Long-read sequencing reveals a hidden Alu-mediated splice defect in CPLANE1, causing orofaciodigital syndrome type VI.

CPLANE1

Two biallelic splice-site variants in CPLANE1, including an Alu element insertion close to an exon-intron boundary, each causing exon skipping and reduced mRNA levels

Orofaciodigital syndrome type VI is a recessive ciliopathy combining excessive polydactyly, molar tooth sign, cleft lip and developmental delay, caused by pathogenic variants in CPLANE1. The authors describe a patient who remained genetically unexplained after routine testing including short-read whole genome sequencing. Long-read sequencing revealed two biallelic splice-site variants in CPLANE1: the c.8633-4_8633-3del deletion and an Alu element insertion close to an exon-intron boundary. Transcript analysis showed that each variant independently resulted in exon skipping, and quantitative expression studies revealed reduced total CPLANE1 mRNA in patient-derived fibroblasts, allowing reclassification of c.8633-4_8633-3del from a variant of uncertain significance to likely pathogenic.

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

The message is about how short-read sequencing fails: a mobile element insertion close to a splice junction is not called, and it was precisely the allele needed to close a recessive case with an otherwise typical phenotype. In practice, faced with a convincing ciliopathy and a single variant identified, the next step is not to sequence more broadly but to go after the second allele — long-read or transcript analysis. A single case obviously does not quantify the diagnostic gain of this strategy.

Analysis by Dr Thibaut Benquey