USP25
ubiquitin specific peptidase 25, the group of Ubiquitin specific peptidases
Basic information
Region (hg38): 21:15729982-15880064
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| 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
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.
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 | 70 | 70 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 70 | 0 | 0 |
Variants in USP25
This is a list of pathogenic ClinVar variants found in the USP25 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-15730425-G-A | not specified | Uncertain significance (Jun 17, 2022) | ||
| 21-15762892-A-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 21-15762898-A-G | not specified | Uncertain significance (Oct 06, 2021) | ||
| 21-15762901-C-G | not specified | Uncertain significance (Oct 14, 2021) | ||
| 21-15762948-A-G | not specified | Uncertain significance (Aug 19, 2024) | ||
| 21-15791543-A-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 21-15791558-A-C | not specified | Uncertain significance (Aug 12, 2024) | ||
| 21-15791580-C-G | not specified | Uncertain significance (Feb 17, 2022) | ||
| 21-15799794-T-G | not specified | Uncertain significance (Jan 23, 2025) | ||
| 21-15799829-C-A | not specified | Uncertain significance (Jun 26, 2024) | ||
| 21-15805127-C-T | not specified | Uncertain significance (Dec 09, 2023) | ||
| 21-15805128-G-A | not specified | Uncertain significance (Jun 03, 2024) | ||
| 21-15805136-C-T | not specified | Uncertain significance (Aug 06, 2024) | ||
| 21-15805145-C-T | not specified | Uncertain significance (Dec 15, 2021) | ||
| 21-15805176-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 21-15808847-G-T | not specified | Uncertain significance (Jun 05, 2024) | ||
| 21-15811146-G-C | not specified | Uncertain significance (Jan 31, 2024) | ||
| 21-15811146-G-T | not specified | Uncertain significance (May 25, 2022) | ||
| 21-15818749-A-G | not specified | Uncertain significance (Jun 18, 2024) | ||
| 21-15824097-A-G | not specified | Uncertain significance (Aug 18, 2023) | ||
| 21-15824100-A-G | not specified | Uncertain significance (Mar 19, 2024) | ||
| 21-15824114-C-T | not specified | Uncertain significance (Dec 05, 2024) | ||
| 21-15824127-A-G | not specified | Uncertain significance (Dec 03, 2024) | ||
| 21-15824972-G-T | not specified | Uncertain significance (Dec 02, 2022) | ||
| 21-15824988-A-G | not specified | Uncertain significance (Jun 11, 2024) |
GnomAD
Source:
| 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:
- 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