Identification and prenatal diagnosis of a novel likely pathogenic ANOS1 variant in a large Chinese Kallmann syndrome family

Abstract

Background This study aimed to systematically analyze a Chinese family with Kallmann syndrome (KS), evaluate the pathogenicity of a candidate variant through co-segregation analysis and bioinformatic predictions, and provide clinical intervention for the family. Methods This study included a Chinese family with KS comprising 40 members in total (37 living, 3 deceased). Whole-genome sequencing (WGS) was performed on the proband, followed by Sanger sequencing for co-segregation analysis with 22 family members. Multiple bioinformatics tools were used to assess evolutionary conservation, and AlphaFold3 modeling was employed to predict the potential impact on protein structure. Based on the genetic findings, prenatal diagnosis was subsequently offered to and performed for a female carrier in the family. Results A hemizygous ANOS1:c.1879T>C (p.Ser627Pro) variant was identified. Among the eight males with clinical features of KS in this family, five of whom underwent genetic testing, and all carried the variant. The variant fully co-segregated with KS among the genotyped individuals: all five tested males carried the variant (with their mothers confirmed as carriers), while five unaffected male relatives were wild-type. Bioinformatics analysis predicted that the variant site is evolutionarily conserved across species. AlphaFold3 modeling further suggested that the p. Ser627Pro substitution disrupts the original hydrogen bonding network, potentially leading to protein instability and function impairment. Based on these genetic findings, prenatal diagnosis was performed for a female carrier in the family, and the results showed that the fetus did not carry the variant. Conclusion Combining family co-segregation (PP1) and population frequency data (PM2), the ANOS1 c.1879T>C variant was classified as likely pathogenic, providing important information for genetic counseling. This study demonstrated that even in the absence of functional experiments, comprehensive family analysis can provide crucial clues for variant of uncertain significance (VUS) interpretation. This study also guided prenatal diagnosis, offering a referable strategy for the management of similar rare diseases.