USP51

ubiquitin specific peptidase 51, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): X:55484615-55489848

Links

ENSG00000247746 ∙ NCBI:158880 ∙ ∙ HGNC:23086 ∙ Uniprot:Q70EK9 ∙ 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 USP51 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP51 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	1

Variants in USP51

This is a list of pathogenic ClinVar variants found in the USP51 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-55486818-G-C		not specified	Uncertain significance (Oct 13, 2023)
X-55486967-T-C		not specified	Uncertain significance (May 29, 2024)
X-55487243-G-A		not specified	Uncertain significance (Jun 17, 2024)
X-55487287-G-A			Likely benign (May 01, 2023)
X-55487378-G-C		not specified	Uncertain significance (Dec 09, 2023)
X-55487628-G-A		not specified	Uncertain significance (Jan 26, 2023)
X-55487767-G-T		not specified	Uncertain significance (Jun 28, 2023)
X-55488029-G-A		not specified	Uncertain significance (Apr 20, 2024)
X-55488079-C-T		not specified	Uncertain significance (Apr 08, 2024)
X-55488278-C-A		not specified	Uncertain significance (Apr 24, 2024)
X-55488330-C-T		not specified	Uncertain significance (May 05, 2023)
X-55488448-T-C			Benign (Feb 02, 2018)
X-55488483-T-C		not specified	Uncertain significance (Nov 13, 2023)
X-55488524-G-T		not specified	Uncertain significance (Oct 20, 2021)
X-55488540-G-A		not specified	Uncertain significance (Jan 16, 2024)
X-55488570-G-A		not specified	Uncertain significance (Jun 16, 2024)
X-55488572-G-A		not specified	Uncertain significance (Aug 12, 2022)
X-55488621-G-C		not specified	Uncertain significance (Mar 08, 2024)
X-55488636-G-A		not specified	Uncertain significance (Apr 11, 2023)
X-55488653-G-A		not specified	Uncertain significance (Dec 22, 2023)
X-55488654-A-C		not specified	Uncertain significance (Feb 17, 2022)
X-55488659-C-G		not specified	Uncertain significance (Feb 28, 2024)
X-55488704-C-T		not specified	Uncertain significance (Jan 12, 2024)
X-55488730-C-A		not specified	Uncertain significance (Jul 26, 2022)
X-55488760-T-C			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP51	protein_coding	protein_coding	ENST00000500968	1	4587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.126	0.869	125740	1	5	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	203	254	0.800	0.0000173	4670
Missense in Polyphen		38	91.103	0.41711		1865
Synonymous	-1.48	118	99.3	1.19	0.00000677	1384
Loss of Function	2.48	4	14.0	0.285	0.00000103	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000200	0.000160
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000652	0.0000462
European (Non-Finnish)	0.0000258	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically deubiquitinates 'Lys-14' (H2AK13Ub) and 'Lys-16'(H2AK15Ub) of histone H2A regulating the DNA damage response at double-strand breaks (DSBs) (PubMed:27083998). USP51 is recruited to chromatin after DNA damage and regulates the dynamic assembly/disassembly of TP53BP1 and BRCA1. Exhibits also activity for 'Lys-27' or 'Lys-63'-linked di-ubiquitin (PubMed:27083998). {ECO:0000269|PubMed:27083998}.

Recessive Scores

• pRec: 0.0877

Intolerance Scores

• loftool: 0.0619
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.455
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp51

Gene ontology

• Biological process: DNA repair;ubiquitin-dependent protein catabolic process;regulation of cell cycle process;regulation of double-strand break repair via homologous recombination;histone deubiquitination;protein deubiquitination;regulation of response to DNA damage stimulus;regulation of double-strand break repair via nonhomologous end joining
• Cellular component: chromosome
• Molecular function: chromatin binding;thiol-dependent ubiquitin-specific protease activity;zinc ion binding;histone binding