A multimodal genetic testing approach to a diagnosis of Roberts-SC phocomelia syndrome, an ESCO2 spectrum disorder

Abstract Diagnosis of a genetic syndrome has traditionally relied upon the identification of characteristic phenotypic findings, followed by targeted laboratory testing. Shared clinical manifestations between genetically distinct syndromes and variable expressivity of findings within a single syndrome can complicate the diagnosis. Multiple testing modalities may be necessary, even when the putative gene(s) is known. We describe the multi-pronged genetic testing applied to a patient with a suspected diagnosis of Roberts- SC phocomelia syndrome (RBS). RBS is an autosomal recessive developmental disorder (OMIM 268300) caused by pathogenic variants in the “establishment of sister chromatid cohesion N-acetyltransferase” (ESCO2 ) gene mapped to chromosome 8p21.1. The ESCO2 enzyme product is a conserved protein with acetyltransferase activity required for formation of the cohesin complex, which, among other activities, maintains sister chromatid association during S-phase of the cell cycle. Because of the defective cohesin complex, RBS joins other syndromes referred to as cohesinopathies. The patient, a newborn male, was small for gestational age, with hypertelorism, cleft lip and palate, shortened forearms, absence of the radius and thumbs, and bilateral clubbed feet. All of these findings are established characteristics of RBS. Targeted Next Generation Sequencing revealed a single variant in exon 10 of ESCO2 (c.1654C>T, p.Arg552*) predicted to result in a loss of function. Chromosomal microarray was also performed and showed an estimated 15 Mb region of homozygosity (ROH) extending from 8p11.21 to 8p21.2, which spans ESCO2. The finding of this ROH supported the interpretation of homozygosity for the variant, as did a family history of consanguinity. Additional cytogenetic analysis documented premature sister chromatid separation and repulsion of heterochromatin chromosomal regions characteristic of RBS. These chromosomal findings served as a functional assay supporting pathogenicity of the ESCO2 variant. Interestingly, the only report of an identical variant within exon 10 of ESCO2 was described for two brothers diagnosed with Juberg-Hayward syndrome. Juberg-Hayward was considered allelic to, but a distinct entity from RBS. In contrast, our findings support the conclusion that RBS and Juberg-Hayward are not distinct syndromes, but rather represent variability within an ESCO2 syndrome spectrum. Such unification of diagnoses based on genomic findings has influenc