USP25

ubiquitin specific peptidase 25, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 21:15729982-15880064

Links

ENSG00000155313

∙ NCBI:29761 ∙ OMIM:604736 ∙ HGNC:12624 ∙ Uniprot:Q9UHP3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, idiopathic generalized, susceptibility to, 19	AD	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	Neurologic	38875478

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP25 gene.

not_specified (101 variants)
not_provided (1 variants)
Epilepsy,_idiopathic_generalized,_susceptibility_to,_19 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP25 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001283041.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			103 clinvar			103
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	103	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP25	protein_coding	protein_coding	ENST00000285679	24	150034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.752	0.248	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	453	533	0.849	0.0000264	6931
Missense in Polyphen		63	90.875	0.69326		1158
Synonymous	0.256	188	193	0.977	0.0000100	1875
Loss of Function	5.95	14	66.3	0.211	0.00000376	815

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.000505	0.000496
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000112	0.000109
South Asian	0.000165	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates and thus, functions to process newly synthesized Ubiquitin, to recycle ubiquitin molecules or to edit polyubiquitin chains and prevents proteasomal degradation of substrates. Hydrolyzes both 'Lys-48'- and 'Lys-63'-linked tetraubiquitin chains.;
Pathway: IL-17 signaling pathway - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.660
rvis_EVS: -0.91
rvis_percentile_EVS: 10.12

Haploinsufficiency Scores

pHI: 0.166
hipred: Y
hipred_score: 0.708
ghis: 0.626

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Usp25
Phenotype: hematopoietic system phenotype; immune system phenotype; respiratory system phenotype;

Zebrafish Information Network

Gene name: usp25
Affected structure: pharyngeal arch cartilage
Phenotype tag: abnormal
Phenotype quality: malformed

Gene ontology

Biological process: cellular protein modification process;proteolysis;ubiquitin-dependent protein catabolic process;protein deubiquitination;regulation of protein stability;protein K63-linked deubiquitination;protein K48-linked deubiquitination;negative regulation of ERAD pathway
Cellular component: nucleus;endoplasmic reticulum;cytosol
Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;peptidase activity;ubiquitin protein ligase binding;thiol-dependent ubiquitinyl hydrolase activity;ubiquitin binding;ATPase binding;ubiquitin-specific protease activity involved in negative regulation of ERAD pathway