P.133 - Identification of variants that affect severity of the spinal muscular atrophy phenotype within and outside of the SMN2 gene

Abstract

SMA is caused by loss or mutation of the SMN1 gene and retention of SMN2. The SMN2 gene copy number correlates with phenotypic severity. However, there are exceptions, with type 3 cases having 2 copies of SMN2 or type 1 cases with 3 copies as well as discordant siblings with the same copy number. With effective therapeutics for SMA early introduction of therapy is important in achieving maximum benefit. Newborn screening is progressing towards implementation but precise prediction of phenotype from genotype is critical to optimize timing of treatment. It is often not known if the SMN2 gene is intact or contains variants which can affect the amount of SMN produced. In order to identify deletion junctions as well as intact SMN2 copies and variants within the gene that affect phenotypic severity we have sequenced the entire SMN2/SMN1gene present in 60 patients. In addition, we have employed genomic sequencing in a set of discordant siblings in comparison to concordant siblings in order to identify variants in the genome associated with the milder sibling. The entire SMN2/SMN1 gene along with the CFTR and PLS3 gene was captured and sequenced with an adapted Multiplexed direct genomic selection (MDiGS) technique. The sequences were aligned and variants were determined. To determine SMN2 copy number the SMN read count was split into bins and normalized to the CFTR and PLS3 reads. We defined a deletion occurring in 8 patients, the deletion occurred between two nearly identical repeats located in intron 6 and in sequence located 3 prime of SMN2. We detected a cryptic splice site in intron 6 of a patient with one copy of SMN1 and a missense mutation (A75T) in the SMN2 gene of a patient. We detected 3 variants associated with a milder phenotype in 3 copy SMN2 individuals. Lastly, we have performed genomic sequencing of select discordant and concordant families to identify modifiers of phenotype that act in trans.