Objective:

To apply an integrative multiomic approach to identify novel genetic etiologies and biological mechanisms underlying Chiari I malformation (CM1) and to investigate its overlap with neurodevelopmental disorders (NDDs).

Background:

Chiari I malformation, defined by caudal descent of the cerebellar tonsils through the foramen magnum, is the most common structural anomaly of the human hindbrain. Despite its prevalence and substantial morbidity, the genetic architecture and developmental mechanisms underlying CM1 remain poorly understood, contributing to inconsistent surgical outcomes and persistent neurobehavioral symptoms.

Design/Methods:

We performed an integrative analysis of 1,585 CM1 proband–parent trios (4,857 exomes), natural language processing–derived phenotypic data from medical records, and 176,492 single-cell transcriptomes from the developing human cerebellum. De novo variant (DNV) enrichment was assessed using DenovolyzeR and DeNovoWEST. Functional annotation incorporated protein–protein interaction (PPI) networks, gene ontology, and developmental transcriptomic analyses.

Results:

Damaging DNVs in mutation-intolerant genes were significantly enriched in CM1 cases versus 1,798 control trios (P = 1.91 × 10⁻⁴⁸). Fifteen genes reached exome-wide significance, and 76 additional high-confidence genes harbored multiple damaging DNVs. CM1 genes converged on two primary PPI networks regulating chromatin remodeling and phosphoinositide 3-kinase (PI3K) signaling. Recurrent DNVs in FGFR3, PIK3CA, PIK3R2, PTEN, and AKT3 suggest dysregulated PI3K-AKT-mTOR activity promoting cerebellar overgrowth. Single-cell analysis revealed CM1 gene enrichment in neuroblasts of the nuclear transitory zone and glutamatergic granule cells, implicating early cerebellar developmental disruption.

Conclusions:

This study defines the first large-scale genomic landscape of CM1, revealing rare damaging DNVs in mutation-intolerant genes that regulate chromatin and growth signaling. Findings implicate genetically encoded cranio-cerebellar disproportion as a core pathogenic mechanism, provide a molecular framework for CM1-associated neurodevelopmental phenotypes, and suggest potential non-surgical therapeutic targets.