Exome Sequencing in Prenatally Diagnosed Isolated Neural Tube Defects: A Subtype-Specific Analysis

Objective: To explore potential genetic contributors across different subtypes of isolated neural tube defects (NTDs) - acrania–exencephaly–anencephaly sequence (AEAS), spinal dysraphism, and encephalocele - using exome sequencing (ES) in a prenatal cohort, with the goal of gaining insight into the molecular diversity underlying these distinct phenotypes. Methods: We retrospectively reviewed all fetuses diagnosed prenatally with isolated NTDs at Tel Aviv Sourasky Medical Center between September 2020 and July 2025. Detailed anatomical ultrasound excluded additional malformations. Chromosomal microarray (CMA) and trio-based ES were performed using standard protocols. Variant interpretation followed ACMG/AMP guidelines, integrating phenotypic concordance via Human Phenotype Ontology (HPO) terms. Results: The cohort comprised 23 fetuses: 10 with AEAS (9 acrania, 1 exencephaly), 8 with spinal dysraphism (5 myelomeningocele, 3 meningocele), and 5 with encephalocele. Across the cohort, exome sequencing yielded pathogenic or likely pathogenic variants in 26% (6/23) of cases and a variant of uncertain significance in 4% (1/23). Detection rates varied by subtype, highest in encephalocele (60%), followed by spinal dysraphism (25%) and AEAS (20%). However, these findings reflect diagnostic associations rather than definitive causal relationships. Identified genes included PPP1R12A, ARHGAP35, PIEZO2, KIAA0586, TSC2, and CLCN7, representing diverse pathways in cytoskeletal organization, ciliary function, mechanotransduction, and mTOR signaling. Notably, recurrent PPP1R12A variants were found in 2 fetuses: one with AEAS and one with encephalocele, suggesting a shared morphogenetic pathway affecting cranial fold formation and mesenchymal remodeling. Conclusion: Our findings indicate that these distinct types of NTD, namely AEAS, spinal dysraphism, and encephalocele, may represent partially divergent embryologic and genetic entities rather than a single phenotypic continuum. Subtype-specific analysis revealed differing molecular patterns, emphasizing the value of trio-based ES in elucidating the etiology of isolated NTDs. Larger studies are needed to refine detection rates and expand our understanding of the genetic architecture underlying these distinct malformations.