OTUD5
Basic information
Region (hg38): X:48922024-48958386
Links
Phenotypes
GenCC
Source:
- multiple congenital anomalies/dysmorphic syndrome (Moderate), mode of inheritance: XL
- multiple congenital anomalies-neurodevelopmental syndrome, X-linked (Strong), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Multiple congenital anomalies-neurodevelopmental syndrome, X-linked | XL | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal | 33131077; 33523931 |
ClinVar
This is a list of variants' phenotypes submitted to
- Multiple congenital anomalies-neurodevelopmental syndrome, X-linked (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUD5 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 | 5 | |||||
| missense | 34 | 36 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 1 | 1 | 37 | 4 | 1 |
Variants in OTUD5
This is a list of pathogenic ClinVar variants found in the OTUD5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| OTUD5 | protein_coding | protein_coding | ENST00000156084 | 9 | 36344 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00283 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.99 | 44 | 205 | 0.215 | 0.0000164 | 3643 |
| Missense in Polyphen | 3 | 60.517 | 0.049573 | 961 | ||
| Synonymous | 0.0542 | 79 | 79.6 | 0.992 | 0.00000624 | 1188 |
| Loss of Function | 3.85 | 0 | 17.2 | 0.00 | 0.00000132 | 262 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Deubiquitinating enzyme that functions as negative regulator of the innate immune system. Acts via TRAF3 deubiquitination and subsequent suppression of type I interferon (IFN) production. Has peptidase activity towards 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. Can also cleave 'Lys-11'- linked ubiquitin chains (in vitro). {ECO:0000269|PubMed:17991829, ECO:0000269|PubMed:22245969, ECO:0000269|PubMed:23827681}.;
- Pathway
- RIG-I-like receptor signaling pathway - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Gastric Cancer Network 2;RIG-I-like Receptor Signaling;Post-translational protein modification;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Metabolism of proteins;Innate Immune System;Immune System;Negative regulators of DDX58/IFIH1 signaling;Ovarian tumor domain proteases;Deubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.368
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.513
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.772
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Otud5
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland 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); hematopoietic system phenotype; digestive/alimentary phenotype; immune system phenotype; embryo phenotype;
Zebrafish Information Network
- Gene name
- otud5b
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- bent
Gene ontology
- Biological process
- protein deubiquitination;negative regulation of type I interferon production;response to lipopolysaccharide;protein K63-linked deubiquitination;protein K48-linked deubiquitination
- Cellular component
- cytosol
- Molecular function
- thiol-dependent ubiquitin-specific protease activity;Lys63-specific deubiquitinase activity;ubiquitinyl hydrolase activity;Lys48-specific deubiquitinase activity