Journal Article

Pathogenic cryptic variants detectable through exome data reanalysis significantly increase the diagnostic yield in Joubert syndrome

Battini, Roberta, D’Arrigo, Stefano, Taccagni, Cecilia Maria, Borgatti, Renato, Manti, Filippo, Zanni, Ginevra, Caputi, Caterina, D’Abrusco, Fulvio, Garau, Jessica, Giorgio, Elisa, Sirchia, Fabio, Cattaneo, Luca, Valente, Enza Maria, Signorini, Sabrina, Petković Ramadža, Danijela, De Laurentiis, Arianna, Graziano, Claudio, Romaniello, Romina, Bertini, Enrico, Morelli, Federica, Gana, Simone, Boltshauser, Eugen, Boggioni, Monica, Lemke, Johannes R., Serpieri, Valentina, Leuzzi, Vincenzo

2025

Overview

Joubert syndrome (JS) is a genetically heterogeneous neurodevelopmental ciliopathy. Despite exome sequencing (ES), several patients remain undiagnosed. This study aims to increase the diagnostic yield by uncovering cryptic variants through targeted ES reanalysis. We first focused on 26 patients in whom ES only disclosed heterozygous pathogenic coding variants in a JS gene. We reanalyzed raw ES data searching for copy number variants (CNVs) and intronic variants affecting splicing. We validated CNVs through real-time PCR or chromosomal microarray, and splicing variants through RT-PCR or minigenes. Cryptic variants were then searched in additional 44 ES-negative JS individuals. We identified cryptic “second hits” in 14 of 26 children (54%) and biallelic cryptic variants in 3 of 44 (7%), reaching a definite diagnosis in 17 of 70 (overall diagnostic gain 24%). We show that CNVs and intronic splicing variants are a common mutational mechanism in JS; more importantly, we demonstrate that a significant proportion of such variants can be disclosed simply through a focused reanalysis of available ES data, with a significantly increase of the diagnostic yield especially among patients previously found to carry heterozygous coding variants in the KIAA0586 , CC2D2A and CPLANE1 genes.

• Publisher: Springer International Publishing,Nature Publishing Group
• Subject: 631/208/2489/144 / 692/308/2056 / Abnormalities, Multiple - diagnosis / Abnormalities, Multiple - genetics / Adolescent / Behavioral sciences / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Brain / Cell Cycle Proteins / Cerebellum - abnormalities / Cerebellum - pathology / Child / Child, Preschool / Congenital defects / Copy number / Cytogenetics / Cytoplasmic Dyneins - genetics / Cytoskeletal Proteins / DNA Copy Number Variations / DNA microarrays / Exome - genetics / Exome Sequencing / Eye Abnormalities - diagnosis / Eye Abnormalities - genetics / Female / Gene Expression / Genes / Genetic abnormalities / Genetic testing / Genetics / Heterozygote / Human Genetics / Humans / Infant / Kidney Diseases, Cystic - diagnosis / Kidney Diseases, Cystic - genetics / Male / Membrane Proteins / Mutation / Neurodevelopmental disorders / Neurology / Psychiatry / Retina - abnormalities / Retina - pathology / RNA Splicing / Splicing / Whole genome sequencing