Description and phenotype of a novel C5 gene mutation and a novel combination: family report and literature review

Abstract

Background: Patients with C5 mutations are more susceptibility to Gram-negative bacterial infections, particularly Neisseria species.

Objective: To describe the phenotype and clinical features of a family carrying two C5 gene variants, including one novel mutation, and to assess their functional and genetic significance.

Methods: We analyzed the clinical and genetic characteristics of a family with two compounds heterozygous C5 variants. Clinical features were assessed across affected and unaffected family members, and results were correlated with genetic and functional assays.

Results: Genetic testing revealed compound heterozygous variants in the C5 gene: c.713T>C (p.Ile238Thr) and c.1949G>T (p.Gly650Val). The p.Ile238Thr variant, located in exon 7, results in a substitution of isoleucine with threonine. The p.Gly650Val variant, located in exon 15, replaces glycine with valine. Sanger sequencing confirmed the variants were in trans (on separate alleles). The mother carried the same two variants as the patient. Two siblings carried one variant each (Gly650Val and Ile238Thr, respectively), and one sibling was homozygous for the Ile238Thr variant.Clinically, the patient, the mother, and the homozygous sibling had very low serum C5 protein and CH50 levels, correlating with increased susceptibility to Neisseria infections. Siblings carrying only one variant had normal complement function. In silico analysis and molecular modeling indicate that both amino acid substitutions (Ile238Thr and Gly650Val) may disrupt C5 protein structure. The Ile238Thr change introduces a polar residue in place of a hydrophobic one, disrupting the hydrophobic core and opening a loop between beta-sheets. The Gly650Val change substitutes a small residue with a larger one, causing steric hindrance that necessitates structural rearrangements, including shifts in a loop, alpha-helix, and beta-sheet.

Conclusion: We describe a novel C5 variant (Gly650Val) a previously reported variant (Ile238Thr) in unique genotypic combinations (compound heterozygous and homozygous) associated with marked C5 deficiency and increased susceptibility to invasive Neisseria infections. Our findings underscore the importance of combining genetic, functional, and structural data for variant interpretation in complement deficiencies.

Keywords: C5 deficiency; C5 mutation; complement deficiency; novel mutation; phenotype and genotype.

Figure 1

Schematic and structural representation of the human complement component 5 (C5). (A) Representation of the genomic structure of the human C5 gene, highlighting exons 7 and 15 in red, which contain the variants identified in this study. Other relevant C5 variants previously reported in nearby exons were also included (–6). (B) Schematic overview of the C5 protein structure, showing the α- and β-chains where the MG1–MG6 domains are shown in green, the C5a domain in purple, and the MG6–MG8 and C345C domains in blue. The cleavage site between C5a and C5b is marked by an arrow, along with selected key residues. There are also indicated domains where the reported variations are ubicated. (C) Ribbon diagram of the C5 protein structure generated using PyMOL and PDB entry 3CU7 highlighting the position of both C5 variants identified in this study. Domains are colored as in (B).

Figure 2

Sequencing outcomes of the family under study. (A) Pedigree of the family analyzed in this study. Each figure subdivision represents a C5 allele. The left side of each symbol indicates the presence of the p.Ile238Thr variant, while the right side indicates the p.Gly650Val variant. Shading denotes whether the variant is present in heterozygous or homozygous form, resulting in different allele combinations. (B) Sanger results for the c.713T>C (p.Ile238Thr) variant. (C) Sanger findings for the c.1949G>T (p.Gly650Val) variant. Complete results from Sanger Sequencing can be found in Supplementary Figure 1 .

Figure 3

Three-dimensional modeling of residue 238 using PyMOL. (A) The native residue, isoleucine (green), and its surrounding environment (pink) are shown on the left. The right panel shows the substitution with threonine (white). (B) Comparison of AlphaFold-predicted structure (green) with two MODELLER-generated mutants (magenta and pink). (C) Comparison of PDB 3CU7 structure (yellow) with the same two MODELLER-generated mutants (magenta and pink).

Figure 4

Three-dimensional modeling of residue 650 using PyMOL. (A) Left: native glycine residue (green) and its surrounding environment (pink). Right: valine substitution (white), showing potential steric hindrance. (B) Comparison of the AlphaFold prediction (green) with two MODELLER-generated mutants (purple and magenta). (C) Comparison of PDB 3CU7 structure (yellow) with two MODELLER-generated mutants (purple and magenta).