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Disorders/differences of sex development (DSDs) are defined as broad, heterogenous groups of congenital conditions characterized by atypical development of genetic, gonadal, or phenotypic sex accompanied by abnormal development of internal and/or external genitalia. <i>NR5A1</i> gene mutation is one of the principal genetic alterations implicated in causing DSD. This review outlines the role of <i>NR5A1</i> gene during the process of gonadal development in humans, provides an overview of the molecular and functional characteristics of <i>NR5A1</i> gene, and discusses potential clinical phenotypes and additional organ diseases due to <i>NR5A1</i> mutations. <i>NR5A1</i> mutations were analyzed in patients with 46,XY DSD and 46,XX DSD both during the neonatal and pubertal periods. Loss of function of the <i>NR5A1</i> gene causes several different phenotypes, including some associated with disease in additional organs. Clinical phenotypes may vary, even among patients carrying the same <i>NR5A1</i> variant, indicating that there is no specific genotype–phenotype correlation. Genetic tests are crucial diagnostic tools that should be used early in the diagnostic pathway, as early as the neonatal period, when gonadal dysgenesis is the main manifestation of <i>NR5A1</i> mutation. <i>NR5A1</i> gene mutations could be mainly associated with amenorrhea, ovarian failure, hypogonadism, and infertility during puberty. Fertility preservation techniques should be considered as early as possible.