Case Report: Integrative Multiomics to Establish Pathogenicity of novel GBE1 R198T Variant

<ns7:p> Background Glycogen Storage Disease IV (GSD IV) is a rare disease affecting 1 in every 760,000–960,000 live births. GSD IV is caused by mutations in <ns7:italic>GBE1</ns7:italic> , especially if it affects the central catalytic core domain of the glycogen branching enzyme (GBE) protein at 184 <ns7:sup>th</ns7:sup> –600 <ns7:sup>th</ns7:sup> residue. A novel missense mutation, <ns7:italic>GBE1</ns7:italic> R198T, was detected in a 3-year-old boy in Indonesia. This variant has not previously been reported in allele frequency databases or classified as pathogenic. Method In this study, we used an integrative multi-omics diagnostic approach involving phenotype analysis, proband and trio genetic mutation analysis, protein molecular modeling, protein-ligand docking, and protein expression studies. We compared <ns7:italic>GBE1</ns7:italic> R198T mutation with the wild-type and previously well-known pathogenic variants, L224P and Y329S, to analyze the clinical progression and pathogenic effects of R198T. Results Trio mutation analysis revealed that this mutation was inherited from a heterozygous parent. Functional prediction, molecular modeling, and docking analysis supported the R198T pathomechanism to cause structural changes in the GBE protein domain, which is detrimental to GBE ligand binding with maltoheptose (Glc7). An <ns7:italic>in vitro</ns7:italic> study further supported the decrease in <ns7:italic>GBE1</ns7:italic> R198T protein expression compared to that in the WT. In addition, <ns7:italic>GBE1</ns7:italic> R198T band intensity showed similar results to those of the <ns7:italic>GBE1</ns7:italic> L224 variant, indicating potentially similar pathogenic characteristics exhibited by both variants. Conclusions This is the first study to establish the pathogenicity of the <ns7:italic>GBE1</ns7:italic> R198T variant, and the first rare disease functional study reported in Indonesia. </ns7:p>