PurposeThe relationship between the CDK5RAP3 and UFM1 expression and the prolonged outcomes of patients who underwent gastric cancer (GC) surgery was investigated.MethodsSingle-sample gene set enrichment analysis (ssGSEA), unsupervised clustering and other methods were used to verify the relationship between CDK5RAP3 and UFM1 in GC through public databases. Additionally, CDK5RAP3 and UFM1 expression in cancerous and paracancerous tissues of GC was analysed in the context of patient prognosis.ResultsCDK5RAP3 and UFM1 expression was downregulated synchronously, the interaction was observed between the two proteins, and UFM1 and CDK5RAP3 expression was found to be inversely associated to AKT pathway activation. Prognostic analysis showed that the prognosis is poorer for low CDK5RAP3 and UFM1 patients, than for high CDK5RAP3 and/or UFM1 (p