USP26

ubiquitin specific peptidase 26, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): X:133023168-133097109

Links

ENSG00000134588 ∙ NCBI:83844 ∙ OMIM:300309 ∙ HGNC:13485 ∙ Uniprot:Q9BXU7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure, X-linked, 6 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure, X-linked, 6	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	36796361

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP26 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP26 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				9	2	11
missense			28	10	2	40
nonsense						0
start loss						0
frameshift			2			2
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	19	5

Variants in USP26

This is a list of pathogenic ClinVar variants found in the USP26 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-133025483-T-C			Likely benign (Mar 01, 2022)
X-133025506-C-A		not specified	Uncertain significance (May 27, 2022)
X-133025575-A-C		not specified	Uncertain significance (Oct 25, 2024)
X-133025597-C-T		not specified	Uncertain significance (Aug 12, 2021)
X-133025607-C-T		not specified	Likely benign (Dec 20, 2023)
X-133025639-C-T		not specified	Likely benign (Dec 10, 2024)
X-133025748-G-C		Spermatogenic failure, X-linked, 6	Pathogenic (Mar 16, 2023)
X-133025764-C-A		not specified	Uncertain significance (Sep 16, 2021)
X-133025825-T-C		Spermatogenic failure, X-linked, 6	Pathogenic (Mar 16, 2023)
X-133025894-G-A			Likely benign (Apr 01, 2022)
X-133025991-C-T		not specified	Uncertain significance (Jan 05, 2022)
X-133026023-T-C		not specified	Uncertain significance (Apr 22, 2022)
X-133026081-T-A		not specified	Uncertain significance (Dec 10, 2024)
X-133026081-T-C		not specified	Uncertain significance (Aug 15, 2023)
X-133026128-C-T		not specified	Likely benign (Oct 04, 2024)
X-133026133-T-C		USP26-related disorder	Benign (Dec 31, 2019)
X-133026159-C-T			Likely benign (Sep 01, 2022)
X-133026212-T-C		USP26-related disorder	Likely benign (May 10, 2022)
X-133026227-G-A		not specified	Uncertain significance (Dec 05, 2022)
X-133026229-G-C		USP26-related disorder	Likely benign (Mar 20, 2019)
X-133026238-C-A		USP26-related disorder	Likely benign (Mar 20, 2019)
X-133026245-G-A			Likely benign (Dec 31, 2019)
X-133026267-C-G		not specified	Uncertain significance (Oct 06, 2021)
X-133026287-T-C		not specified	Uncertain significance (Mar 12, 2024)
X-133026334-A-G			Likely benign (Apr 02, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP26	protein_coding	protein_coding	ENST00000511190	1	72479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0837	321	317	1.01	0.0000224	6067
Missense in Polyphen		44	67.513	0.65172		1490
Synonymous	-0.300	126	122	1.03	0.00000885	1681
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the ubiquitin-dependent proteolytic pathway in conjunction with the 26S proteasome (By similarity). Deubiquitinates the androgen receptor and regulates the androgen receptor signaling pathway. {ECO:0000250, ECO:0000269|PubMed:20501646}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.0741

Intolerance Scores

• loftool: 0.414
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.0911
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp26

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;ubiquitin-dependent protein catabolic process;protein deubiquitination
• Cellular component: nucleus;nucleoplasm
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity