Rare splice and missense variants with evidence of pathogenicity in consanguineous families with autosomal recessive intellectual disability from Pakistan

Intellectual disability (ID) is a neurodevelopmental disorder affecting up to 1-3% of people worldwide. Genetic factors, including rare de novo or rare homozygous mutations, explain many cases of autosomal dominant or recessive forms of ID. ID is clinically and genetically heterogeneous, with hundreds of genes associated with it. In this study, we performed high-depth whole-genome sequencing of twenty individuals from five consanguineous families from Pakistan, with nine individuals affected by mild or severe ID. We identified one splice and five missense rare variants (at allele frequencies below 0.001%) in a homozygous state in the affected individuals with supporting and moderate evidence of pathogenicity based on guidance from the American College of Medical Genetics and Genomics. These six variants mapped to different genes ( SRD5A3 , RDH11 , RTF2 , PCDHA2 , ADAMTS17 , and TRPC3 ), and only SRD5A3 had previously been known to cause ID. The p.Tyr169Cys mutation inside SRD5A3 was predicted to be deleterious and affect protein structure by multiple in silico tools. In addition, we found one missense mutation, p.Pro1505Ser, inside UNC13B with conflicting evidence of pathogenic and benign effects. Further functional studies are required to confirm the pathogenicity of these variants and understand their role in ID. Our findings provide additional needed information for interpreting rare variants in the genetic testing of ID. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement A.W. was supported by the Higher Education Commission of Pakistan. The sequencing experiments and analyses of sequencing data in this study were supported by the McGill Canada Excellence Research Chair Program in Genomic Medicine (V.M.). V.M. holds a Canada Excellence Research Chair. Calcul Quebec and the Digital Research Alliance of Canada provided the computational resources for this study. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The ORIC (Office of Research Innovation and Commercialization) and DSAR (Director of Advanced Study and Research) boards of the University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan, approved the study ethics protocol. The DNA sequencing and genetic data analyses were also approved by the Research Ethics Office (IRB) of the Faculty of Medicine and Health Sciences at McGill University, Montreal, Canada. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes