USP21

ubiquitin specific peptidase 21, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 1:161159449-161165723

Previous symbols: [ "USP23" ]

Links

ENSG00000143258 ∙ NCBI:27005 ∙ OMIM:604729 ∙ HGNC:12620 ∙ Uniprot:Q9UK80 ∙ 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 USP21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP21 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in USP21

This is a list of pathogenic ClinVar variants found in the USP21 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-161160662-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-161160663-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-161160671-C-T		not specified	Uncertain significance (Oct 06, 2023)
1-161160678-G-A		not specified	Uncertain significance (May 30, 2024)
1-161160751-G-T		not specified	Uncertain significance (Jun 18, 2021)
1-161160753-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-161160795-T-G		not specified	Uncertain significance (Mar 20, 2023)
1-161160804-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-161160855-G-A		not specified	Uncertain significance (Apr 29, 2024)
1-161160870-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-161160947-C-G		not specified	Uncertain significance (Apr 25, 2023)
1-161160953-C-T		not specified	Uncertain significance (Nov 29, 2023)
1-161161068-C-T		not specified	Uncertain significance (Jun 01, 2022)
1-161161070-C-T		not specified	Uncertain significance (May 09, 2022)
1-161161073-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-161161074-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-161161113-G-A		not specified	Uncertain significance (Aug 18, 2023)
1-161161127-T-G		not specified	Uncertain significance (Jan 26, 2023)
1-161161209-C-A		not specified	Uncertain significance (Jun 09, 2022)
1-161162312-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-161162960-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-161162990-G-A		not specified	Uncertain significance (Jul 27, 2022)
1-161163037-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-161163566-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-161163583-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP21	protein_coding	protein_coding	ENST00000368002	12	6274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00264	0.997	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	250	361	0.692	0.0000241	3569
Missense in Polyphen		60	114.22	0.5253		1246
Synonymous	0.430	124	130	0.952	0.00000656	1265
Loss of Function	3.97	12	38.6	0.311	0.00000315	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinates histone H2A, a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A releaves the repression of di- and trimethylation of histone H3 at 'Lys-4', resulting in regulation of transcriptional initiation. Regulates gene expression via histone H2A deubiquitination (By similarity). Also capable of removing NEDD8 from NEDD8 conjugates but has no effect on Sentrin-1 conjugates (PubMed:10799498). Deubiquitinates BAZ2A/TIP5 leading to its stabilization (PubMed:26100909). {ECO:0000250|UniProtKB:Q9QZL6, ECO:0000269|PubMed:10799498, ECO:0000269|PubMed:26100909}.
• Pathway: Necroptosis - Homo sapiens (human);Signal Transduction;Post-translational protein modification;Metabolism of proteins;TNFR1-induced NFkappaB signaling pathway;TNFR1-induced proapoptotic signaling;TNF signaling;Ub-specific processing proteases;Deubiquitination;Death Receptor Signalling (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.653
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.390
• hipred: Y
• hipred_score: 0.651
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Usp21
• Phenotype: homeostasis/metabolism phenotype; 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); embryo phenotype; immune system phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;histone deubiquitination;protein deubiquitination;neuron projection development;positive regulation of transcription, DNA-templated
• Cellular component: cellular_component;nucleoplasm;cytoplasm;cytosol;plasma membrane
• Molecular function: transcription coactivator activity;thiol-dependent ubiquitin-specific protease activity;protein binding;cysteine-type peptidase activity;NEDD8-specific protease activity;thiol-dependent ubiquitinyl hydrolase activity;metal ion binding