We have shown that human glycerol-3P-acyltransferase 2 (GPAT2) is overexpressed in various human cancer cell lines, including breast cancer MDA-MB-231 cells. We also showed that GPAT2 knockdown decreases cell proliferation, anchorage-independent growth, migration, and tumorigenicity, and increases staurosporine-induced apoptosis. GPAT2 features a significant positive correlation with the histological grade of human breast carcinomas. Additionally, it can modulate the expression levels of several non-coding RNAs. Transcriptomic analysis showed that the Wnt5A gene and the Wnt pathway are downregulated after GPAT2 silencing. Furthermore, we found that GPAT2 knockdown in MDA-MB-231 cells impacts the expression levels of several long non-coding RNAs (LncRNAs). Following the identification, selection, and annotation of differentially expressed LncRNAs in GPAT2-silenced cells versus control cells, we identified three LncRNAs (LINC1085, CTD2066L21.3, and NOVA1.AS1) predictive of overall survival in patients with breast cancer. Moreover, we identified specific miRNAs associated with the selected LncRNAs. Specifically, we found that hsa-mir-106a-5p, associated with NOVA1.AS1, shows a significant positive correlation with breast cancer patient survival and a strong negative correlation with the Wnt signaling pathway, thereby establishing this pathway as a candidate to explain the effect of GPAT2 expression on MDA cells. In this work, we knocked down Wnt5A in MDA cells using shRNA methodology. By performing cell proliferation and wound healing assays, we were able to reproduce the phenotype obtained by silencing GPAT2 in this same cell line. Importantly, the expression level of GPAT2 was not affected by Wnt5A silencing.