Extension of the Pompe mutation database by linking disease-associated variants to clinical severity

Abstract

Pompe disease is an autosomal recessive lysosomal storage disorder caused by disease-associated variants in the acid alpha-glucosidase (GAA) gene. The current Pompe mutation database provides a severity rating of GAA variants based on in silico predictions and expression studies. Here, we extended the database with clinical information of reported phenotypes. We added additional in silico predictions for effects on splicing and protein function and for cross reactive immunologic material (CRIM) status, minor allele frequencies, and molecular analyses. We analyzed 867 patients and 562 GAA variants. Based on their combination with a GAA null allele (i.e., complete deficiency of GAA enzyme activity), 49% of the 422 disease-associated variants could be linked to classic infantile, childhood, or adult phenotypes. Predictions and immunoblot analyses identified 131 CRIM negative and 216 CRIM positive variants. While disease-associated missense variants were found throughout the GAA protein, they were enriched up to seven-fold in the catalytic site. Fifteen percent of disease-associated missense variants were predicted to affect splicing. This should be confirmed using splicing assays. Inclusion of clinical severity rating in the Pompe mutation database provides an invaluable tool for diagnosis, prognosis of disease progression, treatment regimens, and the future development of personalized medicine for Pompe disease.

Keywords: cardiac and skeletal muscle disorder; genotype-phenotype relationship; glycogen storage disease type II; lysosomal storage disease; www.pompecenter.nl.

Figure 1

The Pompe disease GAA variant database. (a) Flowchart for determining the clinical severity rating in the updated database. (b) Screenshot of the updated Pompe disease GAA variant database home page at http://www.pompevariantdatabase.nl

Figure 2

Frequencies of GAA variants and patients with specific GAA variants, stratified for disease severity. (a) Frequencies of unique variants, classified at the RNA level (upper panel) and protein level (lower panel). The consequences of variants that affect pre‐mRNA splicing was only included in specific categories (e.g., deletion, insertion, frameshift) at the protein level if experimental evidence was available. A list of all included categories is shown in Table S6. (b) Frequencies of variant types in patients, classified at the RNA level (upper panel) and protein level (lower panel). Two GAA alleles per patient were counted. Please note that 1) only one GAA allele could be counted in patients with an unknown second GAA variant; and that 2) the allele was counted twice in patients with a homozygous genotype

Figure 3

Distribution of CRIM positive and CRIM negative variants per variant type at the RNA level (a) and protein level (b). Left panels in (a) and (b): predicted variants; right panels: experimentally tested variants. CRIM, cross reactive immunologic material

Figure 4

Distribution of missense variants along the GAA protein. (a) Cartoon of the GAA gene indicating the locations of exons. Dark brown regions indicate the 5′ and 3′ untranslated regions. The translation start codon is indicated as c.1 in exon 2. The second cartoon indicates the GAA protein domains and the sites modified by M6P residues. (b) The distribution of disease‐associated variants in GAA protein domains according to frequency and clinical severity rating. Numbers are corrected for the length of each domain. (c) as (b), but now for all GAA variants, including both disease‐associated and non‐disease‐associated missense variants, listed in the ExAc database