Identification of the novel COL5A1 c.3369_3431dup, p.(Glu1124_Gly1144dup) variant in a patient with incomplete classical Ehlers–Danlos syndrome: The importance of phenotype-guided genetic testing

Background: Classical Ehlers–Danlos syndrome (cEDS) is a connective tissue disorder mainly caused by heterozygous COL5A1 or COL5A2 variants encoding type V collagen and rarely by the p.(Arg312Cys) missense substitution in COL1A1 encoding type I collagen. The current EDS nosology specifies that minimal suggestive criteria are marked skin hyperextensibility plus atrophic scarring together with either generalized joint hypermobility or at least three minor criteria comprising additional cutaneous and articular signs. To reach a final diagnosis, molecular testing is required. Herein, we report on a 3-year-old female who came to our attention with an inconclusive next generation sequencing (NGS) panel comprising all cEDS-associated genes. Methods: Despite the patient did not formally fulfill the nosological criteria because the skin was only slightly hyperextensible, we made a cEDS diagnosis, mainly for the presence of typical atrophic scars. We investigated COL5A1 intragenic deletions/duplications by Multiplex Ligation-dependent Probe Amplification (MLPA), excluded the recessive classical-like EDS type 2 by AEBP1 Sanger analysis, and retested COL5A1 with the Sanger method. Results: Molecular analyses revealed the novel COL5A1 c.3369_3431dup p.(Glu1124_Gly1144dup) intermediate-sized duplication with a predicted dominant negative effect that was missed both by NGS and MLPA. Conclusions: This report highlights that some cEDS patients might not display overt skin hyperextensibility and the importance of clinical expertise to make such a diagnosis in patients with an incomplete presentation. Our results also exemplify that NGS is not a fool-proof technology and that Sanger sequencing achieves the diagnostic goal when there is a sufficiently clear phenotypic indication.