HDAC7

histone deacetylase 7, the group of Histone deacetylases, class IIA

Basic information

Region (hg38): 12:47782721-47833132

Previous symbols: [ "HDAC7A" ]

Links

ENSG00000061273 ∙ NCBI:51564 ∙ OMIM:606542 ∙ HGNC:14067 ∙ Uniprot:Q8WUI4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HDAC7 gene.

• Inborn genetic diseases (47 variants)
• not provided (7 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			46	3		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	46	6	1

Variants in HDAC7

This is a list of pathogenic ClinVar variants found in the HDAC7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-47784130-T-A		not specified	Uncertain significance (Aug 23, 2021)
12-47784193-C-T		not specified	Uncertain significance (Jul 05, 2023)
12-47785451-T-G		not specified	Uncertain significance (May 10, 2022)
12-47785465-G-A		not specified	Uncertain significance (Sep 16, 2021)
12-47787725-G-C		not specified	Uncertain significance (May 24, 2023)
12-47787745-G-C		not specified	Uncertain significance (Aug 17, 2022)
12-47787745-G-T		not specified	Uncertain significance (Aug 08, 2022)
12-47787746-G-C		not specified	Uncertain significance (Sep 22, 2023)
12-47788081-G-A			Likely benign (Jul 01, 2022)
12-47789871-C-T		not specified	Uncertain significance (Dec 18, 2023)
12-47789880-T-C		not specified	Uncertain significance (Dec 15, 2022)
12-47789897-A-T		not specified	Uncertain significance (May 13, 2022)
12-47791294-G-A		not specified	Uncertain significance (Sep 25, 2023)
12-47791313-G-A			Benign (Jul 06, 2018)
12-47791592-G-C		not specified	Uncertain significance (Jan 17, 2023)
12-47791598-C-T		not specified	Uncertain significance (Mar 14, 2023)
12-47791615-C-T		not specified	Uncertain significance (Dec 21, 2023)
12-47791646-C-T		not specified	Uncertain significance (Jul 20, 2022)
12-47791678-T-C		not specified	Uncertain significance (Dec 08, 2023)
12-47791885-G-A		not specified	Uncertain significance (Jan 08, 2024)
12-47791960-C-T		not specified	Uncertain significance (Jan 29, 2024)
12-47791989-G-C		not specified	Uncertain significance (Nov 09, 2022)
12-47793371-G-T		not specified	Uncertain significance (Jan 03, 2024)
12-47793420-G-C		not specified	Uncertain significance (Jan 02, 2024)
12-47793428-C-T		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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