Broad phenotypes in heterozygous NR5A1 46,XY patients with a disorder of sex development: an oligogenic origin?

Abstract

SF-1/NR5A1 is a transcriptional regulator of adrenal and gonadal development. NR5A1 disease-causing variants cause disorders of sex development (DSD) and adrenal failure, but most affected individuals show a broad DSD/reproductive phenotype only. Most NR5A1 variants show in vitro pathogenic effects, but not when tested in heterozygote state together with wild-type NR5A1 as usually seen in patients. Thus, the genotype-phenotype correlation for NR5A1 variants remains an unsolved question. We analyzed heterozygous 46,XY SF-1/NR5A1 patients by whole exome sequencing and used an algorithm for data analysis based on selected project-specific DSD- and SF-1-related genes. The variants detected were evaluated for their significance in literature, databases and checked in silico using webtools. We identified 19 potentially deleterious variants (one to seven per patient) in 18 genes in four 46,XY DSD subjects carrying heterozygous NR5A1 disease-causing variants. We constructed a scheme of all these hits within the landscape of currently known genes involved in male sex determination and differentiation. Our results suggest that the broad phenotype in these heterozygous NR5A1 46,XY DSD subjects may well be explained by an oligogenic mode of inheritance, in which multiple hits, individually non-deleterious, may contribute to a DSD phenotype unique to each heterozygous SF-1/NR5A1 individual.

Fig. 1

Algorithm used for data analysis after whole exome sequencing (WES) of patients harboring heterozygous NR5A1/SF-1 disease-causing variants. Number of variants and genes retrieved after each filtering step of the analysis are indicated. Short information on filtering steps is also provided. Capital letters A−H identify the analysis steps. pt patient, a annotation per variant: gene, transcript, protein, change (nucleotide, amino acid, codon (HGVS coding sequence name)), position (chromosome, coordinate, exonic/intronic), genotype (heterozygote, homozygote, hemizygote), type (snv, deletion, insertion), consequence (splice region (acceptor/donor), stop gain, stop loss, frameshift, nonsense, missense, synonymous, intronic), dbSNP id, read depth, filter pass, quality control, allele freq global minor (minor allele frequency (MAF)), frequency in EVS, Cosmic, ClinVar, etc., prediction of impact (PolyPhen-2, SIFT)

Fig. 2

Additional, likely disease-causing genetic variants identified in four 46,XY patients with disorder of sex development harboring heterozygous NR5A1/SF-1 disease-causing variants depicted with respect to the known pathway of male sex determination and differentiation. The scheme shows an overview of involved genes and their interrelationship. It emphasizes on SF-1, which seems to play an important role throughout all developmental processes (indicated by a thick line). Genetic variants identified by whole exome sequencing in the studied patients are given in specific colors. In violet: candidate gene in patient 1; in blue: candidate genes in patient 2; in green: candidate genes in patient 3; in red: candidate genes in patient 4; in gray: known genes involved in sexual development. Interrogation mark (?): function/timing/location is not clear; arrows: regulation/co-activation; dotted arrows: gene with binding regions for SF-1, SRY, and/or SOX9; lines: interaction/partnership; dashed lines: related genes, but thus far unclear how exactly; thick dashed arrows: hormone production