HDAC10

histone deacetylase 10, the group of Histone deacetylases, class IIB

Basic information

Region (hg38): 22:50245183-50251405

Links

ENSG00000100429 ∙ NCBI:83933 ∙ OMIM:608544 ∙ HGNC:18128 ∙ Uniprot:Q969S8 ∙ 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 HDAC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDAC10 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						0
missense			52	2		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	52	4	0

Variants in HDAC10

This is a list of pathogenic ClinVar variants found in the HDAC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50245229-G-C			Likely benign (Oct 09, 2018)
22-50245269-G-T			Likely benign (Jul 17, 2018)
22-50245530-A-G		not specified	Uncertain significance (Dec 12, 2022)
22-50245698-C-G		not specified	Uncertain significance (Apr 08, 2023)
22-50245951-G-A		not specified	Uncertain significance (Feb 17, 2023)
22-50245969-G-A		not specified	Uncertain significance (Dec 21, 2023)
22-50245995-T-C		not specified	Uncertain significance (Dec 14, 2022)
22-50246017-G-C		not specified	Uncertain significance (Dec 13, 2022)
22-50246309-G-C		not specified	Uncertain significance (Apr 18, 2023)
22-50246336-C-G		not specified	Uncertain significance (Aug 21, 2023)
22-50246343-C-G		not specified	Uncertain significance (Aug 17, 2021)
22-50246351-C-T		not specified	Uncertain significance (Jun 06, 2023)
22-50246372-T-G		not specified	Uncertain significance (May 16, 2023)
22-50246373-C-A		not specified	Uncertain significance (May 16, 2023)
22-50246704-G-A		not specified	Uncertain significance (Feb 22, 2023)
22-50246709-A-G		not specified	Uncertain significance (Dec 30, 2023)
22-50246923-G-T		not specified	Uncertain significance (Dec 17, 2023)
22-50246927-C-T		not specified	Uncertain significance (Dec 07, 2021)
22-50247706-T-C		not specified	Uncertain significance (Mar 19, 2024)
22-50247730-T-C		not specified	Uncertain significance (Feb 05, 2024)
22-50247938-A-G		not specified	Uncertain significance (Sep 26, 2023)
22-50247962-G-T		not specified	Uncertain significance (Aug 21, 2023)
22-50247971-G-C		not specified	Uncertain significance (Jul 11, 2023)
22-50247995-C-A		not specified	Uncertain significance (Sep 30, 2021)
22-50248008-C-T		not specified	Likely benign (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDAC10	protein_coding	protein_coding	ENST00000216271	20	6223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-31	0.00000355	125324	0	363	125687	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.451	423	398	1.06	0.0000231	4195
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00315	0.00313
Ashkenazi Jewish	0.000309	0.000298
East Asian	0.00110	0.00109
Finnish	0.00203	0.00199
European (Non-Finnish)	0.00141	0.00136
Middle Eastern	0.00110	0.00109
South Asian	0.00148	0.00144
Other	0.00133	0.00131

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.
• Pathway: Viral carcinogenesis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Neural Crest Differentiation;Ectoderm Differentiation;Ethanol effects on histone modifications;Disease;Signal Transduction;HDACs deacetylate histones;Chromatin modifying enzymes;Signaling by NOTCH1;Signaling by NOTCH;Signaling events mediated by HDAC Class II;Chromatin organization;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: 0.154

Intolerance Scores

• loftool: 0.849
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.63

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.486
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• 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: Hdac10
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;regulation of transcription, DNA-templated;protein deacetylation;oligodendrocyte development;histone deacetylation;negative regulation of transcription, DNA-templated;histone H3 deacetylation
• Cellular component: histone deacetylase complex;nucleus;nucleoplasm;cytoplasm
• Molecular function: histone deacetylase activity;protein binding;enzyme binding;NAD-dependent histone deacetylase activity (H3-K14 specific);protein deacetylase activity;histone deacetylase binding