GBA3
protein-codingglucosylceramidase beta 3 (gene/pseudogene), the group of Glycoside hydrolase family 1|Glucosylceramidases
Gene summary
The protein encoded by this gene is a cytosolic enzyme that can hydrolyze several types of glycosides. The enzyme has its highest activity at neutral pH and is predominantly expressed in human liver, kidney, intestine, and spleen. This gene is a polymorphic pseudogene, with the most common allele being the functional allele that encodes the full-length protein. Some individuals contain a single nucleotide polymorphism that results in a premature stop codon in the coding region, and therefore this allele is pseudogenic due to the failure to produce a functional full-length protein. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2022]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~126.7 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 GBA3 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 0 | |||||
| missense | 35 | 1 | 36 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 1 | 0 | 36 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| Ensembl | ENSP00000422220.1 | 3 | Standard | |
| Ensembl | ENSP00000427458.1 | 5 | Standard | |
| Ensembl | ENSP00000423754.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Starch and sucrose metabolism - Homo sapiens (human)
- Metabolism of lipids
- Metabolism
- Glycosphingolipid metabolism
- Sphingolipid metabolism
Biological Process
- glycosphingolipid metabolic process
- glycoside catabolic process
- glycosylceramide catabolic process
- protein stabilization
- cellular oligosaccharide catabolic process
Molecular Function
- glucosylceramidase activity
- beta-galactosidase activity
- protein binding
- beta-glucosidase activity
- glycosylceramidase activity
Cellular Component
- cytosol
- catalytic complex
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Glycosidase probably involved in the intestinal absorption and metabolism of dietary flavonoid glycosides. Able to hydrolyze a broad variety of glycosides including phytoestrogens, flavonols, flavones, flavanones and cyanogens. Possesses beta- glycosylceramidase activity and may be involved in a nonlysosomal catabolic pathway of glycosylceramide. {ECO:0000269|PubMed:11784319, ECO:0000269|PubMed:12594539, ECO:0000269|PubMed:17595169}.;
Recessive Scores
- pRec
- 0.478
Intolerance Scores
- RVIS EVS
- 0.78
- RVIS percentile EVS
- 87.14
Essentials
- Essential (CRISPR2)
- N