Trinucleotide insertion in the SMN2 promoter may not be related to the clinical phenotype of SMA

Abstract Background More than 90% of spinal muscular atrophy (SMA) patients show homozygous deletion of SMN1 (survival motor neuron 1). They retain SMN2 , a highly homologous gene to SMN1 , which may partially compensate for deletion of SMN1 . Although the promoter sequences of these two genes are almost identical, a GCC insertion polymorphism has been identified at c.-320_-321 in the SMN1 promoter. We have also found this insertion polymorphism in an SMN2 promoter in an SMA patient (Patient A) who has SMA type 2/3. Purpose The aims of this study were to determine the frequency of the GCC insertion polymorphism in SMA patients, and to evaluate its effect on SMN transcription efficiency. Patients and methods Fifty-one SMA patients, including Patient A, were involved in this study. SMN2 transcript levels in white blood cells were measured by real-time polymerase chain reaction. Screening of the GCC insertion polymorphism was performed using denaturing high-pressure liquid chromatography. The transcription efficiency of the promoter with the insertion mutation was evaluated using a reporter-gene assay. Results All SMA patients in this study were homozygous for SMN1 deletion. Patient A retained two copies of SMN2 , and showed only a small amount of SMN2 transcript in white blood cells. We detected a GCC insertion polymorphism at c.-320_-321 only in Patient A, and not in 50 other SMA patients. The polymorphism had a slight but significant negative effect on transcription efficiency. Discussion and conclusion Patient A was judged to be an exceptional case of SMA, because the GCC insertion polymorphism rarely exists in SMN1 -deleted SMA patients. The GCC insertion polymorphism did not enhance the transcriptional efficiency of SMN2 . Thus, this GCC insertion polymorphism in the SMN2 promoter may not be associated with the milder phenotype of the patient. Patient A suggests that there are other unknown factors modifying the clinical phenotype of SMA.