GBE1 p.Pro552=
c.1656A>C · rs1340229013 · VCV989805
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000172%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.053 | GERP -0.033, phastCons 0.97 |
| Overall | ||
| CADD | 7.933 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000172%
European (non-Finnish) · 2/1,160,012 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000128%
2/1,565,036 alleles · very rare
exomes 2/1,412,816 · genomes 0/152,220 · 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.Pro552=
- Coding
- c.1656A>C
- MANE Select
- NM_000158
- dbSNP
- rs1340229013
- Type
- single nucleotide variant
- Location
- chr3:81537058 (GRCh38)
- Gene constraint
- LOEUF 1.211 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.30 · 3 PDB
Similar variants
- GBE1 p.Pro552Leu Likely pathogenic ★★ same residue
- 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
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-pro552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown