Amyotrophic lateral sclerosis (ALS) is characterised by the progressive degeneration of motor neurons that typically results in fatality within 3 – 5 years. Recent GWAS studies have identified a number of candidate ALS genes, but validation of these risk factors requires further study. Colleagues have shown that a SNP in the GGNBP2 gene increases ALS risk by 10%, and that this allele is associated with increased GGNBP2 expression. We used Drosophila to characterise this gene’s function in motor neurons and validate it as an ALS risk factor. We identified a fly homologue (Ggnbp2) and used CRISPR to generate a null mutant. Motor neurons in Ggnbp2 mutant flies were smaller and had fewer synapses compared to controls; these phenotypes could be rescued by expressing wild type Ggnbp2 in motor neurons. Overexpression of Ggnbp2 in motor neurons, emulating the human disease, results in the opposite effect where motor neuron size and synapse number is increased. Using a climbing assay to assess motor function, we also observed strong defects in animals overexpressing Ggnbp2. Rescue of Ggnbp2 mutant phenotypes with a human transgene demonstrated that this gene has a conserved function in motor neurons. To better understand the role of Ggnbp2 in motor neurons, we conducted a series of genetic studies and linked it to autophagy, a process commonly defective in ALS. Thus, we demonstrate that GGNBP2 is a bona fide risk factor for ALS and propose that overexpression of this gene could lead to defects in synaptic development and autophagy in humans.