Rare Mendelian disorders, while individually uncommon, collectively represent a substantial global health burden. The prolonged diagnostic journey typically associated with these conditions necessitates efficient and accurate methods of genetic diagnosis. The aim of this study was to identify genetic variants underlying a rare disorder in a patient born to consanguineous parents, using whole exome sequencing and advanced bioinformatics analysis. A structured bioinformatics pipeline in QIAGEN Clinical Insight Interpret Translational was applied, which included rigorous variant filtering based on quality, population frequency, functional prediction, and inheritance models. This analysis resulted in eight prioritized candidate variants across six genes, with two particularly compelling genetic explanations identified: a homozygous missense variant in one gene and two compound heterozygous variants in another gene. Both variant options exhibited high phenotypic concordance and biological plausibility, offering new insights into genotype-phenotype correlations for rare disorders. These findings underscore the diagnostic power of integrating whole exome sequencing with phenotype-driven analyses, significantly contributing to personalized medicine and better clinical management of rare genetic diseases. Future validation studies are recommended to confirm these genetic associations and further enhance diagnostic frameworks.