Identification of Copy Number Variations in Familial Hemiplegic Migraine Genes in Suspected Hemiplegic Migraine Patients

Background: Familial hemiplegic migraine (FHM) is a rare and severe form of migraine disorder featuring aura symptoms that include hemiplegia during attacks. While pathogenic missense variants in CACNA1A, ATP1A2, and SCN1A can cause FHM or its sporadic form, they explain less than 20% of suspected hemiplegic migraine cases, suggesting the involvement of other genes or genetic variations, potentially including copy number variations (CNVs). PPRT2 gene variants including CNVs have also been implicated in hemiplegic migraine. Methods: Multiplex ligation-dependent probe amplification (MLPA) assays were used to investigate the presence of CNVs in the CACNA1A, SCN1A, ATP1A2, and PRRT2 genes in a cohort of 170 unrelated probands suspected to have FHM who had tested negative for pathogenic missense or small indel variants within these genes. Potential CNVs were subsequently confirmed using quantitative PCR. Results: In 15 patients referred for FHM genetic testing, various CNVs in the target genes were detected by MLPA and subsequently validated by quantitative PCR. CACNA1A exon duplications were identified in six patients and deletions found in two. Two patients had ATP1A2 exon deletions, while one had a duplication. For SCN1A, exon deletions were found in three patients and a duplication in one. PRRT2 exon deletions were detected in five patients, with a single nucleotide polymorphism (SNP) array confirming a deletion spanning PRRT2 and neighbouring loci including 26 genes in one of those. Three patients had CNVs in more than one FHM gene. Conclusions: Our study demonstrates the presence of CNVs in FHM genes in a subset of hemiplegic migraine cases (~9%), suggesting a likely role in the disorder and highlighting the need to explore structural variation in addition to the commonly interrogated genetic mutation points. These findings contribute to further understanding of genetic mechanisms that underlie hemiplegic migraine and may inform improved diagnostic and therapeutic strategies.