GBE1 p.Ile282=
c.846A>C · rs959259894 · VCV1085836
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
Conditions
2
Glycogen storage disease IV, classic hepatic
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.98 | GERP -3.5 |
| Overall | ||
| CADD | 2.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,386 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,613,194 alleles · very rare
exomes 5/1,460,952 · genomes 0/152,242 · joint denominator
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
- GBE1
- Protein
- p.Ile282=
- Coding
- c.846A>C
- MANE Select
- NM_000158
- dbSNP
- rs959259894
- Type
- single nucleotide variant
- Location
- chr3:81642927 (GRCh38)
- Gene constraint
- LOEUF 1.211 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.30 · 3 PDB
- Residue 282
- a β-strand
Similar variants
- GBE1 c.1109-1G>T Likely pathogenic ★★ same condition
- GBE1 c.1236+1G>A Likely pathogenic ★★ same condition
- GBE1 c.1336-1G>A Pathogenic/Likely pathogenic ★★ same condition
- GBE1 c.143+1G>A Pathogenic ★★ same condition
- GBE1 c.143+2T>C Pathogenic/Likely pathogenic ★★ same condition
- GBE1 c.144-1G>C Pathogenic/Likely pathogenic ★★ same condition
- GBE1 c.1618+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GBE1 c.1803+2T>C Pathogenic/Likely pathogenic ★★ same condition
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/gbe1-p-ile282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown