Objective <p>This study aims to analyze the clinical features and genetic mutation characteristics of a family with Dentinogenesis Imperfecta Shields type II (DGI-II) and to observe the behavior of the stem cells from human exfoliated deciduous teeth (SHED) to explore the relationship between the locus of dentin sialophosphoprotein (<i>DSPP</i>) mutations and family clinical manifestations.</p> Materials and methods <p>After collecting clinical data from the family, Whole Genome Sequencing (WGS) followed by Sanger sequencing was used to identify pathogenic genes sites. The physical characteristics of the patient’s teeth were examined using Micro-CT, scanning electron microscopy (SEM), and microhardness analysis. The behavior of SHEDs was studied through flow cytometry, adipogenic and osteogenic differentiation, quantitative real-time PCR (qRT-PCR), Western blotting, CCK-8 proliferation assays, colony formation, and cell migration experiments.</p> Results <p>A novel frameshift mutation, <i>DSPP</i> c.2695delA.N899fs, was identified in the family. Micro-CT showed significant wear in the patient’s teeth. SEM results revealed reduced and irregular dentinal tubules. Microhardness analysis showed significantly lower hardness in the patient’s teeth. CCK-8, colony formation, and migration assays demonstrated reduced proliferation and migration capacities in the patient’s SHEDs. qRT-PCR and Western blot results showed lower expression of <i>DSPP</i>,<i> RUNX2</i>,<i> OCN</i>, and <i>ALP</i> compared to controls, but higher DSPP protein level in the patient’s SHEDs. Osteogenic differentiation tests indicated reduced mineralization capacity of the patient’s SHEDs.</p> Conclusion <p>This study identified a novel frameshift mutation, <i>DSPP</i> c.2695delA.N899fs, in a DGI-II family and demonstrated its impact on SHED proliferation, migration, and mineralization. The findings demonstrated that this novel variant disturbs dentinal characteristics and cell behavior of SHED.</p>