Provided are a nucleic acid molecule encoding a Gle1 protein variant comprising a phytic acid-binding pocket, a protein encoded by the nucleic acid molecule and a method using the nucleic acid molecule. The Gle1 protein variant has an increased sensitivity to phytic acid in plants, and also has an effect of highly increasing vegetative growth, seed yield, seed performance and abiotic stress tolerance in plants containing a low level of phytic acid. Therefore, high yield low-InsP6 crops may be cultivated using the nucleic acid molecule.