Clinical and genetic characteristics of a large international cohort of individuals with rare NR5A1/SF-1 variants of sex development

Abstract

Background: Steroidogenic factor 1 (SF-1/NR5A1) is essential for human sex development. Heterozygous NR5A1/SF-1 variants manifest with a broad range of phenotypes of differences of sex development (DSD), which remain unexplained.

Methods: We conducted a retrospective analysis on the so far largest international cohort of individuals with NR5A1/SF-1 variants, identified through the I-DSD registry and a research network.

Findings: Among 197 individuals with NR5A1/SF-1 variants, we confirmed diverse phenotypes. Over 70% of 46, XY individuals had a severe DSD phenotype, while 90% of 46, XX individuals had female-typical sex development. Close to 100 different novel and known NR5A1/SF-1 variants were identified, without specific hot spots. Additionally, likely disease-associated variants in other genes were reported in 32 individuals out of 128 tested (25%), particularly in those with severe or opposite sex DSD phenotypes. Interestingly, 48% of these variants were found in known DSD or SF-1 interacting genes, but no frequent gene-clusters were identified. Sex registration at birth varied, with <10% undergoing reassignment. Gonadectomy was performed in 30% and genital surgery in 58%. Associated organ anomalies were observed in 27% of individuals with a DSD, mainly concerning the spleen. Intrafamilial phenotypes also varied considerably.

Interpretation: The observed phenotypic variability in individuals and families with NR5A1/SF-1 variants is large and remains unpredictable. It may often not be solely explained by the monogenic pathogenicity of the NR5A1/SF-1 variants but is likely influenced by additional genetic variants and as-yet-unknown factors.

Funding: Swiss National Science Foundation (320030-197725) and Boveri Foundation Zürich, Switzerland.

Keywords: Broad phenotype; Differences of sex development (DSD); Genetics of sex determination and differentiation; Intersex; Steroidogenic factor 1 (SF-1/NR5A1).

Fig. 1

Overview of the participants and summary of the NR5A1/SF-1 variants in the international SF1next study cohort. (a) Number of individuals collected from each country comprising the SF1next study cohort are shown (n = 197). (b and c) Identified variants in the NR5A1 gene are shown with respect to the gene and protein sequence. (b) Location of four intronic variants and one whole gene deletion of NR5A1/SF-1 (NC_000009.11). (c) Location of 87 NR5A1/SF-1 variants identified in the SF1next cohort, shown at their protein level (NM_004959.5). Novel variants are shown in bold, while previously reported variants are shown in normal font. The SF-1 protein comprises the DNA-binding domain, which contains two zinc fingers (Zn1 and Zn2), a FTZ-F1 box, the accessory hinge region, and the ligand-binding domain. It harbors two activation functional domains, AF-1 and AF-2. NR5A1, nuclear receptor subfamily 5 group A member 1; UTR, untranslated region.

Fig. 2

Characterization of NR5A1/SF-1 variants identified in the SF1next study cohort. (a) Genotype-phenotype correlation. Each dot represents one individual (n = 197) with the corresponding DSD phenotype of the external genitalia and karyotype, stratified by karyotype and type of data. Filled dots show individuals who required medical care while white filled dots show individuals who came to medical attention because of the genetic workup of their NR5A1/SF-1 positive relatives (i.e., family members with basic data who did not require medical care because of DSD). NR5A1/SF-1 variants affecting the same amino acid residue/intronic region are highlighted in black, purple or blue colour, while others are shown in light grey. (b) Karyotype and DSD phenotype of individuals in the cohort. (c) Summary of the pathogenicity of the 93 different NR5A1/SF-1 variants according to ACMG classification, stratified by DSD phenotype of the identified individuals in the cohort. P, pathogenic, LP, likely pathogenic, VUS, variant of unknown significance, LB, likely benign, B, benign.

Fig. 3

Associated organ anomalies found in individuals with a DSD and NR5A1/SF-1 variants (n = 116). (a) Heatmap depicts frequency of organ anomalies found with specific NR5A1/SF-1 variants. Sufficient information on organ anomalies was available in 116 out of 131 individuals with a DSD. NR5A1/SF-1 variants affecting the same amino acid residue/intronic region are highlighted in blue or purple colour, while others are shown in light grey. The colour of a single cell provides the information on how many individuals are affected (light red to dark red (≥1)) or unaffected (green (≤−1)) by the specific organ anomaly (see value scale). Organ systems with reported anomalies are shown in bold. Number of individuals with reported anomaly divided by the number of individuals with sufficient information per organ system is shown on the right side of the heatmap. Individuals with organ anomalies and without DSD (n = 8) are not reported in the figure; in those, anomalies were found in the blood system and spleen (3/8), metabolism and homeostasis (2/8), endocrine system (1/8), head and neck (1/8), skeletal system (1/8), musculature (1/8), CNS (1/8), cardiovascular system (1/8), connective tissue (1/8), or abdomen (1/8). For white coloured cells no data were available. (b and c) Range of anomalies reported in each organ system according to karyotype (b) or (c) DSD phenotype (n = 38). CNS, Central nervous system; PNS, Peripheral nervous system.