Genetic architecture and prognostic significance of suspected fetal microcephaly: evidence from prenatal exome sequencing in a large prospective cohort

BACKGROUND: Fetal microcephaly (FMIC) is a neurodevelopmental disorder with heterogeneous etiologies and uncertain prenatal prognosis. Discrepancies between prenatal and postnatal head circumference (HC) measurements may confound ultrasound-based diagnosis, underscoring the need for genetic stratification to improve risk assessment. METHODS: This prospective cohort study analyzed data from 301 fetuses with suspected FMIC collected between 2014 and 2022. Trio-prenatal exome sequencing (pES) was performed in 301 fetuses with suspected FMIC and normal results on karyotyping and chromosomal microarray analysis. Diagnostic yield, molecular spectrum, and pathway enrichment were analyzed. Clinical follow-up was conducted to correlate genetic findings with postnatal neurodevelopmental outcomes. RESULTS: Molecular diagnoses were achieved in 41 cases (13.6%). Diagnostic yield was significantly higher in complex FMIC compared with isolated FMIC (15.9% vs. 10.1%, p < 0.01), and peaked in cases with family history (26.7%). Our findings expand the prenatal phenotypic spectrum for six genes (TUBB2A, DUOX2, EBP, FAM111A, FGFR3, PEX1), indicating that microcephaly can be a primary presenting feature in the fetus for conditions where it was previously considered a secondary or postnatal finding. Pathogenic variants were enriched in neurogenesis and extracellular matrix-related pathways, implicating dysregulated cell cycle progression and synaptogenesis. Importantly, HC standard deviation (HC-SD) correlated with diagnostic yield and, as demonstrated by multivariable analysis, served as an independent predictor of postnatal prognosis (aOR: 2.1 per 1-SD decrease; 95% CI: 1.5-3.0), whereas fetal growth restriction appeared nonspecific. CONCLUSIONS: This prospective cohort study provides the largest prenatal genomic and prognostic analysis of FMIC to date, revealing potential genotype-phenotype associations, pathogenic pathways, and prognostic markers. These findings enhance understanding of FMIC mechanisms and provide essential evidence for prenatal genetic counseling and individualized risk assessment.