X-linked intellectual disability (XLID) is a genetically heterogeneous disorder. Currently, 162 genes linked to XLID have been found, but the cause of XLID is still unclear. While the GNAO1 gene is crucial for hypotonia, epilepsy, developmental delay, and movement disorders, the NEXMIF gene, also known as KIAA2022, has associations with XLID, autism, and epilepsy. The subject of the study, a 5-year-old girl has lots of congenital defects, including a cleft palate, anal atresia, hypotonia in her lower limbs, and thumb missing. A variety of eye abnormalities, such as scoliosis, finger malformations, and craniofacial dysmorphism. Radiological tests revealed substantial heart problems, bilateral renal hypoplasia, and brain abnormalities. She met milestones more later than her contemporaries, indicating clear developmental deficits. The NEXMIF and GNAO1 genes both include heterozygous frameshift variants that were discovered through genetic research using next-generation sequencing. The complex and varied clinical signs of XLID are shown in this case. The clinical picture is further complicated by the co-occurrence of mutations in the NEXMIF and GNAO1 genes, which emphasizes the need for an approach to offer suitable therapy solutions. Future studies are necessary to understand the complex interactions between these genes and how they affect XLID and related symptoms.