GBA2 p.Arg870=
c.2610A>G · rs775542106 · VCV744908
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -3.8 |
| Overall | ||
| CADD | 2.588 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,014 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.000496%
8/1,614,012 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,573 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- GBA2
- Protein
- p.Arg870=
- Coding
- c.2610A>G
- MANE Select
- NM_020944
- dbSNP
- rs775542106
- Type
- single nucleotide variant
- Location
- chr9:35737343 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.77
- Residue 870
- a UniProt-annotated variant site (in spg46; loss of glucosylceramide catabolic process)
Similar variants
- GBA2 p.Arg870Ter Likely pathogenic ★★ same residue
- GBA2 p.Arg870Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- GBA2 c.1582+2T>G Likely pathogenic ★★ same type
- GBA2 p.Arg234Ter Pathogenic ★★ same type
- GBA2 p.Arg340Ter Pathogenic ★★ same type
- GBA2 p.Arg574Ter Pathogenic ★★ same type
- GBA2 p.Arg630Trp Pathogenic/Likely pathogenic ★★ same type
- GBA2 p.Arg873His Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/gba2-p-arg870 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown