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<p>Abstract</p> <p>Lipoid proteinosis is a rare autosomal recessive disease characterized by cutaneous and mucosal lesions and hoarseness appearing in early childhood that is caused by homozygous or compound heterozygous mutations in the <it>ECM1 </it>gene located on chromosome 1q21. The aim of the study was to investigate the molecular genetic defect underlying lipoid proteinosis in a consanguineous Pakistani family.</p> <p>Methods</p> <p>Genotyping of seven members of the family was performed by amplifying microsatellite markers, tightly linked to the <it>ECM1 </it>gene. To screen for mutations in the <it>ECM1 </it>gene, all of its exons and splice junctions were PCR amplified from genomic DNA and analyzed by SSCP and sequenced directly in an ABI 3130 genetic analyzer.</p> <p>Results</p> <p>The results revealed linkage of the LP family to the <it>ECM1 </it>locus. Sequence analysis of the coding exons and splice junctions of the <it>ECM1 </it>gene revealed a novel homozygous mutation (c.616C > T) in exon 6, predicted to replace glutamine with stop codon (p.Q206X) at amino acid position 206.</p> <p>Conclusions</p> <p>The finding of a novel mutation in Pakistani family extends the body of evidence that supports the importance of <it>ECM1 </it>gene for the development of lipoid proteinosis.</p>