Intellectual disability type 98 (ID 98) is an X-linked disorder caused by pathogenic variants in the NEXMIF gene, characterized by intellectual disability, epilepsy, and multisystem manifestations. They identified a novel hemizygous NEXMIF variant (c.19391942delinsAT, p.S647Ifs3) in a 5-year-old boy with severe intellectual disability using triple whole-exome sequencing. His mildly disabled mother was a heterozygous carrier of this variant. Prenatal diagnosis in the mother's subsequent pregnancy revealed the same hemizygous variant in the male fetus. After genetic counseling, the family decided to terminate the pregnancy, thereby preventing clinical manifestations of the disease in the child. This case report expands the spectrum of mutations in the NEXMIF gene. Genetic testing is crucial for early diagnosis and informed reproductive counseling of families.