Genetic study of SMA patients without homozygous SMN1 deletions: identification of compound heterozygotes and characterisation of novel intragenic SMN1 mutations

Autosomal recessive spinal muscular atrophy (SMA) is a disease resulting from mutations in the telomeric survival motor neuron gene (SMN1). In our sample of 150 Spanish SMA families, 87% of patients had homozygous deletions of SMN1. To identify patients who retained a single SMN1 copy, SMN dosage analysis was performed by a fluorescent quantitative PCR assay. In five out of 19 patients tested we detected one SMN1 copy. An extensive SMN gene analysis in these patients led to identification of four intragenic mutations, including two novel ones: a frameshift mutation in exon 6 (773insC) and a splice site mutation in intron 6 (c.867+2T-->G). Two previously described mutations were also found: a deletion in exon 3 (430del4), identified in several Spanish patients, and a frequently occurring mutation in exon 6 (813ins/dup11), reported in several populations. Although the spectrum of intragenic mutations is small, only 27 reported up to now, identification of three mutations found exclusively in the Spanish population indicates that the occurrence of different intragenic mutations depends on the ethnic origin of SMA patients. In the remaining patient, who had a single SMN1 copy and three SMN2 copies, we found that the SMN1 allele was non-functional; the patient did not show any SMN1 transcript. Sequencing of the SMN promoter regions revealed various differences between promoters of the patient's four SMN genes, in particular a change in the length of a polyA run removing a putative YY1 binding site, which may affect the expression of SMN genes.