USP41

ubiquitin specific peptidase 41, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 22:20363621-20377251

Links

ENSG00000161133 ∙ NCBI:373856 ∙ ∙ HGNC:20070 ∙ Uniprot:Q3LFD5 ∙ 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 USP41 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP41 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	0	1	0

Variants in USP41

This is a list of pathogenic ClinVar variants found in the USP41 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-20369492-G-A			Likely benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP41	protein_coding	protein_coding	ENST00000454608	12	40181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.08e-11	0.231	125037	2	709	125748	0.00283

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.596	169	192	0.879	0.0000102	2341
Missense in Polyphen		51	56.256	0.90656		770
Synonymous	-0.758	84	75.6	1.11	0.00000447	623
Loss of Function	0.856	19	23.5	0.809	0.00000124	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0325	0.0309
Ashkenazi Jewish	0.00	0.00
East Asian	0.000547	0.000544
Finnish	0.000239	0.000231
European (Non-Finnish)	0.00109	0.00102
Middle Eastern	0.000547	0.000544
South Asian	0.000772	0.000752
Other	0.00221	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May recognize and hydrolyze the peptide bond at the C- terminal Gly of ubiquitin. Involved in the processing of poly- ubiquitin precursors as well as that of ubiquitinated proteins (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0916

Haploinsufficiency Scores

• pHI: 0.101
• ghis: 0.396

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;regulation of protein stability
• Cellular component: cytosol
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity