Linkage studies in families of spinal muscular atrophy patients found that 95% of all cases of spinal muscular atrophy were linked to the 5q13 region of chromosome 5. Two candidate genes within this region were first described: the survival motor neuron (SMN) gene and neuronal apoptosis inhibitory protein gene. Each of these genes was found to be present in at least two copies. Later, the p44 gene (a subunit of the basal transcription factor) was identified as a third candidate gene.
The human SMN gene was described to have 8 exons; however, a full characterization of the SMN gene showed that it has 9 exons. In order not to confuse previously published mutation data, former exon 2 is commonly known as exons 2a and 2b. The gene spans about 20 kb. The stop codon for the predicted protein occurs in exon 7 and exon 8 is not translated. SMN1 has been found to be homozygously absent or interrupted in 98.6% of childhood SMAs and in at least some patients with the adult form. The SMN gene is present in two almost identical copies, one telomeric (SMN1) and one centromeric (SMN2 or cBCD541). Both the centromeric and telomeric copies contain 9 exons. They differ only in 8 nucleotides; 5 are intronic and 3 are exonic, located in exons 6, 7 and 8. The telomeric copy is the functional. Homozygous deletions of exons 7 and 8 of SMN1 were found to occur in >95% of patients with spinal muscular atrophy, but not in normal control populations.