Alu-mediated FANCD2 exonic deletion contributes to Fanconi anaemia

Fanconi anaemia (FA) is a rare genetic disease resulting from a pathogenic variant in the gene related to deoxyribonucleic acid repair. FANCD2-related FA is associated with a severe clinical phenotype compared with other FA genes. Despite advances in genetic diagnostics, complex structural variants and the neighbouring pseudogenes pose challenges for accurate molecular characterization of FA. Here, we report two Chinese siblings with classical FA manifestations. Chromosomal breakage analysis suggested an FA diagnosis, yet exome sequencing failed to identify biallelic pathogenic variants. To resolve cryptic genomic alterations, we performed whole-genome sequencing (WGS), ribonucleic acid sequencing (RNA-seq) and long-read sequencing (LRS). WGS identified a paternally inherited missense variant p.(Met1238Lys) in FANCD2, while LRS and RNA-seq further uncovered a maternally inherited 4 kb deletion in FANCD2, which arose from Alu-mediated homologous recombination. Our findings emphasize the diagnostic challenges of FANCD2-related FA, which can be resolved by LRS and RNA-seq.