USP11

ubiquitin specific peptidase 11, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): X:47232866-47248328

Links

ENSG00000102226 ∙ NCBI:8237 ∙ OMIM:300050 ∙ HGNC:12609 ∙ Uniprot:P51784 ∙ 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 USP11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP11 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		1		7	8	16
missense		1	39	2	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	39	9	9

Variants in USP11

This is a list of pathogenic ClinVar variants found in the USP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-47232979-T-C		not specified	Uncertain significance (Aug 19, 2024)
X-47233011-A-C		not specified	Uncertain significance (Nov 23, 2024)
X-47233024-G-A		not specified	Uncertain significance (Mar 24, 2023)
X-47233041-G-C		not specified	Uncertain significance (Oct 06, 2024)
X-47233043-G-C			Likely benign (Jun 22, 2018)
X-47233055-C-T			Likely benign (Mar 01, 2023)
X-47233060-C-T		not specified	Uncertain significance (Oct 27, 2022)
X-47233066-C-T		not specified	Uncertain significance (Dec 15, 2022)
X-47239077-G-C		not specified	Uncertain significance (Jan 16, 2024)
X-47239175-T-C			Benign (Dec 31, 2019)
X-47239366-G-A		not specified	Uncertain significance (Dec 03, 2021)
X-47239455-C-T		not specified	Uncertain significance (Feb 27, 2025)
X-47239825-G-A			Benign (Dec 31, 2019)
X-47239829-C-T		not specified	Uncertain significance (Jan 31, 2024)
X-47239872-C-T		not specified	Uncertain significance (Jun 07, 2024)
X-47240328-G-A		not specified	Uncertain significance (Oct 04, 2024)
X-47240345-G-C		not specified	Uncertain significance (Sep 17, 2021)
X-47240362-G-A		Abnormal brain morphology	Likely pathogenic (-)
X-47240788-C-T		not specified	Uncertain significance (Dec 19, 2022)
X-47241303-C-T			Likely benign (Apr 16, 2018)
X-47241359-G-C		not specified	Uncertain significance (Mar 25, 2024)
X-47241373-A-G		not specified	Uncertain significance (Feb 24, 2025)
X-47242241-A-G		not specified	Likely benign (Mar 11, 2024)
X-47242260-T-C		not specified	Uncertain significance (Dec 03, 2024)
X-47242288-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP11	protein_coding	protein_coding	ENST00000218348	21	15639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000377	125510	0	2	125512	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.57	225	435	0.518	0.0000379	6324
Missense in Polyphen		65	197.84	0.32855		2795
Synonymous	-0.811	194	180	1.08	0.0000159	1892
Loss of Function	5.38	2	37.6	0.0532	0.00000283	572

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000790	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000526	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains (PubMed:12084015, PubMed:15314155, PubMed:17897950, PubMed:19874889, PubMed:20233726, PubMed:24724799). Inhibits the degradation of target proteins by the proteasome (PubMed:12084015). Cleaves preferentially 'Lys-6' and 'Lys-63'-linked ubiquitin chains. Has lower activity with 'Lys-11' and 'Lys-33'-linked ubiquitin chains, and extremely low activity with 'Lys-27', 'Lys-29' and 'Lys-48'- linked ubiquitin chains (in vitro) (PubMed:24724799). Plays a role in the regulation of pathways leading to NF-kappa-B activation (PubMed:17897950, PubMed:19874889). Plays a role in the regulation of DNA repair after double-stranded DNA breaks (PubMed:15314155, PubMed:20233726). Acts as a chromatin regulator via its association with the Polycomb group (PcG) multiprotein PRC1-like complex; may act by deubiquitinating components of the PRC1-like complex (PubMed:20601937). {ECO:0000269|PubMed:15314155, ECO:0000269|PubMed:17897950, ECO:0000269|PubMed:18408009, ECO:0000269|PubMed:19874889, ECO:0000269|PubMed:20233726, ECO:0000269|PubMed:24724799}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Ub-specific processing proteases;Protein folding;Deubiquitination;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.172
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.71

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.771
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.594

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp11
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: usp11
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination
• Cellular component: nucleus;nucleoplasm;chromosome;cytosol
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity