Rare variants in cause delayed development, intellectual disability, autism, and epilepsy.

encodes the Protein-Tyrosine Phosphatase, Receptor-Type, F Polypeptide-Interacting Protein Alpha-3 (PPFIA3), which is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family involved in synaptic vesicle transport and presynaptic active zone assembly. The protein structure and function are well conserved in both invertebrates and vertebrates, but human diseases related to PPFIA3 dysfunction are not yet known. Here, we report 14 individuals with rare mono-allelic variants presenting with features including developmental delay, intellectual disability, hypotonia, autism, and epilepsy. To determine the pathogenicity of variants , we generated transgenic fruit flies expressing either human PPFIA3 wildtype (WT) or variant protein using GAL4-UAS targeted gene expression systems. Ubiquitous expression with Actin-GAL4 showed that the variants had variable penetrance of pupal lethality, eclosion defects, and anatomical leg defects. Neuronal expression with elav-GAL4 showed that the variants had seizure-like behaviors, motor defects, and bouton loss at the 3 instar larval neuromuscular junction (NMJ). Altogether, in the fly overexpression assays, we found that the variants in the N-terminal coiled coil domain exhibited stronger phenotypes compared to those in the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly α leads to embryonic lethality. This lethality is partially rescued by the expression of human WT, suggesting human PPFIA3 protein function is partially conserved in the fly. However, the variants failed to rescue lethality. Altogether, the human and fruit fly data reveal that the rare variants are dominant negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.