Is GAA p.Pro779fs (c.2334_2335dup) pathogenic?

GAA p.Pro779fs (c.23342335dup) is classified Likely pathogenic in GAA (ClinVar, Single submitter, 1 submitter; last evaluated 2026-07-01). Associated with glycogen storage disease II.

What condition is associated with GAA p.Pro779fs (c.2334_2335dup)?

GAA p.Pro779fs (c.2334_2335dup) is associated with glycogen storage disease II (ClinVar).

GAA p.Pro779fs

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.2334_2335dup · VCV4876639

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

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 17 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP 1.3, phastCons 1

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

Variant & gene context

Gene: GAA
Protein: p.Pro779fs
Coding: c.2334_2335dup
MANE Select: NM_000152
Type: Duplication
Location: chr17:80117601 (GRCh38)
Gene constraint: LOEUF 1.008 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.32 · 19 PDB

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.Pro779Gln Uncertain significance ★★ ⚠ same residue
GAA p.Pro779= Likely benign ★★ same residue
GAA p.Ala150fs Likely pathogenic ★★★ same condition
GAA p.Ala610fs Pathogenic ★★★ same condition
GAA p.Asn87fs Pathogenic ★★★ same condition
GAA p.Gln914fs Likely pathogenic ★★★ same condition
GAA p.Glu721fs Likely pathogenic ★★★ same condition
GAA p.Ile257fs 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/gaa-p-pro779fs (accessed [today's date]).

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