We investigate a 5d gauge theory on S1 with point interactions. The point interactions describe extra boundary conditions and provide three generations, the charged lepton mass hierarchy, the lepton flavor mixing and tiny degenerated neutrino masses after choosing suitable boundary conditions and parameters. The existence of the restriction in the flavor mixing, which appears from the configuration of the extra dimension, is one of the features of this model. Tiny Yukawa couplings for the neutrinos also appears without the see-saw mechanism nor symmetries in our model. The magnitude of CP violation in the leptons can be a prediction and is consistent with the current experimental data. © Owned by the authors, published by EDP Sciences, 2015.