USP33
ubiquitin specific peptidase 33, the group of Ubiquitin specific peptidases
Basic information
Region (hg38): 1:77695986-77759852
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 USP33 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 | 38 | 38 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 38 | 0 | 0 |
Variants in USP33
This is a list of pathogenic ClinVar variants found in the USP33 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-77697387-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-77697404-T-A | not specified | Uncertain significance (May 24, 2024) | ||
| 1-77697454-A-C | not specified | Uncertain significance (Dec 28, 2022) | ||
| 1-77697904-T-C | not specified | Uncertain significance (Feb 14, 2024) | ||
| 1-77701401-T-C | not specified | Uncertain significance (Jun 16, 2024) | ||
| 1-77701435-T-C | not specified | Uncertain significance (Jun 09, 2022) | ||
| 1-77701437-G-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 1-77701461-G-A | not specified | Uncertain significance (May 26, 2024) | ||
| 1-77701462-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-77714662-C-T | not specified | Uncertain significance (Jan 22, 2024) | ||
| 1-77714669-C-G | not specified | Uncertain significance (May 31, 2023) | ||
| 1-77714740-T-G | not specified | Uncertain significance (Oct 30, 2023) | ||
| 1-77714756-C-G | not specified | Uncertain significance (Apr 26, 2023) | ||
| 1-77714760-T-C | not specified | Uncertain significance (Mar 11, 2022) | ||
| 1-77715846-G-C | not specified | Uncertain significance (Apr 30, 2024) | ||
| 1-77717909-A-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 1-77717963-C-T | not specified | Uncertain significance (Dec 14, 2021) | ||
| 1-77717971-G-A | Uncertain significance (Nov 01, 2022) | |||
| 1-77722040-T-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 1-77722076-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 1-77722100-T-C | not specified | Uncertain significance (Feb 10, 2022) | ||
| 1-77722154-T-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-77723366-T-C | not specified | Uncertain significance (Jul 14, 2022) | ||
| 1-77723437-G-C | not specified | Uncertain significance (Nov 17, 2023) | ||
| 1-77725634-G-C | not specified | Uncertain significance (Jan 23, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| USP33 | protein_coding | protein_coding | ENST00000370793 | 24 | 63866 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.862 | 0.138 | 125725 | 0 | 20 | 125745 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.10 | 341 | 469 | 0.727 | 0.0000225 | 6223 |
| Missense in Polyphen | 99 | 195.68 | 0.50593 | 2649 | ||
| Synonymous | -0.425 | 168 | 161 | 1.04 | 0.00000840 | 1686 |
| Loss of Function | 5.50 | 11 | 55.0 | 0.200 | 0.00000285 | 685 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000605 | 0.0000605 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000709 | 0.0000703 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000177 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Deubiquitinating enzyme involved in various processes such as centrosome duplication, cellular migration and beta-2 adrenergic receptor/ADRB2 recycling. Involved in regulation of centrosome duplication by mediating deubiquitination of CCP110 in S and G2/M phase, leading to stabilize CCP110 during the period which centrioles duplicate and elongate. Involved in cell migration via its interaction with intracellular domain of ROBO1, leading to regulate the Slit signaling. Plays a role in commissural axon guidance cross the ventral midline of the neural tube in a Slit-dependent manner, possibly by mediating the deubiquitination of ROBO1. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination of beta-arrestins (ARRB1 and ARRB2) and beta-2 adrenergic receptor (ADRB2). Plays a central role in ADRB2 recycling and resensitization after prolonged agonist stimulation by constitutively binding ADRB2, mediating deubiquitination of ADRB2 and inhibiting lysosomal trafficking of ADRB2. Upon dissociation, it is probably transferred to the translocated beta- arrestins, leading to beta-arrestins deubiquitination and disengagement from ADRB2. This suggests the existence of a dynamic exchange between the ADRB2 and beta-arrestins. Deubiquitinates DIO2, thereby regulating thyroid hormone regulation. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. {ECO:0000269|PubMed:12865408, ECO:0000269|PubMed:19363159, ECO:0000269|PubMed:19424180, ECO:0000269|PubMed:23486064}.;
- Pathway
- Developmental Biology;Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination;Regulation of expression of SLITs and ROBOs;Signaling by ROBO receptors;Axon guidance
(Consensus)
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.541
- rvis_EVS
- -1.44
- rvis_percentile_EVS
- 3.96
Haploinsufficiency Scores
- pHI
- 0.713
- hipred
- Y
- hipred_score
- 0.639
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.758
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp33
- Phenotype
- hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- usp33
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- curled
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;endocytosis;axon guidance;regulation of G protein-coupled receptor signaling pathway;cellular response to starvation;regulation of autophagy;cell migration;protein deubiquitination;negative regulation of protein binding;positive regulation of protein binding;protein stabilization;centrosome duplication;protein K63-linked deubiquitination;protein K48-linked deubiquitination
- Cellular component
- nucleoplasm;cytoplasm;Golgi apparatus;centrosome;cytosol;focal adhesion;VCB complex;cell body;perinuclear region of cytoplasm
- Molecular function
- G protein-coupled receptor binding;cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;zinc ion binding;Ral GTPase binding;thiol-dependent ubiquitinyl hydrolase activity;ubiquitin binding