GBE1 p.Lys39=
c.117G>A · rs769399819 · VCV1360394
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP -1.1, phastCons 0.88 |
| Overall | ||
| CADD | 9.345 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,798 alleles
Overall
6.2e-05%
1/1,613,062 alleles · very rare
exomes 1/1,460,694 · genomes 0/152,368 · 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.Lys39=
- Coding
- c.117G>A
- MANE Select
- NM_000158
- dbSNP
- rs769399819
- Type
- single nucleotide variant
- Location
- chr3:81761401 (GRCh38)
- Gene constraint
- LOEUF 1.211 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.30 · 3 PDB
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-lys39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown