YOD1
YOD1 deubiquitinase, the group of OTU domain containing
Basic information
Region (hg38): 1:207043849-207052980
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (47 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the YOD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018566.4. 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 | 1 | |||||
| missense | 47 | 47 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 47 | 1 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| YOD1 | protein_coding | protein_coding | ENST00000315927 | 2 | 9132 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.135 | 0.846 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.524 | 174 | 195 | 0.894 | 0.00000994 | 2247 |
| Missense in Polyphen | 43 | 70.28 | 0.61184 | 885 | ||
| Synonymous | -1.03 | 86 | 74.6 | 1.15 | 0.00000378 | 725 |
| Loss of Function | 2.03 | 3 | 9.87 | 0.304 | 4.24e-7 | 123 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000170 | 0.000163 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000616 | 0.0000615 |
| Middle Eastern | 0.000170 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin. May play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes. May recruit PLAA, UBXN6 and VCP to damaged lysosome membranes decorated with K48-linked ubiquitin chains and remove these chains allowing autophagosome formation (PubMed:27753622). {ECO:0000269|PubMed:19818707, ECO:0000269|PubMed:23827681, ECO:0000269|PubMed:27753622}.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.0740
Intolerance Scores
- loftool
- 0.106
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.63
Haploinsufficiency Scores
- pHI
- 0.155
- hipred
- Y
- hipred_score
- 0.754
- ghis
- 0.465
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Yod1
- Phenotype
Zebrafish Information Network
- Gene name
- yod1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- curled
Gene ontology
- Biological process
- macroautophagy;protein deubiquitination;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;protein K29-linked deubiquitination;protein K11-linked deubiquitination;protein K63-linked deubiquitination;protein K48-linked deubiquitination;negative regulation of retrograde protein transport, ER to cytosol;protein K27-linked deubiquitination;protein K33-linked deubiquitination
- Cellular component
- cytoplasm;cytosol
- Molecular function
- nucleic acid binding;thiol-dependent ubiquitin-specific protease activity;protein binding;ubiquitin protein ligase binding;metal ion binding;Lys63-specific deubiquitinase activity;ubiquitin-specific protease activity involved in negative regulation of retrograde protein transport, ER to cytosol;Lys48-specific deubiquitinase activity