USO1

USO1 vesicle transport factor, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 4:75724576-75814286

Links

ENSG00000138768 ∙ NCBI:8615 ∙ OMIM:603344 ∙ HGNC:30904 ∙ Uniprot:O60763 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USO1 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						0
missense				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in USO1

This is a list of pathogenic ClinVar variants found in the USO1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-75806549-G-A		USO1-related disorder	Likely benign (Jul 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USO1	protein_coding	protein_coding	ENST00000538159	25	85606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.334	0.666	124607	0	30	124637	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	367	443	0.829	0.0000214	6308
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000123	0.000111
Finnish	0.0000515	0.0000464
European (Non-Finnish)	0.000148	0.000142
Middle Eastern	0.000123	0.000111
South Asian	0.000177	0.000131
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Golgi Cisternae Pericentriolar Stack Reorganization;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Arf1 pathway;Mitotic Prophase;COPI-mediated anterograde transport;M Phase;Cell Cycle;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.897
• hipred: N
• hipred_score: 0.426
• ghis: 0.607

Essentials

• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.764

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Uso1
• Phenotype: cellular 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)

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;transcytosis;COPII vesicle coating;Golgi vesicle docking;vesicle fusion with Golgi apparatus;membrane fusion
• Cellular component: Golgi membrane;fibrillar center;endoplasmic reticulum;Golgi apparatus;Golgi stack;cytosol;ER to Golgi transport vesicle membrane;membrane;transport vesicle;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;protein transporter activity;cadherin binding