USP24

ubiquitin specific peptidase 24, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 1:55066358-55215378

Links

ENSG00000162402 ∙ NCBI:23358 ∙ OMIM:610569 ∙ HGNC:12623 ∙ Uniprot:Q9UPU5 ∙ 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 USP24 gene.

• Inborn genetic diseases (54 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP24 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				1	4	5
missense			53	1	1	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	2	5

Variants in USP24

This is a list of pathogenic ClinVar variants found in the USP24 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-55072819-G-A			Benign (Apr 19, 2018)
1-55073899-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-55073913-G-A		Short stature	Likely pathogenic (Nov 18, 2001)
1-55077293-A-T		not specified	Uncertain significance (Jul 09, 2021)
1-55077300-T-C		not specified	Uncertain significance (Nov 22, 2021)
1-55078555-T-C		not specified	Uncertain significance (Oct 19, 2021)
1-55078560-A-T		not specified	Uncertain significance (Mar 22, 2023)
1-55079557-C-G		not specified	Uncertain significance (Sep 26, 2023)
1-55079614-G-A		not specified	Uncertain significance (Feb 14, 2023)
1-55079638-C-T		not specified	Uncertain significance (May 04, 2022)
1-55079651-T-C		not specified	Likely benign (Aug 05, 2023)
1-55081351-T-C		not specified	Uncertain significance (Aug 14, 2023)
1-55081417-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-55081420-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-55083306-C-G		not specified	Uncertain significance (Jun 24, 2022)
1-55083354-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-55083797-A-G		not specified	Uncertain significance (Sep 01, 2021)
1-55085962-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-55086021-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-55089711-A-G		not specified	Uncertain significance (Jan 24, 2024)
1-55092095-A-G		not specified	Uncertain significance (Jun 22, 2023)
1-55092879-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-55095280-G-A		not specified	Uncertain significance (Jun 01, 2023)
1-55095286-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-55096552-T-C		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP24	protein_coding	protein_coding	ENST00000294383	68	148755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.41e-14	125440	0	19	125459	0.0000757

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.99	759	1.26e+3	0.604	0.0000654	17022
Missense in Polyphen		140	358.1	0.39096		4915
Synonymous	0.616	438	455	0.963	0.0000242	4887
Loss of Function	10.2	14	149	0.0942	0.00000827	1906

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000175	0.000160
Ashkenazi Jewish	0.000102	0.0000993
East Asian	0.000111	0.000109
Finnish	0.0000494	0.0000462
European (Non-Finnish)	0.0000805	0.0000793
Middle Eastern	0.000111	0.000109
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-specific protease that regulates cell survival in various contexts through modulating the protein stability of some of its substrates including DDB2, MCL1 or TP53. Plays a positive role on ferritinophagy where ferritin is degraded in lysosomes and releases free iron. {ECO:0000269|PubMed:23159851, ECO:0000269|PubMed:29695420}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• rvis_EVS: -2.16
• rvis_percentile_EVS: 1.44

Haploinsufficiency Scores

• pHI: 0.695
• hipred: Y
• hipred_score: 0.563
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp24
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: usp24
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;thiol-dependent ubiquitinyl hydrolase activity