UCHL5
ubiquitin C-terminal hydrolase L5, the group of Ubiquitin C-terminal hydrolases|INO80 complex
Basic information
Region (hg38): 1:193012249-193060080
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UCHL5 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 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in UCHL5
This is a list of pathogenic ClinVar variants found in the UCHL5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-193021159-A-G | not specified | Uncertain significance (Jun 05, 2024) | ||
| 1-193021195-T-A | not specified | Uncertain significance (Oct 18, 2021) | ||
| 1-193023024-T-C | not specified | Uncertain significance (Dec 21, 2023) | ||
| 1-193023840-G-A | Benign (Jul 21, 2018) | |||
| 1-193023870-C-T | not specified | Uncertain significance (Oct 03, 2023) | ||
| 1-193023873-T-C | not specified | Uncertain significance (Mar 30, 2024) | ||
| 1-193023941-C-G | not specified | Uncertain significance (Dec 06, 2021) | ||
| 1-193028139-T-C | not specified | Uncertain significance (May 09, 2022) | ||
| 1-193028145-G-C | not specified | Uncertain significance (May 31, 2023) | ||
| 1-193029223-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-193029302-T-C | not specified | Uncertain significance (Dec 02, 2022) | ||
| 1-193029587-T-C | not specified | Uncertain significance (Apr 05, 2023) | ||
| 1-193059240-C-T | Likely benign (Apr 01, 2022) | |||
| 1-193059250-T-C | not specified | Uncertain significance (Jan 12, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UCHL5 | protein_coding | protein_coding | ENST00000367455 | 11 | 47858 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00126 | 0.997 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.94 | 99 | 170 | 0.582 | 0.00000791 | 2192 |
| Missense in Polyphen | 20 | 57.752 | 0.34631 | 759 | ||
| Synonymous | 0.0100 | 59 | 59.1 | 0.998 | 0.00000301 | 550 |
| Loss of Function | 2.76 | 9 | 23.4 | 0.385 | 0.00000121 | 278 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000150 | 0.000149 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.0000559 | 0.0000544 |
| Finnish | 0.0000926 | 0.0000924 |
| European (Non-Finnish) | 0.0000447 | 0.0000439 |
| Middle Eastern | 0.0000559 | 0.0000544 |
| South Asian | 0.000131 | 0.0000980 |
| Other | 0.000177 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Protease that specifically cleaves 'Lys-48'-linked polyubiquitin chains. Deubiquitinating enzyme associated with the 19S regulatory subunit of the 26S proteasome. Putative regulatory component of the INO80 complex; however is inactive in the INO80 complex and is activated by a transient interaction of the INO80 complex with the proteasome via ADRM1. {ECO:0000269|PubMed:16906146, ECO:0000269|PubMed:18922472}.;
- Pathway
- TGF-Ncore;TGF-beta Signaling Pathway;Signal Transduction;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Deubiquitination;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs
(Consensus)
Recessive Scores
- pRec
- 0.137
Intolerance Scores
- loftool
- 0.683
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.207
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.670
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Uchl5
- 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; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- uchl5
- Affected structure
- pharyngeal arch cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- DNA repair;DNA recombination;ubiquitin-dependent protein catabolic process;negative regulation of endopeptidase activity;protein deubiquitination;lateral ventricle development;midbrain development;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;forebrain morphogenesis;regulation of proteasomal protein catabolic process
- Cellular component
- nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;Ino80 complex;cytosolic proteasome complex
- Molecular function
- RNA binding;thiol-dependent ubiquitin-specific protease activity;endopeptidase inhibitor activity;protein binding;proteasome binding