Spinal muscular atrophy type I associated with a novel splicing variant that disrupts the expression of the functional transcript.

Introduction: Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by pathogenic variants in the gene. The majority of SMA patients harbor a homozygous deletion of exon 7 (95%). Heterozygosity for a conventional variant and a deletion is rare (5%) and not easily detected, due to the highly homologous gene interference. mainly produces a truncated non-functional protein (SMN-d7) instead of the full-length functional (SMN-FL). We hereby report a novel splicing variant in an infant with severe SMA.

Methods: MLPA was used for exon dosage determination. Sanger sequencing approaches and long-range PCR were employed to search for an variant. Conventional and improved Real-time PCR assays were developed for the qualitative and quantitative RNA analysis.

Results: The novel splice-site variant c.835-8_835-5delinsG, was identified in compound heterozygosity with exons 7/8 deletion. RNA studies revealed complete absence of exon 7, thus confirming a disruptive effect of the variant on splicing. No expression of the functional -FL transcript, remarkable expression of the d7 and increased levels of the -FL/-d7 transcripts were observed.

Discussion: We verified the occurrence of a non-deletion variant and supported its pathogenicity, thus expanding the variants spectrum. We discuss the updated SMA genetic findings in the Cypriot population, highlighting an increased percentage of intragenic variants compared to other populations.