Genotype determination at the survival motor neuron locus in a normal population and SMA carriers using competitive PCR and primer extension

Hum Mutat. 2000 Sep;16(3):253-63. doi: 10.1002/1098-1004(200009)16:3<253::AID-HUMU8>3.0.CO;2-8.


Precise quantitation of SMN1 copy number is of great interest in many clinical applications such as direct detection of SMA carriers or detection of an SMA-affected patient with a hemizygous deletion of the SMN1 gene. We describe a method that combines two independent nonradioactive PCR assays: determination of the relative ratio of the SMN1 and SMN2 genes using a primer extension assay and of the total SMN copy number using competitive PCR. Consistency of the results of two independent approaches ensures the reliability of the deduced genotype and thus avoids false interpretation of borderline results that can occur in quantitative assays. In all, 135 subjects were tested, including 91 normal controls and 44 SMA-affected children or SMA carriers. Two main genotypes were observed in controls: 2T/2C (45%) and 2T/1C (32%). A wide variability at the SMN locus is observed with nine different genotypes and up to six SMN genes. SMA carriers showed three frequent genotypes, 1T/2C (50%), 1T/3C (29%), and 1T/1C (18%). Normal chromosomes with two SMN1 genes per chromosome are not infrequent and thus, about 3% of SMA carriers are not detected using SMN1 copy number quantitation. Finally, as this method does not detect point mutations (4% of SMN1 gene mutations), reliability ranges from 93% to 100% depending on data available from the propositus.

Publication types

  • Comparative Study

MeSH terms

  • Child, Preschool
  • Cyclic AMP Response Element-Binding Protein
  • DNA Primers / genetics*
  • Gene Dosage
  • Genetic Carrier Screening*
  • Genetic Markers / genetics
  • Genotype
  • Humans
  • Motor Neurons / physiology*
  • Muscular Atrophy, Spinal / genetics*
  • Nerve Tissue Proteins / genetics*
  • Phenotype
  • Polymerase Chain Reaction / methods*
  • Polymerase Chain Reaction / standards
  • RNA-Binding Proteins
  • Reproducibility of Results
  • SMN Complex Proteins
  • Survival of Motor Neuron 1 Protein
  • Survival of Motor Neuron 2 Protein


  • Cyclic AMP Response Element-Binding Protein
  • DNA Primers
  • Genetic Markers
  • Nerve Tissue Proteins
  • RNA-Binding Proteins
  • SMN Complex Proteins
  • SMN1 protein, human
  • SMN2 protein, human
  • Survival of Motor Neuron 1 Protein
  • Survival of Motor Neuron 2 Protein