USP20

ubiquitin specific peptidase 20, the group of Ubiquitin specific peptidases|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:129834698-129881828

Links

ENSG00000136878 ∙ ∙ OMIM:615143 ∙ HGNC:12619 ∙ Uniprot:Q9Y2K6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP20 gene.

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	5
missense			79	2	1	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: gnomAD

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: dbNSFP

• 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