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.

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.

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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in HDAC11

This is a list of pathogenic ClinVar variants found in the HDAC11 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-13481284-C-T		not specified	Uncertain significance (Jul 15, 2021)
3-13481293-C-A		not specified	Uncertain significance (Jan 26, 2022)
3-13481371-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-13481393-A-C		not specified	Uncertain significance (Dec 03, 2024)
3-13483464-A-T		not specified	Uncertain significance (Sep 20, 2024)
3-13496784-C-T		not specified	Uncertain significance (Apr 09, 2024)
3-13498552-G-A		not specified	Uncertain significance (Apr 08, 2024)
3-13500766-G-T		not specified	Uncertain significance (Mar 05, 2024)
3-13501883-C-T		not specified	Uncertain significance (Jul 14, 2023)
3-13502929-A-G		not specified	Uncertain significance (Oct 12, 2021)
3-13502969-G-A		not specified	Uncertain significance (Aug 06, 2024)
3-13502969-G-T		not specified	Uncertain significance (Mar 23, 2023)
3-13504105-C-T		not specified	Uncertain significance (Dec 07, 2021)
3-13504106-G-A		not specified	Uncertain significance (Aug 22, 2022)
3-13504122-G-T		not specified	Uncertain significance (Oct 10, 2023)
3-13504190-A-G		not specified	Uncertain significance (Apr 09, 2024)
3-13504513-C-T		not specified	Uncertain significance (Sep 03, 2024)
3-13504516-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-13504517-G-A		not specified	Likely benign (Apr 04, 2024)
3-13504546-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-13504613-T-C		not specified	Uncertain significance (May 17, 2023)
3-13504627-C-G		not specified	Uncertain significance (Jan 17, 2024)
3-13504633-G-A		not specified	Likely benign (Aug 02, 2022)
3-13504646-A-G		not specified	Uncertain significance (Dec 14, 2022)
3-13504658-C-T		not specified	Uncertain significance (May 21, 2024)

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)