HDAC11

histone deacetylase 11, the group of Histone deacetylases, class IV

Basic information

Region (hg38): 3:13479724-13506424

Links

ENSG00000163517

∙ NCBI:79885 ∙ OMIM:607226 ∙ HGNC:19086 ∙ Uniprot:Q96DB2 ∙ 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 HDAC11 gene.

not_specified (46 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDAC11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024827.4. 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						0
missense			42 clinvar	4 clinvar		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	4	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDAC11	protein_coding	protein_coding	ENST00000295757	10	26693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00693	0.990	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	167	229	0.729	0.0000151	2239
Missense in Polyphen		51	91.33	0.55841		1006
Synonymous	-0.0558	89	88.3	1.01	0.00000541	713
Loss of Function	2.57	7	19.1	0.366	0.00000117	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000180	0.000180
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000343	0.0000327
Other	0.000163	0.000163

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. {ECO:0000269|PubMed:11948178}.;
Pathway: Viral carcinogenesis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Valproic Acid Pathway, Pharmacodynamics;Pathway_PA165964473;Neural Crest Differentiation;Disease;Signal Transduction;Signaling by NOTCH1;Signaling by NOTCH;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: 0.143

Intolerance Scores

loftool: 0.598
rvis_EVS: -0.67
rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

pHI: 0.148
hipred: Y
hipred_score: 0.756
ghis: 0.636

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.843

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Hdac11
Phenotype: neoplasm; immune system phenotype;

Gene ontology

Biological process: chromatin organization;oligodendrocyte development;histone deacetylation;histone H3 deacetylation
Cellular component: histone deacetylase complex;nucleus;plasma membrane
Molecular function: histone deacetylase activity;transcription factor binding;NAD-dependent histone deacetylase activity (H3-K14 specific)