USP54

ubiquitin specific peptidase 54, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 10:73497538-73626117

Previous symbols: [ "C10orf29" ]

Links

ENSG00000166348 ∙ NCBI:159195 ∙ ∙ HGNC:23513 ∙ Uniprot:Q70EL1 ∙ 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 USP54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP54 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		1
missense			78	5		83
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	78	8	0

Variants in USP54

This is a list of pathogenic ClinVar variants found in the USP54 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73498691-G-C		not specified	Uncertain significance (May 31, 2023)
10-73498705-C-T		not specified	Likely benign (Oct 31, 2024)
10-73498804-C-T		not specified	Uncertain significance (Jun 03, 2022)
10-73498808-A-G		not specified	Uncertain significance (Mar 31, 2024)
10-73498853-G-T		not specified	Uncertain significance (Oct 20, 2023)
10-73498943-C-T		not specified	Uncertain significance (Nov 21, 2022)
10-73498952-C-T		not specified	Uncertain significance (Apr 26, 2023)
10-73498953-C-A		not specified	Uncertain significance (Oct 07, 2024)
10-73498967-G-A		not specified	Uncertain significance (Apr 25, 2023)
10-73499080-C-T		not specified	Uncertain significance (Sep 06, 2022)
10-73499081-G-A		not specified	Uncertain significance (Nov 12, 2024)
10-73499129-C-T		not specified	Uncertain significance (Oct 21, 2024)
10-73499138-T-C		not specified	Uncertain significance (Jun 01, 2023)
10-73500658-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-73500741-C-T		not specified	Uncertain significance (Mar 28, 2024)
10-73500760-G-C		not specified	Uncertain significance (Mar 01, 2023)
10-73500795-C-T		not specified	Uncertain significance (Oct 03, 2024)
10-73500799-G-A		USP54-related disorder	Likely benign (May 23, 2022)
10-73500805-C-T		not specified	Uncertain significance (Jun 18, 2024)
10-73504852-A-T		not specified	Uncertain significance (May 23, 2024)
10-73504855-T-C		not specified	Uncertain significance (Sep 01, 2021)
10-73504869-G-A		not specified	Uncertain significance (Dec 22, 2023)
10-73504894-C-T		not specified	Uncertain significance (Sep 30, 2021)
10-73504912-G-A		not specified	Uncertain significance (Jan 23, 2023)
10-73504920-C-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP54	protein_coding	protein_coding	ENST00000339859	22	128416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.39e-11	1.00	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	729	910	0.801	0.0000477	11079
Missense in Polyphen		269	383.78	0.70091		4768
Synonymous	2.01	291	338	0.861	0.0000174	3281
Loss of Function	4.84	32	78.2	0.409	0.00000423	879

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000355
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000399	0.000326
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000399	0.000326
South Asian	0.000262	0.000261
Other	0.000339	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has no peptidase activity.

Intolerance Scores

• loftool: 0.835
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.38

Haploinsufficiency Scores

• pHI: 0.255
• hipred: N
• hipred_score: 0.343
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp54
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein deubiquitination
• Molecular function: protein binding;thiol-dependent ubiquitinyl hydrolase activity