Antithrombin (AT) deficiency is an autosomal dominant disorder, and the identification of mutant AT variants has provided a useful aid to our full understanding of the anticoagulant function of serine protease inhibitors (SERPIN) and the molecular mechanisms of AT deficiency. Genome-wide exon sequencing of a member of a Chinese family with deep vein thrombosis revealed a 4 amino acid deletion mutation in exon 4 of the SERPINC1 gene. This mutation caused the development of type I AT deficiency by leading to intracellular aggregation of AT proteins, and intracellular aggregation of AT increased endoplasmic reticulum (ER) stress, which further inhibited AT release. Moreover, ER stress activated ER stress-related degradation pathways, which further enhanced the intracellular degradation of AT. Finally, the secretion of AT was found to be enhanced by further inhibition of the ER stress pathway. In this study, a novel deletion mutation in the SERPINC1 gene was identified for the first time, and it was determined that the mutation caused the development of type I AT deficiency through a novel mechanism-raising ER stress; therefore, this study may provide a new therapeutic idea for the intervention of AT deficiency.