GBA3

glucosylceramidase beta 3 (gene/pseudogene), the group of Glycoside hydrolase family 1|Glucosylceramidases

Basic information

Region (hg38): 4:22692913-22819575

Links

ENSG00000249948 ∙ NCBI:57733 ∙ OMIM:606619 ∙ HGNC:19069 ∙ Uniprot:Q9H227 ∙ 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 GBA3 gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBA3 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in GBA3

This is a list of pathogenic ClinVar variants found in the GBA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-22693031-G-A		not specified	Uncertain significance (Dec 21, 2022)
4-22693071-A-G		not specified	Uncertain significance (Oct 06, 2021)
4-22735989-G-A		not specified	Uncertain significance (May 30, 2023)
4-22736019-G-A		not specified	Uncertain significance (Jun 16, 2023)
4-22736031-C-T		not specified	Uncertain significance (May 31, 2023)
4-22736107-A-G		not specified	Uncertain significance (Jan 08, 2024)
4-22736145-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-22736184-A-G		not specified	Uncertain significance (Jul 09, 2021)
4-22736185-C-T		not specified	Uncertain significance (Sep 14, 2023)
4-22747305-A-T		not specified	Uncertain significance (Nov 08, 2022)
4-22747380-C-T		not specified	Uncertain significance (Dec 16, 2021)
4-22747404-G-A		not specified	Uncertain significance (May 15, 2023)
4-22747427-G-C		not specified	Uncertain significance (Aug 19, 2023)
4-22747511-G-T		not specified	Uncertain significance (Oct 06, 2022)
4-22747551-C-T		not specified	Uncertain significance (May 18, 2022)
4-22747593-A-C		not specified	Uncertain significance (Feb 22, 2023)
4-22747603-T-G		not specified	Uncertain significance (Sep 15, 2021)
4-22747652-A-G		not specified	Likely benign (Sep 16, 2021)
4-22747686-C-T		not specified	Uncertain significance (Oct 02, 2023)
4-22747811-G-C		not specified	Uncertain significance (Jun 28, 2023)
4-22747853-C-T		not specified	Uncertain significance (Aug 12, 2021)
4-22747880-G-A		not specified	Uncertain significance (Jul 14, 2021)
4-22747917-T-G		not specified	Uncertain significance (Nov 10, 2022)
4-22747998-C-A		not specified	Uncertain significance (Aug 17, 2022)
4-22748882-C-A		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.478

Intolerance Scores

• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.14

Haploinsufficiency Scores

• pHI: 0.0915

Essentials

• essential_gene_CRISPR2: N

Gene ontology

• Biological process: glycosphingolipid metabolic process;glycoside catabolic process;glycosylceramide catabolic process;protein stabilization;cellular oligosaccharide catabolic process;positive regulation of exo-alpha-sialidase activity
• Cellular component: cytosol;catalytic complex
• Molecular function: glucosylceramidase activity;beta-galactosidase activity;protein binding;beta-glucosidase activity;glycosylceramidase activity;scopolin beta-glucosidase activity