VP.79 Challenges in genetic diagnosis of LAMA2-MD - when the pieces do not fit

Pathogenic variants in the LAMA2 gene can cause muscular dystrophy (MD) associated with variable degrees of severity. We describe an infant with a congenital phenotype: severe hypotonia and weakness at birth, elevated creatine kinase levels, brain white-matter alterations and reduced merosin expression in muscle biopsy. Next-generation sequencing (NGS) targeting a panel of genes involved in hereditary myopathies revealed a rare homozygous missense variant in exon 39 of the LAMA2 gene. Detailed genotype-phenotype evaluation associated with an incongruent bioinformatics analysis led us to proceed to full LAMA2 cDNA analysis. A partial retention of intron 14 was identified, thought to be the primary genetic defect accountable for the patient´s phenotype. Further investigation enabled us to conclude that this splicing event was instigated by the presence of a homozygous intronic substitution located 117bp downstream of exon 14, which created a cryptic splice site. To our knowledge, this splicing variant represents the first pathogenic variant located further from the LAMA2 exon-intron boundaries. Besides the importance of cDNA studies, this work highlights the need for critical judgment of any identified variants of unknown significance (VUS) in the definition of the correct and causal genotype.