USP22
ubiquitin specific peptidase 22, the group of Ubiquitin specific peptidases|SAGA complex
Basic information
Region (hg38): 17:20999596-21043760
Previous symbols: [ "USP3L" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 USP22 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 | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in USP22
This is a list of pathogenic ClinVar variants found in the USP22 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-21006921-C-T | not specified | Uncertain significance (Jun 22, 2024) | ||
| 17-21006929-A-G | not specified | Uncertain significance (Oct 09, 2024) | ||
| 17-21007940-T-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| 17-21011172-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 17-21011184-G-A | not specified | Uncertain significance (Sep 12, 2023) | ||
| 17-21011188-C-T | not specified | Likely benign (May 28, 2024) | ||
| 17-21018030-C-T | not specified | Uncertain significance (Feb 22, 2025) | ||
| 17-21019087-T-C | not specified | Uncertain significance (Jun 16, 2023) | ||
| 17-21028572-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
| 17-21028644-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-21042691-C-A | not specified | Uncertain significance (Jan 23, 2025) | ||
| 17-21042707-C-G | not specified | Uncertain significance (Jul 02, 2024) | ||
| 17-21042717-G-C | not specified | Uncertain significance (Aug 27, 2024) | ||
| 17-21042798-T-C | not specified | Uncertain significance (Jul 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| USP22 | protein_coding | protein_coding | ENST00000261497 | 13 | 44164 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.552 | 0.448 | 124788 | 0 | 8 | 124796 | 0.0000321 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.56 | 130 | 305 | 0.426 | 0.0000180 | 3472 |
| Missense in Polyphen | 24 | 108.75 | 0.22069 | 1274 | ||
| Synonymous | 1.20 | 111 | 128 | 0.865 | 0.00000872 | 941 |
| Loss of Function | 3.91 | 6 | 28.6 | 0.210 | 0.00000154 | 323 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000291 | 0.0000291 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000553 | 0.0000530 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complex SAGA. Catalyzes the deubiquitination of both histones H2A and H2B, thereby acting as a coactivator. Recruited to specific gene promoters by activators such as MYC, where it is required for transcription. Required for nuclear receptor-mediated transactivation and cell cycle progression. {ECO:0000269|PubMed:18206972, ECO:0000269|PubMed:18206973, ECO:0000269|PubMed:18469533}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Chromatin modifying enzymes;HATs acetylate histones;Ub-specific processing proteases;Deubiquitination;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- 0.153
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.42
Haploinsufficiency Scores
- pHI
- 0.183
- hipred
- Y
- hipred_score
- 0.771
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.755
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp22
- Phenotype
- skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- usp22
- Affected structure
- brain
- Phenotype tag
- abnormal
- Phenotype quality
- bulbous
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;cell cycle;embryo development ending in birth or egg hatching;histone ubiquitination;histone deubiquitination;protein deubiquitination;histone H4 acetylation;positive regulation of transcription, DNA-templated;positive regulation of mitotic cell cycle
- Cellular component
- SAGA complex;nucleoplasm;nuclear speck;SAGA-type complex
- Molecular function
- transcription coactivator activity;thiol-dependent ubiquitin-specific protease activity;protein binding;zinc ion binding;H4 histone acetyltransferase activity;enzyme binding;nuclear receptor transcription coactivator activity;thiol-dependent ubiquitinyl hydrolase activity