Isogenic pairs of cell lines derived from human pluripotent stem cells (hPSCs) enable the precise assessment of mutation-specific phenotypes through differentiation to target cells, as this method of disease modeling excludes the bias of genetic variation. However, the extremely low efficiency of precise gene editing based on homology-directed repair (HDR) with Cas9 in hPSCs remains a technical hurdle for this approach. Herein, we took advantage of currently available base editors (BEs) in hPSCs to epitomize the isogenic disease model from hPSCs with a pathophysiological indicator. Using this method, we established 14 hPSCs that harbor point mutations on the GNE gene, including four different mutations found in GNE myopathy patients. Because BEs activated p53 to a lesser degree than Cas9, we observed a higher editing efficiency with BEs. Four different mutations in the epimerase or kinase domains of GNE revealed mutation-specific hyposialylation, which was closely correlated to pathological clinical phenotypes. These mutation-specific hyposialylation patterns were evident in GNE protein structure modeling. Furthermore, treatment with a drug candidate currently under clinical trials showed a mutation-specific drug response in GNE myopathy disease models. These data suggest that isogenic disease models from hPSCs using BEs could serve as a useful tool for mimicking the pathophysiology of GNE myopathy and for predicting drug responses.