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AKNA is identified as a gene that regulates inflammation, immune response, and Epithelial–Mesenchymal Transition (EMT), which plays an important role in the progression of epithelial ovarian cancer. In this study, we analyzed the genotype and allele distribution as well as 3D modeling of one of the AKNA rs10817595 (−1372 C>A). The distribution of genotypes and alleles was analyzed using the T-ARMS PCR method on 63 ovarian cancer samples and 65 controls. AKNA mRNA expression was analyzed using qRT-PCR on 35 low-grade and 28 high-grade samples. Fifteen low-grade and 12 high-grade samples were analyzed for AKNA protein levels using immunohistochemistry. A 3D model of protein structure was constructed using AlphaFold. Significant differences in AKNA protein levels were found. However, no significant correlation was found for relative AKNA mRNA expression with protein levels. This result is thought to be related to decreased immune system response, increased inflammation, and increased EMT in epithelial ovarian cancer. AKNA gene variant (−1372 C>A) can cause a decrease in mRNA and protein levels in the low-grade and high-grade groups, so it has the potential as a genetic susceptibility factor in epithelial ovarian cancer.