoplasm, allowing the expression of myocyte enhancer factors (By similarity). May be involved in Epstein-Barr virus (EBV) latency, possibly by repressing the viral BZLF1 gene. Positively regulates the transcriptional repressor activity of FOXP3 (PubMed:17360565). {ECO:0000250|UniProtKB:Q8C2B3, ECO:0000269|PubMed:12239305, ECO:0000269|PubMed:17360565}.;
- Pathway
- Viral carcinogenesis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Cell Cycle;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;Disease;Signal Transduction;SUMOylation of DNA damage response and repair proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;TCR;Signaling by NOTCH1;Signaling by NOTCH;AndrogenReceptor;TGF-beta super family signaling pathway canonical;SUMOylation;Signaling events mediated by HDAC Class II;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;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;Intracellular signaling by second messengers;Diseases of signal transduction;HIF-1-alpha transcription factor network;Regulation of Androgen receptor activity;NOTCH1 Intracellular Domain Regulates Transcription
(Consensus)
Intolerance Scores
- loftool
- 0.229
- rvis_EVS
- -0.04
- rvis_percentile_EVS
- 50.52
Haploinsufficiency Scores
- pHI
- 0.110
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.531
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.869
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hdac7
- Phenotype
- craniofacial phenotype; muscle phenotype; homeostasis/metabolism 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- hdac7a
- Affected structure
- hematopoietic progenitor cell differentiation
- Phenotype tag
- abnormal
- Phenotype quality
- decreased occurrence
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;vasculogenesis;cell-cell junction assembly;protein sumoylation;negative regulation of interleukin-2 production;negative regulation of osteoblast differentiation;histone H3 deacetylation;positive regulation of cell migration involved in sprouting angiogenesis;negative regulation of NIK/NF-kappaB signaling
- Cellular component
- histone deacetylase complex;nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- chromatin binding;transcription corepressor activity;protein kinase C binding;protein binding;SUMO transferase activity;protein kinase binding;NAD-dependent histone deacetylase activity (H3-K14 specific);activating transcription factor binding;metal ion binding;repressing transcription factor binding;14-3-3 protein binding