The genetic etiology of brain disorders is highly heterogeneous, characterized by abnormalities in the development of the central nervous system that lead to diminished physical or intellectual capabilities. The process of determining which gene drives disease, known as "gene prioritization," is not entirely understood. Genome-wide searches for gene-disease associations are still underdeveloped due to reliance on previous discoveries and evidence sources with false positive or negative relations. This paper introduces DeepGenePrior, a model based on deep neural networks that prioritizes candidate genes in genetic diseases. Using the well-studied Variational AutoEncoder (VAE), we developed a score to measure the impact of genes on target diseases. Unlike other methods that use prior data to select candidate genes, based on the "guilt by association" principle and auxiliary data sources like protein networks, our study exclusively employs copy number variants (CNVs) for gene prioritization. By analyzing CNVs from 74,811 individuals with autism, schizophrenia, and developmental delay, we identified genes that best distinguish cases from controls. Our findings indicate a 12% increase in fold enrichment in brain-expressed genes compared to previous studies and a 15% increase in genes associated with mouse nervous system phenotypes. Furthermore, we identified common deletions in ZDHHC8, DGCR5, and CATG00000022283 among the top genes related to all three disorders, suggesting a common etiology among these clinically distinct conditions. DeepGenePrior is publicly available online at http://git.dml.ir/z%5frahaie/DGP to address obstacles in existing gene prioritization studies identifying candidate genes. Author summary: DeepGenePrior is a deep learning-based method for prioritizing genes in genetic diseases. Conventional tools utilize the guilt by association principle, which relies on prior knowledge to identify novel genes. In contrast, our method does not use any prior information. Furthermore, other tools rely on auxiliary data, including false positive or negative relations, which may lead to erroneous associations. Another group of methods relies on hypothesis testing, and fundamental issues regarding this group have been widely discussed in different papers. We compared the results of DeepGenePrior with both statistical and machine learning studies against biological and classification benchmarks. Our method's results outperformed current works in three brain disorders: autism, schizophrenia, and developmental delay. [ABSTRACT FROM AUTHOR]