Domain-associated phenotypic patterns with MACF1 variants

While heterozygous de novo missense variants in the microtubule-binding GAR domain of Microtubule-actin cross-linking factor 1 (MACF1) cause Lissencephaly 9 with Complex Brainstem Malformations (LIS9) [MIM 618325], the phenotypic impact of variants outside this domain remains unclear.

We assembled a cohort of 5 affected individuals from 4 unrelated families with biallelic non-GAR domain MACF1 variants who exhibit partially overlapping yet unique phenotypic traits. A sixth individual with a de novo, heterozygous frameshift variant was additionally identified. Combined with previously reported cases, we analyzed genotype and phenotype data from 22 individuals using Human Phenotype Ontology (HPO)-based unsupervised hierarchical clustering.

Clustering revealed two distinct phenotypic signatures, suggesting domain-associated effects. Variants outside the GAR domain associate with broader neurodevelopmental phenotypes and craniofacial and skeletal involvement. Enrichment analysis (p < 0.001) using OMIM HPO sets supported these findings. In contrast to the GAR domain's strong correlation with LIS9, biallelic non-GAR domain MACF1 variants were linked to distinct developmental anomalies.

These results expand the phenotypic spectrum of MACF1-related disorders and provide preliminary evidence for domain-associated MACF1 variant effects. While limited by sample size and lack of functional validation, these findings should be considered hypothesis-generating and underscore the utility of HPO-based clustering for systematic phenotype comparison as additional cases emerge. Comprehensive genetic and phenotypic assessments are essential for understanding the role of MACF1 in development, informing diagnosis, and guiding future research on cytoskeletal regulation in neurodevelopment.