Chondrodysplasia punctata is a rare hereditary disorder that affects bone development. The disease is primarily caused by mutations in the emopamil binding protein (EBP) gene, leading to X-linked dominant metabolic enzyme abnormalities. This study aims to report a novel EBP mutation in X-linked dominant chondrodysplasia punctata type 2 (CDPX2), expanding the genetic spectrum of the disease and highlighting the critical role of combined clinical and genetic diagnosis in guiding prenatal counseling and postnatal management. Multiple prenatal ultrasounds revealed misalignment of the spinal column and short femur. Postnatally, the infant exhibited craniofacial defects, short limbs, congenital ichthyosis, and alopecia. Radiographic examination revealed multiple punctate calcifications bilaterally in the pyramids, ischium, pubis, and calcaneus. Whole-exome sequencing of the family revealed a heterozygous mutation, c.204G>A (p.Trp68Ter), in the EBP gene in the affected infant, which is a new pathogenic mutation. The infant received continuous positive airway pressure support for respiratory distress, which was discontinued after 7 days due to clinical improvement. At discharge, respiratory status was stable. Follow-up at 3 months showed significant growth delay: weight 4.6 kg (<3rd percentile) and length 54.5 cm (9th percentile). This case underscores that meticulous physical examination combined with genetic analysis is critical for diagnosing CDPX2. Early identification of EBP mutations enables accurate prenatal counseling and risk assessment for future pregnancies.

X-linked dominant chondrodysplasia punctata (CDPX2) is a rare congenital disorder caused by pathogenic variants in EBP on Xp11.23. We encountered a girl and her mother with CDPX2-compatible phenotypes including punctiform calcification in the neonatal period of the girl, and asymmetric limb shortening and ichthyosis following the Blaschko lines in both subjects. Although Sanger direct sequencing failed to reveal a disease-causing variant in EBP, whole genome sequencing (WGS) followed by Manta analysis identified a ~ 4.5 kb insertion at EBP exon 2 of both subjects. The insertion was associated with the hallmarks of retrotransposition such as an antisense poly(A) tail, a target site duplication, and a consensus endonuclease cleavage site, and the inserted sequence harbored full-length SVA_F1 element with 5'- and 3'-transductions containing the Alu sequence. The results imply the relevance of retrotransposition to the human genetic diseases and the usefulness of WGS in the identification of retrotransposition.