Identification of a Duplication in the RP17 Locus in an Individual With Pathogenic CEP290 Variants: Implications for RP17 Variant Classification.

Compound heterozygous CEP290 variants cause pseudoexon inclusion and exon 36 skipping in patient-derived retinal cells, whereas the RP17 locus duplication disrupts neither chromatin looping nor GDPD1 expression.

Structural variants in the RP17 locus are associated with dominant retinitis pigmentosa; the authors assessed the pathogenicity of a novel duplication of this locus identified in a proband with cone dystrophy and biallelic CEP290 variants. The 324-kb duplication was present in the proband and in his clinically unaffected father, whereas the proband showed reduced visual acuity, foveal abnormalities, diminished cone density and absent light-adapted electroretinogram responses with preserved dark-adapted responses. In photoreceptor precursor cells and retinal organoids derived from patient pluripotent stem cells, the compound heterozygous CEP290 variants caused pseudoexon inclusion and exon 36 skipping, shown by RT-PCR and long-read cDNA sequencing, together with altered ciliation and impaired trafficking of L/M opsin and rhodopsin. In contrast to pathogenic RP17 structural variants, in silico modelling predicted no disruption of chromatin looping and GDPD1 expression was not upregulated in patient organoids, leading to classification of the duplication as likely benign.

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

This is an exemplary demonstration of what structural variant classification now requires: neither size nor location within a known locus is sufficient, a cellular model and a mechanistic readout are needed, here chromatin looping and GDPD1 expression. The unaffected carrier father was already a strong signal, but the retinal organoids settle the question, at a level of evidence out of reach for a diagnostic laboratory. The transferable lesson is to be wary of a structural variant found in a heavily studied locus in a patient whose recessive genotype already explains the whole phenotype.

Analysis by Dr Thibaut Benquey