Insertion of rare autism variants in synaptic genes induce novel behavioral phenotypes in C. elegans

Neurodevelopmental conditions and disorders, including autism, involve a complex interplay of genetic, environmental, and developmental factors. Despite this complexity, genetic studies have identified more than 150 candidate genes that increase risk for autism and related neurodevelopmental and neuropsychiatric conditions. Unsurprisingly, synaptic genes are a large proportion of these genes, likely due to their roles in the formation and maintenance of synaptic architecture, function, and the plasticity of neurons and circuits. The association of synaptic genes with autism and similar conditions is driven by all types of genetic variation, including inherited and de novo rare variants that have unknown impacts on the function of the gene. Here we insert 4 conserved rare variants in the C. elegans orthologs of NLGN4X, NRXN1, and SHANK3, and define their impact on gene function compared to known loss of function variants using behavioral assays. We find that the rare variants impact multiple foraging behaviors, with each gene and variant having a unique pattern of behavioral changes and functional impact. The NLGN4X(A283T) variant induced clear loss of function, while NLGN4X(G84R) induces a loss of function in one behavior, but a gain of function in another behavior. The NRXN1(L18Q) variant induced remarkable loss and gain of functions with distinct impacts across each behavior. The SHANK3(L143P) variant induced partial loss of function in a single behavior. We also identify for the first time that loss of function of shn-1/SHANK3 alters social feeding and food response behaviors. We uncover a remarkably complex impact of rare variants in synaptic genes, with differential impacts across behaviors, highlighting the importance of broad behavioral analysis and the nuanced effects of missense variants compared to loss of function alleles. Together, we define the complex functional impact of each variant on gene function, compare the impact of variants and genes across multiple behaviors, and provide further support for the use of C. elegans to define the impact of genetic variation derived from human neurodevelopmental and neuropsychiatric disorders.