Chromosomal translocation resolves a diagnostic odyssey for familial Ruvalcaba syndrome.

In 1971, Ruvalcaba and colleagues reported a new syndrome in two brothers with severe intellectual disability, dysmorphic features, osseous dysplasia, and overlapping features in two intellectually disabled female maternal first cousins. No genetic cause was identified. We report on updated genomic studies and clinical follow-up in this family, including one of the original probands and their niece, whose own lifelong diagnostic odyssey had been unresolved for over four decades. Trio exome sequencing and copy number variant analysis in an original proband revealed an unbalanced chromosome translocation with a 3.18 Mb terminal deletion of 2q37.3qter and 6.54 Mb terminal duplication of 5q35.2qter. His unaffected sister had no evidence of a chromosomal imbalance, and her affected daughter has the reciprocal terminal duplication at 2q37.3qter and terminal deletion at 5q35.2qter. We used optical genome mapping and Hi-C analysis to further characterize the t(2;5)(q37.3;q35.2) translocation as well as RNA-seq analysis and genome-wide methylation profiling to elucidate the functional consequences of the genomic alterations. Candidate genes for the observed phenotypes include HDAC4, KIF1A, D2HGDH, FLT4, HNRNPH1, and NSD1.