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<p>Abstract</p> <p>Background</p> <p>Autosomal recessive primary microcephaly is a disorder of neurogenic mitosis that causes reduction in brain size. It is a rare heterogeneous condition with seven causative genes reported to date. Mutations in <it>WD repeat protein 62 </it>are associated with autosomal recessive primary microcephaly with cortical malformations. This study was initiated to screen <it>WDR62 </it>mutations in four consanguineous Pakistani families with autosomal recessive primary microcephaly.</p> <p>Methods</p> <p>As part of a large study to detect the genetic basis of primary microcephaly in Pakistan, homozygosity mapping and DNA sequencing was used to explore the genetic basis of autosomal recessive primary microcephaly in four families.</p> <p>Results</p> <p>Four out of 100 families recruited in the study revealed linkage to the <it>MCPH2 </it>locus on chromosome 19, which harbor <it>WDR62 </it>gene. DNA sequencing in these <it>MCPH2 </it>linked families result in the identification of a novel nonsense mutation (p.Q648X) and three previously known mutations.</p> <p>Conclusion</p> <p>Our data indicate that <it>WDR62 </it>mutations cause about 4% of autosomal recessive primary microcephaly in Pakistan.</p>