USP20
Basic information
Region (hg38): 9:129834698-129881828
Links
Phenotypes
GenCC
Source:
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 USP20 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 | 5 | |||||
missense | 79 | 82 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 79 | 2 | 6 |
Variants in USP20
This is a list of pathogenic ClinVar variants found in the USP20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-129852572-A-T | not specified | Uncertain significance (May 17, 2023) | ||
9-129852572-A-ACCTTTGC | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
9-129858474-A-G | not specified | Uncertain significance (Jul 11, 2022) | ||
9-129858488-G-A | not specified | Uncertain significance (Jul 17, 2023) | ||
9-129858510-T-G | not specified | Uncertain significance (Oct 20, 2024) | ||
9-129858527-G-A | not specified | Uncertain significance (Dec 06, 2024) | ||
9-129858536-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
9-129858551-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
9-129858576-C-A | Benign (Feb 26, 2018) | |||
9-129860944-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
9-129861554-A-G | not specified | Uncertain significance (Aug 20, 2023) | ||
9-129861558-A-G | not specified | Uncertain significance (Mar 01, 2024) | ||
9-129863223-C-T | Benign (Aug 08, 2017) | |||
9-129865358-A-G | not specified | Uncertain significance (Feb 22, 2023) | ||
9-129868044-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
9-129868063-C-T | not specified | Uncertain significance (Mar 13, 2023) | ||
9-129868092-G-T | not specified | Uncertain significance (Apr 09, 2024) | ||
9-129868129-G-A | not specified | Uncertain significance (Jul 26, 2024) | ||
9-129868140-C-T | not specified | Uncertain significance (Nov 21, 2023) | ||
9-129868177-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
9-129868178-G-A | Benign (May 23, 2018) | |||
9-129868203-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
9-129868212-C-T | not specified | Uncertain significance (May 06, 2024) | ||
9-129868218-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
9-129868236-G-A | not specified | Uncertain significance (Nov 10, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
USP20 | protein_coding | protein_coding | ENST00000315480 | 23 | 47131 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000729 | 1.00 | 124778 | 0 | 44 | 124822 | 0.000176 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.43 | 502 | 601 | 0.836 | 0.0000409 | 5946 |
Missense in Polyphen | 149 | 209.99 | 0.70955 | 2142 | ||
Synonymous | 0.535 | 250 | 261 | 0.958 | 0.0000198 | 1767 |
Loss of Function | 4.66 | 18 | 55.4 | 0.325 | 0.00000288 | 586 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000481 | 0.000480 |
Ashkenazi Jewish | 0.0000998 | 0.0000993 |
East Asian | 0.000278 | 0.000278 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000206 | 0.000194 |
Middle Eastern | 0.000278 | 0.000278 |
South Asian | 0.000164 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Deubiquitinating enzyme involved in beta-2 adrenergic receptor (ADRB2) recycling. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination 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, possibly 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. Deubiquitinates HIF1A, leading to stabilize HIF1A and enhance HIF1A-mediated activity. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. {ECO:0000269|PubMed:12056827, ECO:0000269|PubMed:12865408, ECO:0000269|PubMed:15776016, ECO:0000269|PubMed:19424180}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- loftool
- 0.754
- rvis_EVS
- -0.37
- rvis_percentile_EVS
- 28.29
Haploinsufficiency Scores
- pHI
- 0.184
- hipred
- Y
- hipred_score
- 0.548
- ghis
- 0.542
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.927
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp20
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- usp20
- Affected structure
- pharyngeal arch cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;endocytosis;regulation of G protein-coupled receptor signaling pathway;protein deubiquitination;protein K63-linked deubiquitination;protein K48-linked deubiquitination
- Cellular component
- cytoplasm;centrosome;cytosol;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;thiol-dependent ubiquitinyl hydrolase activity