A validated in vitro expression and functional analysis system can help classify novel GAA variants associated with Pompe disease (PD), according to a new study published in the journal Frontiers in Genetics.  

To “fill the growing unmet need for novel variant classification and molecular diagnostic confirmation” for people who have a positive result in newborn screening for PD, researchers from Duke University in Durham, North Carolina, developed the in vitro system based on guidelines established by the Clinical Genome Resource Sequence Variant Interpretation Working Group.

The team led by Priya S. Kishnani, MD, MBBS, validated the system using 12 pathogenic variants as controls. They then analyzed 8 GAA variants of uncertain significance or novel variants identified in patients who had a positive newborn screen for PD but no evidence of infantile-onset disease.

Continue Reading

The pathogenic controls had GAA activities between 0 and 11%, the “benign or likely benign controls” had GAA activities between 54% and 100%, and the “pseudodeficiency variant” had a GAA activity level of 17%.

Read more about the types of PD

Using these ranges, the researchers were able to classify 2 of the 8 variants they tested as likely pathogenic and to provide further evidence of the classification of 2 other variants as likely pathogenic. Finally, they were able to reclassify 1 variant as pathogenic based on other supporting evidence. 

The researchers pointed out that they were not able to reclassify 3 variants given conflicting and inadequate data.

Even though more work is necessary to refine their system “this tool can be utilized for variant classification to meet the growing need for novel GAA variant classification in the era of newborn screening for PD,” they added.

PD is a rare genetic disease characterized by a deficiency or absence of the GAA enzyme. With the addition of the disease to newborn screening panels in the US, more and more novel variants and variants of uncertain significance are being identified in the GAA gene, making diagnosis difficult, especially for late-onset disease in which no symptoms are apparent at birth.


Goomber S, Huggins E, Rehder CW, Cohen JL, Bali DS, Kishnani PS. Development of a clinically validated in vitro functional assay to assess pathogenicity of novel GAA variants in patients with Pompe disease identified via newborn screening. Front Genet. Published online September 30, 2022. doi:10.3389/fgene.2022.1001154