title: 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.
  
  
  OBJECTIVE
  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.
  
  
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
authors.forename: Nur Imma Fatimah
authors.initials: NI
authors.lastname: Harahap
authors.affiliation: Kobe Pharmaceutical University, Kobe 658-8558, Japan.
authors.forename: Atsuko
authors.initials: A
authors.lastname: Takeuchi
authors.affiliation: Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Department of Pediatrics, Universiti Sains Malaysia, Kelantan 16150, Malaysia.
authors.forename: Surini
authors.initials: S
authors.lastname: Yusoff
authors.affiliation: Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Tominaga
authors.affiliation: Department of Pediatrics, Bell Land General Hospital, Sakai 599-8247, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Okinaga
authors.affiliation: Department of Pediatric Neurology, Morinomiya Hospital, Osaka 536-0023, Japan.
authors.forename: Yukihiro
authors.initials: Y
authors.lastname: Kitai
authors.affiliation: Kobe Pharmaceutical University, Kobe 658-8558, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Takarada
authors.affiliation: Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kubo
authors.affiliation: Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
authors.forename: Kayoko
authors.initials: K
authors.lastname: Saito
authors.affiliation: Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
authors.forename: Nihayatus
authors.initials: N
authors.lastname: Sa'adah
authors.affiliation: Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
authors.forename: Dian Kesumapramudya
authors.initials: DK
authors.lastname: Nurputra
authors.affiliation: Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0871, Japan.
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Nishimura
authors.affiliation: Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toyonaka, Japan.
authors.forename: Toshio
authors.initials: T
authors.lastname: Saito
authors.affiliation: Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0871, Japan. Electronic address: nishio@med.kobe-u.ac.jp.
authors.forename: Hisahide
authors.initials: H
authors.lastname: Nishio
mesh_terms: D000293:Adolescent; D000328:Adult; D001483:Base Sequence; D002648:Child; D002675:Child, Preschool; D005260:Female; D017353:Gene Deletion; D018628:Gene Dosage; D006801:Humans; D007223:Infant; D008297:Male; D008969:Molecular Sequence Data; D009134:Muscular Atrophy, Spinal / Q000175:diagnosis* / Q000235:genetics*; D009154:Mutation; D010641:Phenotype; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D055533:Survival of Motor Neuron 1 Protein / Q000235:genetics*; D055540:Survival of Motor Neuron 2 Protein / Q000235:genetics; D055815:Young Adult
chemical_list: C526471:SMN1 protein, human; C526477:SMN2 protein, human; D055533:Survival of Motor Neuron 1 Protein; D055540:Survival of Motor Neuron 2 Protein
keywords: Polymorphism; Promoter; SMN1; SMN2; Spinal muscular atrophy