GAA c.2483del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
glycogen storage disease II
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.7, phastCons 1 |
| Non-coding constraint | Z 3.94 | 1 kb window · o/e 0.72 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- GAA
- Coding
- c.2483del
- MANE Select
- NM_000152
- dbSNP
- rs2510402010
- Type
- Deletion
- Location
- chr17:80118192 (GRCh38)
- Gene constraint
- LOEUF 1.008 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.32 · 19 PDB
Disease context
glycogen storage disease II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycogen storage disease due to acid maltase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- GAA c.1551+3_1551+6del Pathogenic ★★★ same condition
- GAA c.2189+459_*546del Pathogenic ★★★ same condition
- GAA c.2481+110_2646+39del Pathogenic ★★★ same condition
- GAA p.Ala14fs Pathogenic ★★★ same condition
- GAA p.Ala382fs Pathogenic ★★★ same condition
- GAA p.Arg154_Thr155del Likely pathogenic ★★★ same condition
- GAA p.Arg154_Thr156del Likely pathogenic ★★★ same condition
- GAA p.Arg385fs 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/gaa-c-2483del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown