Journal Article

A hypomorphic SRD5A2 haplotype with a potential founder effect: composed of common variants in individuals with 5α-reductase type 2 deficiency from South China

Gui, Chunrong, Shi, Meizhen, Yuan, Dejian, Zhou, Xu, Ma, Yunting, Zhao, Sen, Fan, Xin, Xie, Bobo, Tao, Qiuxing, Lei, Xiaoyun, Chen, Shaoke, Wei, Xianda, Gui, Baoheng, Su, Yuna, Cheng, Zifeng

2026

Overview

Background Disorders of sex development (DSDs) exhibit high genetic and phenotypic heterogeneity, and genotype–phenotype correlations are not fully understood. 5α-Reductase type 2 (5α-RD2) deficiency, a common form of DSD, is caused by SRD5A2 inactivation. This study investigated the role of SRD5A2 haplotypes in DSD, focusing on their corresponding phenotypes, structural changes and impacts on enzyme activity. Methods This study enrolled 216 individuals with DSD who underwent genetic analysis and 2,794 controls. Linkage disequilibrium analysis was performed in individuals with 5α-RD2 deficiency to identify SRD5A2 haplotypes, and haplotype frequencies were analysed across cohorts. The clinical manifestations of individuals with different SRD5A2 haplotypes were characterized. Structural predictions were employed to investigate the impacts of haplotypes on the 5α-RD2 structure and interactions with ligands. Functionally, kinetic assays were conducted to validate the effects of different haplotypes on enzyme activity. Results A SRD5A2 haplotype composed of c.265C > G and c.680G > A (Hap3: G-A) was identified, and the haplotype frequency was 64.71% in individuals with 5α-RD2 deficiency, 2.59% and 1.22% in non-5α-RD2 deficiency DSD cases without or with known DSD-related gene variants, respectively, and 1.57% in in-house controls. Globally, Hap3: G-A was enriched in southern Chinese individuals and showed high population differentiation, indicating a potential founder effect of the haplotype. The majority of homozygotes of Hap3: G-A presented microphallus, and nearly half of them manifested isolated microphallus. Structurally, Hap3: G-A was predicted to result in an increase in the solvent-accessible surface area (10.72 Å 2 ), a redistribution of hydrogen bonds within 5α-RD2, and a loss of key hydrogen bonds with NADPH. Functionally, kinetic assays showed that the catalytic efficiency of the enzyme encoded by Hap3: G-A was between that of Hap1: G-G and that of Hap2: C-A. Conclusions Hap3: G-A, which is prevalent in individuals with 5α-RD2 deficiency, suggests a potential founder effect. Structurally, compared with other haplotypes, Hap3: G-A seems to have a combined effect on the structure and interaction of 5α-RD2, rather than have merely additive effects of its constituent variants. Functionally, kinetic assays suggested a hypomorphic effect of Hap3: G-A. These findings provide valuable insights for understanding genotype–phenotype correlations, genetic counselling, early intervention and clinical management of individuals with 5α-RD2 deficiency or even other DSDs. Highlights On the basis of 216 DSD individuals and 2,794 controls, a novel SRD5A2 haplotype (Hap3: G-A), which is composed of common variants and is especially prevalent in DSD patients with 5α-RD2 deficiency, was identified, indicating the potential founder effect of Hap3: G-A. The majority of 5α-RD2 deficiency individuals with homozygous Hap3: G-A presented microphallus. Three-dimensional structure and model construction predicted that Hap3: G-A resulted in an increase in the solvent-accessible surface area, redistribution of hydrogen bonds within 5α-RD2, and loss of key hydrogen bonds with NADPH. Functionally, kinetic assays showed that the catalytic efficiency of the enzyme encoded by Hap3: G-A was between those of Hap1: G-G and Hap2: C-A, suggesting a hypomorphic effect of this haplotype. Plain Language Summary Individuals with disorders of sex development (DSDs) present variable genotypes and phenotypes, and the genotype–phenotype correlation remains poorly understood. 5α-Reductase type 2 (5α-RD2) deficiency, a common form of DSD, is caused by SRD5A2 inactivation. In this study, genetic testing and analysis were performed in 216 individuals with DSD and 2,794 non-DSD controls. A novel SRD5A2 haplotype (Hap3: G-A) was identified, and the haplotype frequency was 64.71% in individuals with 5α-RD2 deficiency, 2.59% and 1.22% in non-5α-RD2 deficiency DSD cases without or with known DSD-related gene variants, respectively, and 1.57% in in-house controls. Globally, Hap3: G-A was enriched in southern Chinese individuals and showed high population differentiation, indicating a potential founder effect of the haplotype. Analyzing the phenotype spectrum of individuals with 5α-RD2 deficiency, we found that the majority of homozygotes of Hap3: G-A presented microphallus, and nearly half of them manifested isolated microphallus. Structurally, Hap3: G-A was predicted to result in an increase in the solvent-accessible surface area, the redistribution of hydrogen bonds within 5α-RD2, and the loss of key hydrogen bonds with NADPH. Compared with other haplotypes, Hap3: G-A seemed to have a combined effect on the structure and interaction of 5α-RD2, rather than simply additive effects of its constituent variants. Functionally, kinetic assays showed that the catalytic efficiency of the enzyme encoded by Hap3: G-A was between that of Hap1: G-G and that of Hap2: C-A, suggesting a hypomorphic effect of this haplotype. These findings provide valuable insights for understanding genotype–phenotype correlations, genetic counselling, early intervention and clinical management of individuals with 5α-RD2 deficiency or even other DSDs.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: 3-Oxo-5-alpha-Steroid 4-Dehydrogenase - chemistry / 3-Oxo-5-alpha-Steroid 4-Dehydrogenase - deficiency / 3-Oxo-5-alpha-Steroid 4-Dehydrogenase - genetics / 3-Oxo-5-alpha-Steroid 4-Dehydrogenase - metabolism / 5α-Reductase type 2 deficiency / Biomedical and Life Sciences / Biomedicine / China / Clitoris / Cryptorchidism / Disorders of sex development / Endocrinology / Enzymatic activity / Enzymes / Families & family life / Female / Females / Founder Effect / Genetic analysis / Genetic counseling / Genomes / Genotype & phenotype / Genotypes / Haplotypes / Homozygotes / Human Physiology / Humans / Hydrogen bonding / Hypomorphic haplotype / Hypospadias - genetics / Ligands / Linkage analysis / Linkage Disequilibrium / Male / Membrane Proteins - chemistry / Membrane Proteins - deficiency / Membrane Proteins - genetics / Membrane Proteins - metabolism / Pathogenesis / Pediatrics / Phenotypes / Population differentiation / Software / Solvents / South China / SRD5A2 / Steroid 5α-reductase / Surface area / Testosterone