What you carry at this position in your DNA and what research says about it.
Pompe Disease Risk: 9/10 evidence, 5 publications.
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Sample genotype (not yours): G/G
Typical Pompe Disease Risk
Two copies of the typical gene are present, meaning there is no elevated risk of Pompe disease. The body produces fully functional acid alpha-glucosidase enzyme to break down glycogen normally.
What this genotype means: Normal acid alpha-glucosidase enzyme activity; No elevated risk of Pompe disease; Will not pass this variant to children.
Sample genotype (not yours): A/A
Highly Elevated Pompe Disease Risk
Two copies of the pathogenic variant are present, which is linked to Pompe disease. This condition causes progressive muscle weakness due to glycogen accumulation.
What this genotype means: Severe deficiency of acid alpha-glucosidase enzyme; High risk of developing Pompe disease; Progressive muscle and respiratory weakness.
Sample genotype (not yours): G/A
Healthy Pompe Disease Carrier
One copy of the pathogenic variant is present, making this a healthy carrier status. There is no risk of developing Pompe disease, but the variant can be passed to children.
What this genotype means: Healthy carrier of Pompe disease; No personal risk of Pompe disease symptoms; 50% chance of passing the variant to offspring.
Gene function and biological role
Gene Function: The GAA gene provides instructions for producing an enzyme called acid alpha-glucosidase, which is active in lysosomes [1]. This enzyme is responsible for breaking down glycogen, a complex sugar, into glucose [1]. When glycogen is not properly degraded, it accumulates to toxic levels in cells, particularly in muscle tissues [2]. This buildup causes progressive cellular damage and impairs normal muscle function [2]. Mutations in this gene can lead to Pompe disease, also known as glycogen storage disease type II [3].
Variant Impact: A nonsense mutation designated as p.Trp126Ter defines this genetic change in the GAA gene [3]. This alteration introduces a premature stop codon early in the protein-coding sequence, halting the production of the acid alpha-glucosidase enzyme [3]. As a result, the cell produces a severely shortened, non-functional protein that is quickly degraded [4]. Without functional enzyme activity, glycogen cannot be broken down and instead accumulates inside lysosomes [4]. This variant is classified as pathogenic and is a known cause of Pompe disease when inherited from both parents [5].
Key Insight: A single letter change in this gene completely halts the production of a vital enzyme, leading to severe muscle damage if two copies are inherited.
Location: GAA. Chromosome 17 · 17q25.3 · 80.1 Mb
Estimated prevalence by population
No frequency data available
This variant is not present in the gnomAD database.
Showing effects for G/G genotype
Rare Genetic Disorders
Inherited Metabolic Disorders
Pompe Disease. Evidence: 9/10. Source: PMID 25681614. Typical Risk.
GAA Enzyme Activity. Evidence: 9/10. Source: PMID 22252923. Normal Activity.
Congenital Malformations
Carrier Status. Evidence: 9/10. Source: PMID 18425781. Non-Carrier.
Lifestyle, Fitness & Aging
Muscle Strength & Power
Muscle Health. Evidence: 9/10. Source: PMID 17056254. Typical Muscle Health.
Showing effects for A/A genotype
Pompe Disease. Evidence: 9/10. Source: PMID 25681614. Highly Elevated Risk.
GAA Enzyme Activity. Evidence: 9/10. Source: PMID 22252923. Severely Deficient.
Carrier Status. Evidence: 9/10. Source: PMID 18425781. Affected.
Muscle Health. Evidence: 9/10. Source: PMID 17056254. Progressive Weakness.
Showing effects for G/A genotype
GAA Enzyme Activity. Evidence: 9/10. Source: PMID 22252923. Slightly Reduced.
Carrier Status. Evidence: 9/10. Source: PMID 18425781. Healthy Carrier.
What this genotype means for the people who carry it
Sample genotype: GG (Homozygous)
Two normal copies of the GAA gene are present in this genotype. The body produces normal levels of the acid alpha-glucosidase enzyme, which is essential for clearing glycogen from muscle cells [1]. Consequently, there is no genetic risk of developing Pompe disease or passing this specific pathogenic variant to offspring [2]. Muscle health and cellular glycogen clearance function typically [1]. No special medical monitoring or dietary interventions related to this variant are necessary [3].
Normal acid alpha-glucosidase enzyme activity; No elevated risk of Pompe disease; Will not pass this variant to children.
Sample genotype: AA (Homozygous)
Two copies of the pathogenic A allele result in a complete or near-complete lack of functional acid alpha-glucosidase enzyme [1]. This severe deficiency prevents the breakdown of glycogen, leading to its toxic accumulation in lysosomes, particularly within cardiac and skeletal muscle tissues [2]. This buildup causes progressive muscle weakness, respiratory difficulties, and, in infantile-onset cases, severe heart enlargement [3]. Symptoms can present in infancy or later in childhood or adulthood depending on any residual enzyme activity [4]. Early diagnosis is critical, as enzyme replacement therapy can help manage the progression of the disease [1].
Severe deficiency of acid alpha-glucosidase enzyme; High risk of developing Pompe disease; Progressive muscle and respiratory weakness.
Sample genotype: GA (Heterozygous)
One copy of the pathogenic A allele is present, which defines a healthy carrier status for Pompe disease [1]. Because Pompe disease is inherited in an autosomal recessive manner, a single normal G allele is sufficient to produce enough functional enzyme to prevent any symptoms [2]. Enzyme activity may be slightly lower than average, but this is not clinically significant and does not impact muscle health [3]. However, there is a 50% chance of passing this pathogenic variant to offspring [1]. If a partner is also a carrier of a GAA mutation, there is a risk of having an affected child, making carrier screening relevant for family planning [2].
Healthy carrier of Pompe disease; No personal risk of Pompe disease symptoms; 50% chance of passing the variant to offspring.
Variants with shared genetic architecture
rs1057516426 · GAA Gene · Chr 17 · Pompe Disease Risk
rs1064794288 · GAA Gene · Chr 17 · Pompe Disease Risk
rs1064796703 · GAA Gene · Chr 17 · Pompe Disease Risk
Novel GAA mutations in patients with Pompe disease.
Content updated August 2026.
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