Recently, the structure of two genes encoding isoenzymes responsible for 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4-isomerase (3 beta HSD) activity in the human was elucidated. This activity is an essential step in the biosynthesis of all classes of steroid hormones. In the classic severe form of 3 beta HSD deficiency, patients present with adrenal insufficiency, various degrees of salt loss, and incomplete masculinization in males. Here we report the characterization of the molecular basis of congenital adrenal hyperplasia due to 3 beta HSD deficiency in a male pseudohermaphrodite born from consanguineous parents and having no clinical salt loss. To analyze the structure of the type I and II 3 beta HSD genes of the patient, DNA fragments, generated by polymerase chain reaction amplification of the four exons and the exon-intron boundaries of these genes, were directly sequenced. The patients carried a homozygous missense mutation converting Asn100 to Ser in exon 3 of his type II 3 beta HSD gene. His parents were heterozygous for the same point mutation. The absence of clinical salt loss associated with a male pseudohermaphroditism suggested that 3 beta HSD activity was impaired to different levels in the testes and adrenal. To elucidate whether this N100S missense mutation affected preferentially a steroidogenic pathway, enzymatic activity was analyzed by in vitro analysis of mutant recombinant enzyme generated by site-directed mutagenesis after its transient expression in COS-1 cells. Using homogenates from transfected cells, the N100S 3 beta HSD enzyme showed a Km value for pregnenolone of 25 +/- 3 mumol/L compared with 3.5 +/- 0.2 mumol/L for the normal human type II 3 beta HSD enzyme. Similar results were obtained using dehydroepiandrosterone as substrate. In addition to decreasing apparent affinity, the N100S mutation decreased the relative specific activity (Vmax), leading to a relative specificity (relative Vmax/Km) 2.7% and 11% that of normal type II 3 beta HSD using pregnenolone or dehydroepiandrosterone as substrate, respectively. Moreover, the mutant N100S protein had an apparent decreased affinity for NAD+, with a Km value of 650 +/- 66 mumol/L compared with 20 +/- 2 mumol/L for normal type II 3 beta HSD. Except for the hypothetical effect of local factors, these findings suggest that a very weak residual activity of the normal type II 3 beta HSD enzyme could prevent salt loss, but it was insufficient for normal male sex differentiation.(ABSTRACT TRUNCATED AT 400 WORDS)