Gastric cancer (GC) with ovarian metastasis (OM) represents a distinct subtype of peritoneal metastasis in female patients, characterized by limited therapeutic options and poor prognosis, with molecular features and mechanisms that remain unknown. We performed whole-exome sequencing (WES) analysis of matched GC samples, with OM or peritoneal metastasis (PM), to identify mutational profiles that contribute to OM. We further validate these findings through in vitro and in vivo experiments. We characterized specific mutated genes in GC with OM, including , , , , , , and . Moreover, these genomic mutations are recurrent in both GC and ovarian cancer. We further identified the E620K mutation of , a Rho guanine nucleotide exchange factor, as a novel risk locus in GC with OM. Ectopic expression of the E620K mutant increased cell migration, invasion and colony formation in vitro, as well as OM in animals bearing GC xenograft tumors. Mechanistically, E620K mutation upregulated expression through Rap1 signaling pathway activation and promoted tumor-derived ITGA6-high exosome formation, which were preferentially uptaken by ovarian fibroblasts. Reciprocally, ovarian fibroblasts educated by ITGA6high exosomes exhibited cancer-associated fibroblasts (CAFs) phenotypes and enhanced tumor cell proliferation, thereby initiating the early stage of pre-metastatic niche formation. Our study provides comprehensive clinical exome profiling, identifies mutation as a new driver, and reveals that ITGA6 acts as an early predictive marker in GC with OM.