Background and purpose: Congenital Myasthenic Syndrome (CMS) is a rare genetic disease with autosomal recessive inheritance pattern which is caused by mutations in the COLQ gene. Molecular diagnosis of the disease using direct mutation analysis is expensive and time consuming. Alternatively, linkage analysis using Single Nucleotide Polymorphic markers (SNP) provides a suitable method in carrier detection and prenatal diagnosis of the disease in families with an affected individual. The aim of this study was to investigate the informative situation of rs6442530 marker in COLQ gene.

Materials and methods: In this experimental study, using bioinformatics investigations, rs6442530 marker located in intron 1 of COLQ gene was selected for genotyping studies. For this purpose, 152 healthy individuals from Isfahan population were genotyped using ARMS PCR technique. Then the allelic frequencies, the Hardy-Weinberg equilibrium and heterozygosity of the marker were estimated using the Genepop software. Finally the amount of Polymorphism Information Content (PIC) was computed by PIC Calculator software for the marker.

Results: The results indicated 43.4% Minor Allele Frequency (MAF), 48.684211% heterozygosity rate and 0.3706 PIC for rs6442530 marker in Isfahan population. Hardy Weinberg Equilibrium showed the presence of equilibrium for rs6442530 in this population.

Conclusion: Together, according to the results (MAF>0.2 and PIC close to 0.375) rs6442530 marker could be suggested as an appropriate marker for molecular diagnosis of CMS in Isfahan population.