Extended Database Links Pompe Mutations to Predicted Clinical Severity

A database with mutations associated with Pompe disease has been extended and links different gene variants with their potential clinical severity to better predict outcomes.

The study, “Extension of the Pompe mutation database by linking disease-associated variants to clinical severity,” appeared in the journal Human Mutation.

Pompe disease is caused by mutations in the GAA gene and is divided into classic infantile-onset, non-classic infantile-onset and late-onset forms. The gene codes for an enzyme (a special protein) called acid alpha-glucosidase, responsible for breaking down glycogen into the simpler sugar glucose, which can be used by cells. Mutations in the GAA gene hinder the enzyme’s production and activity and lead to glycogen accumulation up to toxic levels.

Patients with no detectable GAA protein are termed cross reactive immunologic material (CRIM) negative and have CRIM negative variants in both gene copies. In turn, CRIM positive patients have at least one gene copy producing the protein, but defects in its structure or intracellular transport make it inactive. Both CRIM negative and CRIM positive without GAA enzyme activity have the classic infantile type, while patients with partial enzyme activity have one of the other forms of the disease.

The current Pompe mutation database provides a prediction of how severe the different GAA variants are based on computer-based methods and in vitro tests. The mutations are divided into six categories, from “very severe” to “non-pathogenic.”

A team at the Erasmus University Medical Center, in the Netherlands, used software called Alamut to analyze GAA variants for their effects on RNA processing and protein function. RNA is made from DNA, and is then used to produce proteins. Then, the scientists assessed the literature to predict CRIM status.

The researchers analyzed 867 patients and a total of 562 GAA variants. Of these variants, 422 were listed as disease-associated, 49% of which had a second GAA copy that was a null allele — a gene variant leading to a protein without detectable enzyme activity.

Molecular analysis found that most mutations were missense variants, which lead to a difference in one nucleotide, the building blocks of DNA and RNA. Though the team cautioned that appropriate assays are required for confirmation, 15% of the disease-associated missense variants were predicted to affect RNA editing, or splicing.

The number of unique variants did not widely differ across the three disease types, ranging from 136 in adult to 154 in childhood and 173 in classic infantile patients.

However, when patients with a certain type of variant were divided by disease onset form, the team found that the percentage of cases with a splicing variant increased from less than 1% in the classic infantile group to 44% in the adult group. This effect was driven by the large proportion (86%) of childhood and adult Caucasian patients with the splicing variant IVS1, which causes skipping of exon 2 during RNA editing. Exons are the DNA bits containing information to generate proteins.

Subsequent predictions and molecular analyses identified 130 CRIM negative and 216 CRIM positive variants. Most commonly, CRIM negative and positive variants were classified as nonsense variants — causing early termination of gene expression and a shorter protein — or missense mutations.

Disease-associated variants were found throughout the GAA protein and RNA. However, missense variants were up to seven times more frequent in the catalytic site, which is the part of the enzyme where its substrate (target) binds.

As for association with Pompe disease types and geographical regions, variants linked to the classic infantile form include frequent mutations such as c.525del (Caucasian) and c.1935C>A (Asian). Those associated with the childhood form include c.1857C>G and c.796C>T (both Asian), and c.-32-3C>A (Latin American). In turn, mutations associated with the adult phenotype include c.2647-7G>A (Caucasian).

“The improved database should help doctors, genetic counselors, and scientists to better predict disease outcome in patients diagnosed with Pompe disease,” the scientists stated. “As well as providing new insight into variant severity, it will also improve prediction of prognosis in newborn screening programs, and support decision-making on therapeutic intervention.”