Most gastrointestinal stromal tumors (GISTs) are associated with molecular changes in two genes, KIT and platelet-derived growth factor receptor‑α (PDGFRA). However, only 5–10% of GISTs harbor PDGFRA mutation. Most tumors carry substitution affecting codon D842 in exon 18, which entails imatinib resistance. The other substitutions in this codon are extremely rare mutations (only 13 reported cases) involving D842Y substitution. This report presents a case of gastric GIST infiltrating liver segment III in a 70-year-old man. The tumor was studied histologically, immunohistochemically, and genetically. Mutational analysis revealed PDGFRA exon 18 mutation—p.(D842Y), c.2524G > T. Diagnosis of GIST with a high risk of progression was made. Due to subsequent liver metastases, imatinib therapy was commenced, which resulted in a minor disease response at a higher dose of imatinib. Our case is a unique, comprehensive report of in vivo PDGFRA D842Y-mutated GIST partial sensitivity to imatinib.