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.

• not_specified (188 variants)
• USP54-related_disorder (4 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_001391956.1. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			178	11		189
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	178	13	0

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