Antithrombin (AT) is one of the physiological anticoagulants that are mainly synthesized in the liver. As a protease inhibitor belonging to the serpin superfamily, AT is able to inactivate thrombin and inhibit activated coagulation factors IX, X, XI, and XII (FIXa, FXa, FXIa, and FXIIa).[1] Moreover, it has been found that AT can inhibit activated FVII (FVIIa) by accelerating dissociation of FVIIa–tissue factor complex and preventing it from recombining.[2] The AT gene (SERPINC1), located on chromosome 1 at q23.1–23.9 and spreads 13.5 kb, is composed of seven extrons and six introns.[3] Hereditary AT deficiency is a rare thrombotic disorder caused by defects in SERPINC1 gene.[4] It is inherited in an autosomal-dominant manner with an incidence of roughly 0.02 to 0.25% in the general population and 2 to 5% in patients with a history of venous thromboembolism (VTE).[1] [5] The most common thrombotic manifestations of patients with AT deficiency are VTEs, and their risks of VTE are approximately 20 times higher than those of nondeficient individuals.[6] And the consequences of thrombophilia caused by AT deficiency are more severe than those of protein C and S protein deficiency,[2] so it should be given sufficient attention. Herein, we identified a case of hereditary AT deficiency. The proband was a 24-year-old Chinese male. He came to our hospital for treatment due to left lower extremity pain with swelling for 3 days. Color Doppler ultrasound showed thrombosis in the left iliac vein and the left femoral vein, which suggested deep-vein thrombosis (DVT) in the left lower extremity. Routine coagulation tests showed that his activated partial thromboplastin time, prothrombin time, thrombin time, and fibrinogen were within the normal reference ranges, but D-dimer increased to 18.9 mg/L (reference range: 0–0.50 mg/L). Further coagulation examinations revealed that AT:A and AT antigen (AT:Ag) of the proband were decreased to 43% (reference range: 98–119%) and 107 mg/L (reference range: 250–360 mg/L), respectively. Heparin was initially used for anticoagulant therapy, and then the proband was given to the left lower extremity deep vein thrombus aspiration and catheter thrombolysis. Pedigree survey found that his father had a history of DVT at the age of 35, and his mother and elder sister were asymptomatic. After obtaining written informed consent, venous blood samples were collected from the proband, his family members, and 100 healthy volunteers. Ethical approval was obtained from the Ethics Committee of the First Affiliated Hospital of Wenzhou Medical University (China). AT:A, protein C (PC:A), and protein S activity (PS:A) levels were measured by chromogenic substrate assay. AT:Ag was determined by enzyme linked immunosorbent assay (ELISA). Referring to conditions described in a previous article,[7] all of the seven exons and intron–exon boundaries of the SERPINC1 gene were amplified by a polymerase chain reaction (PCR), then the PCR products were sent for direct sequencing. In his family, his father had a decreased AT:A level with 50% and a parallel decreased AT:Ag with 130 mg/ L, while the AT:A and AT:Ag of his mother and elder sister were within the normal ranges ([Table 1]). The PC:A and PS:A levels of all the family members were within normal ranges. Sequencing analysis identified a heterozygous point mutation c.938T > C causing p.Met281Thr substitution in exon 5 of SERPINC1 in both the proband and his father, while not in his mother and elder sister. There was no liver and/or kidney disease in this family, and their anticoagulant indicators such as PC and PS were normal, thus we initially believed that the heterozygous mutation was responsible for type I AT deficiency in this family. To further investigate the pathogenic characteristics of this mutation, we performed bioinformatics and structural analyses of AT. The p.Met281Thr mutation was predicted to be “disease causing,” “deleterious,” “probably damaging,” and “damaging” corresponding to four online bioinformatics softwares “MutationTaste,” “PROVEAN,” “PolyPhen-2,” and “SIFT,” respectively, indicating that this mutation was damaging. The conservative analysis was performed on ClustalX-2.1-win software and the results are shown in [Fig. 1]; the mutation site Met281 was highly conserved among both the homologous species ([Fig. 1A]) and serpin superfamily ([Fig. 1B]), indicating that it plays a vital role in the function and structure of AT molecules, which also confirms the results of bioinformatics analysis. Besides, the PyMol software package was used to visualize the local structural effects of the new missense mutation and molecular graphic images are shown in [Fig. 2]. AT is a structurally related globular protein that consists of nine α-helices and three β-sheets (A, B, and C). In this research, Met281 is located in the strand 3 β-sheet B (s3B) of AT protein, and from the structural analysis we can know that this methionine was deeply buried and formed two different hydrogen bonds with Leu272 ([Fig. 2A]). Once the base T at position c.938 was replaced by C, the nonpolar methionine at position 281 will be replaced by a polar threonine and resulting in the formation of another hydrogen bond with Leu272 ([Fig. 2B]), which might affect the integrity of local intermolecular structures. Interestingly, Picard et al reported another two mutations, p.Leu285Ser and p.Pro286Leu, located in the s3B, which were also associated with a type I AT deficiency.[8] They indicated that these two nonconservative substitutions had a significant effect on protein synthesis and/or folding, resulting in the absence of secretion. Since Met281, Leu285, and Pro286 are all located in the same secondary structure region s3B and adjacent, we speculated that the pathogenic mechanism of Met281Thr was the same...