BACKGROUND: Hypohidrotic ectodermal dysplasia (HED) mainly results from gene mutations in the EDA/EDAR/NF-κB pathway. Function analysis of the mutations in the collagen domain of ectodysplasin A (EDA)result in HED has been rarely studied. This study aimed at determining the mechanism by which the novel collagen domain mutation of EDA results in HED. METHODS: We analyzed the DNAs from a Chinese family with HED and performed bioinformatics analysis. A new three-dimensional structure model of the EDA trimer was built and used to predict the effect of the mutations on EDA. We performed a western blot to detect EDA1 proteins in cell lysates and supernatants. We then performed coimmunoprecipitation to determine whether the mutation would affect the interaction of EDA1 with the EDA receptor (EDAR). Dual luciferase reporter assay and immunofluorescence were performed to detect the effect of the mutant EDA1 protein on nuclear factor kappa B (NF-κB) activation. RESULTS: A novel missense mutation (c.593G > A, p. Gly198Glu) in the collagen domain of EDA was detected. The mutation was predicted to be disease-causing. A three-dimensional structure model of the EDA trimer was first built in this study, in which the mutation site is located around the receptor binding domain. Functional studies showed that there was no difference in the secretion activity between the mutant EDA1 and the wild-type EDA1. However, the receptor-binding activity and the transcription activation of NF-κB were impaired by the mutation. CONCLUSION: We identified a novel mutation (c.593G > A, p. Gly198Glu) in the collagen domain of EDA. Bioinformatics analysis and functional studies showed this mutation was damaging, indicating that mutations in the collagen domain of EDA could result in HED by affecting the receptor-binding activity of EDA and the transcriptional activity of NF-κB.