USP22

ubiquitin specific peptidase 22, the group of Ubiquitin specific peptidases|SAGA complex

Basic information

Region (hg38): 17:20999596-21043760

Previous symbols: [ "USP3L" ]

Links

ENSG00000124422 ∙ NCBI:23326 ∙ OMIM:612116 ∙ HGNC:12621 ∙ Uniprot:Q9UPT9 ∙ 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 USP22 gene.

• not_specified (31 variants)

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. These statistics are base on transcript: NM_000015276.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			35	1		36
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	37	1	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

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

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