Novel estrogen-related gene variants identified by whole-exome sequencing in pregnancy-associated intrahepatic cholestasis

Intrahepatic cholestasis of pregnancy (ICP) is associated with an increased risk of adverse fetal outcomes, including fetal morbidity and mortality. It is a complex liver disorder influenced by genetic interactions, estrogen levels, and environmental factors. Although elevated estrogen levels are known to contribute to ICP pathogenesis, the role of genetic variants in estrogen-related genes remains poorly characterized. Accordingly, we conducted whole-exome sequencing (WES) in 249 patients with ICP, focusing on eight key estrogen-related genes (<i>ESR1/2, CYP17A1/19A1, CYP1A2/1B1/3A4</i>, and <i>COMT</i>). Variants were validated by Sanger sequencing and functionally characterized using comprehensive bioinformatics analyses (PolyPhen-2, SIFT, and MutationTaster) combined with molecular modeling. Our whole-exome sequencing analysis of 249 patients with ICP identified 235 variants across eight estrogen-related genes, with three novel <i>CYP17A1</i> missense mutations (p.Pro28Thr, p.Phe93Leu, and p.Arg347Leu) demonstrating particularly significant findings. These variants exhibited the following characteristics: (1) complete absence in 1,237 controls and all public genomic databases (1000 Genomes, ExAC, and dbSNP); (2) evolutionary conservation of the affected residues, with unanimous pathogenic predictions from all algorithms (PolyPhen-2: damaging; SIFT: deleterious; MutationTaster: disease-causing); (3) molecular modeling demonstrating structural perturbations in critical functional domains, including steroid-binding and redox partner interaction sites. Furthermore, analysis of placental tissue revealed significantly reduced <i>CYP17A1</i> expression in ICP cases <i>versus</i> controls (<i>P</i> < 0.05), suggesting functional impairment of estrogen metabolic pathways. We identified three novel pathogenic <i>CYP17A1</i> variants associated with ICP through whole-exome sequencing, elucidated their structural and functional effects on estrogen metabolism, and demonstrated significantly reduced placental <i>CYP17A1</i> expression, thereby providing crucial insights into the genetic basis of ICP pathogenesis.