BackgroundDevelopmental and epileptic encephalopathy 9 (DEE9) is characterized by early infantile seizures and mild‐to‐severe neuropsychiatric symptoms. Despite being an X‐linked dominant disorder, DEE9 mainly affects heterozygous females or mosaic males, while hemizygous males are less affected. PCDH19 gene has been documented as the causative gene.MethodsKaryotyping analysis and copy number variation sequencing (CNV‐seq) were performed on a pregnant woman with epilepsy, together with her husband, son, and fetus.ResultsA disease‐causing microdeletion, seq[GRCh37] del(X)(q21.31q22.1) (90310001–100360000), was identified in the pregnant woman and her female fetus. The microdeletion includes the entire PCDH19 gene and is classified as “pathogenic” according to the American College of Medical Genetics and Genomics guidelines.ConclusionIn this case study, we have not only identified the epilepsy type of the woman as DEE9 but have also made an unfavorable prognosis for her fetus. Our findings from this prenatal case provide valuable clinical resources for prenatal diagnosis and genetic counseling, while also implying the potential of CNV‐seq as a viable method for uncovering PCDH19‐related epilepsy.