Predicted Benign and Synonymous Variants in CYP11A1 Cause Primary Adrenal Insufficiency Through Missplicing

Abstract

Primary adrenal insufficiency (PAI) is a potentially life-threatening condition that can present with nonspecific features and can be difficult to diagnose. We undertook next generation sequencing in a cohort of children and young adults with PAI of unknown etiology from around the world and identified a heterozygous missense variant (rs6161, c.940G>A, p.Glu314Lys) in CYP11A1 in 19 individuals from 13 different families (allele frequency within undiagnosed PAI in our cohort, 0.102 vs 0.0026 in the Genome Aggregation Database; P < 0.0001). Seventeen individuals harbored a second heterozygous rare disruptive variant in CYP11A1 and two had very rare synonymous changes in trans (c.990G>A, Thr330 = ; c.1173C>T, Ser391 =). Although p.Glu314Lys is predicted to be benign and showed no loss-of-function in an Escherichia coli assay system, in silico and in vitro studies revealed that the rs6161/c.940G>A variant, plus the c.990G>A and c.1173C>T changes, affected splicing and that p.Glu314Lys produces a nonfunctional protein in mammalian cells. Taken together, these findings show that compound heterozygosity involving a relatively common and predicted “benign” variant in CYP11A1 is a major contributor to PAI of unknown etiology, especially in European populations. These observations have implications for personalized management and demonstrate how variants that might be overlooked in standard analyses can be pathogenic when combined with other very rare disruptive changes.

Long-term outcome of partial P450 side-chain cleavage enzyme deficiency in three brothers: the importance of early diagnosis

“…Consistent with previous reports, pubertal development (although delayed in the two older brothers) was normal in the sibship, with normal testicular volumes and Leydig cell function (19,24,25,26).…”

“…The partial nature of P450scc deficiency in this family is consistent with most of the published cases with similar genetic findings (19,24,25,26).…”

“…Next-generation sequencing studies were performed as part of an initiative to assess the prevalence of CYP11A1 deficiency in PAI in 2016. In this study, HaloPlex targeted Gene Panel analysis was performed as described (26).…”

“…Recently, Maharaj and colleagues reported that the missense mutation rs6161, c.940G>A, p.Glu314Lys, previously predicted to be a benign variant, results in PAI in the context of compound heterozygosity when combined with variations harboring disruptive changes (26). In all, 28 cases of P450scc deficiency related to the presence of the rs6161, c.940G>A, p.Glu314Lys variant have been described, 19 by Maharaj et al (26) and 9 from other centres (19,24,25).…”

Primary adrenal insufficiency: New genetic causes and their long‐term consequences

“…64 Although the c.940G>A variant is predicted to cause a benign protein change (p.E314K), detailed molecular studies have shown that it generates a novel splice site so that missplicing occurs. 64,65 This variant is carried by approximately 1:140 people of European descent, but is likely to cause adrenal insufficiency only when inherited with a very rare disruptive change on the other allele. Partial CYP11A1 insufficiency can also occur in other populations, such as due to the p.R451W variant common in central Turkey.…”