Computational Approach to PCR Primer Design for Genetic Analysis of TRAPPC9 Exon 20

Abstract

 Intellectual disability (ID) is a neurodevelopmental disorder defined by an intelligence quotient (IQ) of 70 or below and deficits in at least two domains of adaptive functioning. It is broadly classified into syndromic (S-ID) and non-syndromic forms, with S-ID associated with additional clinical features. This study aims to investigate the molecular basis of syndromic intellectual disability by targeting known genetic contributors such as those involved in Fragile X syndrome, Down syndrome, Prader-Willi syndrome, 
fetal alcohol spectrum disorders, and autism. Individuals with suspected ID from Tehsil Daska, Pakistan, were recruited for this research. Blood samples were collected, and genomic DNA was extracted using standard protocols. Molecular analyses included gel 
electrophoresis, primer design using Primer3 Plus, PCR amplification, and Sanger sequencing. Exon 20 of the TRAPPC9 gene, associated with autosomal recessive intellectual disability, was examined; no mutations were detected in this region, indicating that causative variants may lie in other exons or genes. This study highlights the need for broader genetic screening in populations with limited molecular diagnostic access. Identifying causative mutations in ID-related genes may support earlier diagnosis, better genetic counseling, and pave the way for targeted therapeutic strategies.