Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics · 2026
[Analysis of a Chinese pedigree affected with Hereditary factor Ⅴ deficiency due to compound heterozygous variants of F5 gene].
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Feng Yujie, Cheng Xiaoli, Liu Jiayun, Zhu Lin
Аннотация
OBJECTIVE: To analyze the clinical characteristics and causative variation sites in a pedigree with hereditary coagulation factor Ⅴ (FⅤ) deficiency.
METHODS: A pedigree with hereditary FⅤ deficiency who visited Xijing Hospital on March 2, 2025, was selected as the study subject. Clinical data of the pedigree were collected using a retrospective analysis method. Venous blood samples were collected from the proband and family members to obtain platelet-poor plasma and genomic DNA. FⅤ activity (FⅤ:C) was measured by coagulation assay, and FⅤ antigen (FⅤ:Ag) was measured by ELISA for all members. Sanger sequencing was used to detect all exons and flanking sequences of the F5 gene in all members to screen for variations. Thrombin generation assay was performed to evaluate the overall coagulation potential of the proband and parents. Multiple online software tools, including ClustalX-2.1-win, PolyPhen-2, PROVEAN, I-Mutant v2.0, SIFT, Mutation Taster, and Swiss-Pdb Viewer, were used to assess the conservation of the variation sites and their impact on protein structure and function. The pathogenicity of the variation sites was evaluated according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines for the interpretation of sequence variants. This study was approved by the Medical Ethics Committee of Xijing Hospital (Ethics No.: KY20252367).
RESULTS: The proband's FⅤ:C level was only 1.3%, and the FⅤ:Ag level was only 2.4%. The proband was found to carry the c.653T>C (p.Phe218Ser) variant in exon 5 and the c.5660A>T (p.Glu1887Val) variant in exon 18 of the F5 gene. According to the ACMG guidelines, these two variants were classified as "Pathogenic" (PS4+PM2_Supporting+PP1+PP3+PP4+PP5) and "Likely Pathogenic" (PM1+PM2_Supporting+PM3+PP1+PP2+PP3+PP4), respectively. The proband's father and grandfather carried the p.Phe218Ser variant in heterozygous state, and the mother and maternal grandmother carried the p.Glu1887Val variant in heterozygous state. The paternal grandmother and maternal grandfather were wild-type. Thrombin generation assay showed delayed thrombin generation and reduced thrombin output in the proband and parents, indicating impaired coagulation function. Bioinformatics analysis revealed that Phe218 and Glu1887 are highly conserved. Both the p.Phe218Ser and p.Glu1887Val variants were predicted to be deleterious, potentially disrupting local protein conformation and stability, which may lead to functional defects.
CONCLUSION: The compound heterozygous variants p.Phe218Ser and p.Glu1887Val may cause a significant decrease in FⅤ:C and FⅤ:Ag by disrupting the structure and function of the FⅤ protein.
METHODS: A pedigree with hereditary FⅤ deficiency who visited Xijing Hospital on March 2, 2025, was selected as the study subject. Clinical data of the pedigree were collected using a retrospective analysis method. Venous blood samples were collected from the proband and family members to obtain platelet-poor plasma and genomic DNA. FⅤ activity (FⅤ:C) was measured by coagulation assay, and FⅤ antigen (FⅤ:Ag) was measured by ELISA for all members. Sanger sequencing was used to detect all exons and flanking sequences of the F5 gene in all members to screen for variations. Thrombin generation assay was performed to evaluate the overall coagulation potential of the proband and parents. Multiple online software tools, including ClustalX-2.1-win, PolyPhen-2, PROVEAN, I-Mutant v2.0, SIFT, Mutation Taster, and Swiss-Pdb Viewer, were used to assess the conservation of the variation sites and their impact on protein structure and function. The pathogenicity of the variation sites was evaluated according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines for the interpretation of sequence variants. This study was approved by the Medical Ethics Committee of Xijing Hospital (Ethics No.: KY20252367).
RESULTS: The proband's FⅤ:C level was only 1.3%, and the FⅤ:Ag level was only 2.4%. The proband was found to carry the c.653T>C (p.Phe218Ser) variant in exon 5 and the c.5660A>T (p.Glu1887Val) variant in exon 18 of the F5 gene. According to the ACMG guidelines, these two variants were classified as "Pathogenic" (PS4+PM2_Supporting+PP1+PP3+PP4+PP5) and "Likely Pathogenic" (PM1+PM2_Supporting+PM3+PP1+PP2+PP3+PP4), respectively. The proband's father and grandfather carried the p.Phe218Ser variant in heterozygous state, and the mother and maternal grandmother carried the p.Glu1887Val variant in heterozygous state. The paternal grandmother and maternal grandfather were wild-type. Thrombin generation assay showed delayed thrombin generation and reduced thrombin output in the proband and parents, indicating impaired coagulation function. Bioinformatics analysis revealed that Phe218 and Glu1887 are highly conserved. Both the p.Phe218Ser and p.Glu1887Val variants were predicted to be deleterious, potentially disrupting local protein conformation and stability, which may lead to functional defects.
CONCLUSION: The compound heterozygous variants p.Phe218Ser and p.Glu1887Val may cause a significant decrease in FⅤ:C and FⅤ:Ag by disrupting the structure and function of the FⅤ protein.