USP24
Basic information
Region (hg38): 1:55066359-55215378
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (196 variants)
- not_provided (6 variants)
- Short_stature (3 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. These statistics are base on transcript: NM_000015306.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 5 | |||||
missense | 194 | 199 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 194 | 5 | 5 |
Highest pathogenic variant AF is 0.00000425199
GnomAD
Source:
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:
- 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
- loftool
- 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