Biallelic CYB5A disruptions in 46, XY DSD: Novel missense and deep intronic variants.

CYB5A

Loss of cytochrome b5, a cofactor of CYP17A1 17,20-lyase activity; deep intronic CYB5A deletion activating cryptic splice sites and pseudo-exon inclusion

The authors report two Vietnamese 46,XY siblings with a female phenotype and low testosterone and estradiol, in whom whole genome sequencing (WGS) identified two novel compound heterozygous CYB5A variants. The first is a paternally inherited missense variant (p.Val34Glu), the second a maternally inherited deep intronic deletion (c.129+862_129+863del) predicted by SpliceAI to create cryptic splice sites. A minigene assay in HEK293T cells confirmed activation of these sites and inclusion of a pseudo-exon between exons 1 and 2, introducing a premature stop codon with predicted nonsense-mediated decay. Both variants were classified as likely pathogenic under ACMG/AMP.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

A textbook case of what genome sequencing adds: the deep intronic deletion was not accessible without intronic coverage, and the combination of SpliceAI and a minigene assay makes it interpretable. The data are limited to one family and a minigene assay, with no patient RNA analysis mentioned. In a suggestive 46,XY DSD with a single CYB5A variant, searching for a second intronic allele is justified.

Analysis by Dr Thibaut Benquey