USO1
protein-codingUSO1 vesicle transport factor, the group of Armadillo like helical domain containing
Gene summary
The protein encoded by this gene is a peripheral membrane protein which recycles between the cytosol and the Golgi apparatus during interphase. It is regulated by phosphorylation: dephosphorylated protein associates with the Golgi membrane and dissociates from the membrane upon phosphorylation. Ras-associated protein 1 recruits this protein to coat protein complex II (COPII) vesicles during budding from the endoplasmic reticulum, where it interacts with a set of COPII vesicle-associated SNAREs to form a cis-SNARE complex that promotes targeting to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~89.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to USO1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003715.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 6 | 1 | 7 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 13 | 1 | 0 | 14 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003706.2 | 24 | MANE Select | |
| Ensembl | ENSP00000444850.2 | 24 | MANE Select | |
| RefSeq | NP_001276978.1 | 26 | Standard | |
| Ensembl | ENSP00000264904.7 | 26 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Post-translational protein modification
- Metabolism of proteins
- Golgi Cisternae Pericentriolar Stack Reorganization
Biological Process
- intracellular protein transport
- endoplasmic reticulum to Golgi vesicle-mediated transport
- Golgi organization
- transcytosis
- COPII vesicle coating
Molecular Function
- RNA binding
- protein binding
- protein transporter activity
- cadherin binding
Cellular Component
- Golgi membrane
- fibrillar center
- endoplasmic reticulum
- Golgi apparatus
- Golgi stack
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000538159
- Coding exons
- 25
- Length
- 85606
- Individuals with no LoFs
- 124607
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 124637
- p
- 0.000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 367 | 443 | 0.829 | 0.0000214 | 6308 |
| Missense (PolyPhen) | 77 | 116.06 | 0.66346 | 1623 | ||
| Synonymous | 0.891 | 145 | 159 | 0.910 | 0.00000780 | 1759 |
| Loss of Function | 5.19 | 12 | 52.6 | 0.228 | 0.00000245 | 740 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00012 | 0.00011 | rare |
| Finnish | 0.000052 | 0.000046 | rare |
| European (Non-Finnish) | 0.00015 | 0.00014 | rare |
| South Asian | 0.00018 | 0.00013 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: General vesicular transport factor required for intercisternal transport in the Golgi stack; it is required for transcytotic fusion and/or subsequent binding of the vesicles to the target membrane. May well act as a vesicular anchor by interacting with the target membrane and holding the vesicular and target membranes in proximity. {ECO:0000250|UniProtKB:P41542}.;
Recessive Scores
- pRec
- 0.107
Essentials
- Essential (CRISPR2)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.764
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |