Is GAA p.Pro425fs (c.1274del) pathogenic?

GAA p.Pro425fs (c.1274del) is classified Pathogenic in GAA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-02). Very rare (popmax 0.0011%, sas); Associated with glycogen storage disease II.

What condition is associated with GAA p.Pro425fs (c.1274del)?

GAA p.Pro425fs (c.1274del) is associated with glycogen storage disease II (ClinVar).

How common is GAA p.Pro425fs (c.1274del) in the general population?

GAA p.Pro425fs (c.1274del) is very rare (popmax 0.0011%, sas) (gnomAD).

GAA p.Pro425fs

Q: How is Glycogen storage disease due to acid maltase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1274del · rs2510364922 · VCV2839746

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

glycogen storage disease II

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.2	GERP 0.67, phastCons 0.99

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/90,564 alleles

Overall 6.86e-05% 1/1,457,528 alleles · very rare

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: GAA
Protein: p.Pro425fs
Coding: c.1274del
MANE Select: NM_000152
dbSNP: rs2510364922
Type: Deletion
Location: chr17:80108774 (GRCh38)
Gene constraint: LOEUF 1.008 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.32 · 19 PDB
Residue 425: an α-helix

Full GAA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 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 p.Pro425Leu Uncertain significance ★★ ⚠ same residue
GAA p.Pro425Ser Uncertain significance ★★ ⚠ same residue
GAA p.Pro425= Likely benign ★★ same residue
GAA p.Pro425Thr Uncertain significance ★ ⚠ same residue
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

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-p-pro425fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown