A novel pathogenic synonymous DHCR7 variant unveiled by aberrant splicing in Smith-Lemli-Opitz syndrome

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Abstract
Synonymous mutations, once regarded as silent, are increasingly recognized as pathogenic through disruption of mRNA splicing. Here, we report a prenatal case with classic features of Smith-Lemli-Opitz syndrome (SLOS), including increased nuchal translucency, enlarged kidneys, and fetal growth restriction. Whole-exome sequencing identified compound heterozygous DHCR7 variants: a previously reported missense variant, NM_001360.3:c.1220A > G (p.Asn407Ser), and a novel synonymous variant, NM_001360.3:c.963G > A (p.Gln321 =). Functional validation using minigene assays and patient-derived cDNA demonstrated that c.963G > A causes aberrant splicing, resulting in a premature termination codon and production of a truncated protein lacking the sterol-sensing domain, which contains multiple recurrent pathogenic missense sites. These findings establish the deleterious effect of this synonymous change, analogous to the well-characterized splice-site variant NM_001360.3:c.964 − 1G > C (historically referred to as IVS8 − 1G > C). In sum, this study provides the first definitive evidence that a synonymous DHCR7 variant can act as a likely pathogenic allele through splicing disruption. Moreover, it offers critical molecular insight and a refined framework for interpreting synonymous variants—particularly variants of uncertain significance—with important implications for clinical diagnosis, genetic counseling, and prenatal care.
Funding Information
  • Hubei Provincial Department of Science and Technology (2025AFC116)
  • Key Project of Scientific Research of the Education Department of Hubei Province (D20234303)
  • Scientific Research Project of Jingchu University of Technology (ZD202303)
  • Ningbo Science and Technology Project (2023Z178)

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