RARE DOSAGE ABNORMALITIES - COPY NUMBER VARIATIONS FLANKING THE SHOX GENE

Abstract

Background: Molecular defects in the SHOX gene including deletions, duplications or pathogenic point mutations are responsible for well-known pathologies involving short stature as a clinical manifestation: Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Turner syndrome or idiopathic short stature. Duplications flanking the SHOX gene (upstream or downstream of the intact SHOX gene involving conserved non-coding cis-regulatory DNA elements - CNEs) have been described but their clinical involvement is still difficult to understand.

Results: We describe two cases with short stature and normal GH-IGF1 status. Multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (arrayCGH) identified in both cases heterozygous duplications involving downstream regions of SHOX gene, within CNEs (CNE8, CNE9 and CNE4, CNE5, CNE6, ECR1, CNE8, CNE9 and surrounding areas, respectively). One of the cases showed a maternally inherited duplication. Although every case has several particularities, we consider that duplications in these non-coding regions of SHOX gene may explain the short stature phenotype.

Conclusion: To our knowledge, these are the first Romanian-reported cases of ISS with a large duplication of downstream SHOX enhancers CNEs region. The spectrum of phenotypic consequences and the exact mechanism of the presumed clinical expression of these genetic alterations still needs to be evaluated and described.

Keywords: CNE; SHOX; deletion; duplication; idiopathic short stature; regulatory element.

Figure 1

Pedigree of the second patient. The proband is indicated by arrow. -/+ indicate the wild type and the variant alleles.

Figure 2

Genomic context of highly conserved non-coding DNA elements (CNEs) in SHOX upstream and downstream regions and indication of lengths and positioning of duplications in our patients. The upper scale illustrates the distance from the Xp/Yp telomere (hg19/GRCh37) (adapted from https://www.ncbi.nlm.nih.gov/genome/gdv/browser/gene/?id=108410392).