AGL p.Val552=
c.1656A>G · rs2524636181 · VCV2979035
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
glycogen storage disease III
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 · A>T here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 4.701 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AGL
- Protein
- p.Val552=
- Coding
- c.1656A>G
- MANE Select
- NM_000642
- dbSNP
- rs2524636181
- Type
- single nucleotide variant
- Location
- chr1:99879967 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.88 · 1 PDB
- Residue 552
- the 'amylo-1,6-glucosidase' region; a β-strand
Disease context
glycogen storage disease III — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycogen storage disease due to glycogen debranching enzyme deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy
- Prevalence
- 1-9 / 100 000 (United States)
Similar variants
- AGL c.1283+2T>C Likely pathogenic ★★ same condition
- AGL c.1284-1G>A Likely pathogenic ★★ same condition
- AGL c.1284-2A>G Likely pathogenic ★★ same condition
- AGL c.1423+1G>A Pathogenic ★★ same condition
- AGL c.1423+1G>C Pathogenic ★★ same condition
- AGL c.1423+1G>T Pathogenic/Likely pathogenic ★★ same condition
- AGL c.1612-1G>A Pathogenic/Likely pathogenic ★★ same condition
- AGL c.1735+1G>T 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/agl-p-val552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown