The SHOX gene is located on both sex chromosomes, X and Y, within the pseudoautosomal region 1 (PAR1). Gross deletions at the SHOX locus lead to protein insufficiency and are manifested by growth disorders such as Leri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), and idiopathic short stature (ISS). In cases of the SHOX gene duplication, the phenotype may range from tall to short stature and LWD. This study describes a family with various SHOX locus alterations and diverse phenotypic manifestations. The proband inherited both deletion and duplication in the SHOX locus from her parents and shows typical features of LWD. The proband's father carries SHOX gene deletion and displays Madelung's deformity but normal height. The proband's mother has SHOX gene duplication without any abnormalities in phenotype. One of the proband's sons inherited deletion, while the other inherited duplication of the gene. Some family members also have the c.845_851dup variant in the CYP26C1 gene, previously described as a modifier of the SHOX gene. It is difficult to assess its effect. At present, it is not possible to predict the future phenotype of the proband's children due to the high phenotypic variability associated with SHOX locus alterations.

Haploinsufficiency of the short stature homeobox-containing (SHOX) gene leads to a phenotypic spectrum ranging from Leri-Weill dyschondrosteosis (LWD) to SHOX-deficient short stature. SHOX nullizygosity leads to Langer mesomelic dysplasia. Pathogenic variants can include whole or partial gene deletions or duplications, point mutations within the coding sequence, and deletions of upstream and downstream regulatory elements. Here we report two families: a non-consanguineous family with a deletion downstream of SHOX, in which the homozygous proband presented with isolated Madelung deformity, without LWD or short stature, as well as a 9-year-old girl with Madelung deformities, mesomelia, a dominant family history of Madelung deformity and a heterozygous deletion of the CNE9 region in the 3' downstream region of SHOX. These case reports provide additional information on the effects of 3' downstream deletions of SHOX, by demonstrating the limited phenotype associated with the recurrent 47.5 kb deletion in a homozygous state and the CNE9 deletion in a heterozygous state.

SHOX gene haploinsufficiency is a frequent cause of idiopathic short stature (ISS), while complete deficiency of this gene product causes the severe Langer mesomelic dysplasia (LMD). Mutations in the SHOX gene are among the well-known genetic factors responsible for short stature. This study investigated the genetic cause of LMD and ISS in two and five individuals in one family. Exome sequencing was conducted in the proband. Candidate variant was evaluated in silico for their impact. Sanger sequencing was employed for variant segregation analysis among available family members. A novel SHOX gene splice donor variant (c.486 + 2T > C) was found in homozygous form in individuals with LMD, and in heterozygous form in individuals with ISS. The mutation is likely to disrupt normal splicing as it affects a nearly invariantly conserved nucleotide at a canonical splice location. The variant was absent from gnomAD. The mutation segregated perfectly with ISS, LMD, and normal stature in this family. This study describes a new SHOX splice-site variant causing LMD and ISS, and demonstrates a strong genotype-phenotype correlation.

Short stature or shortening of the limbs can be the result of a variety of genetic variants. Achondroplasia is the most common cause of disproportionate short stature and is caused by pathogenic variants in the fibroblast growth factor receptor 3 gene (FGFR3). Short stature homeobox (SHOX) deficiency is caused by loss or defects of the SHOX gene or its enhancer region. It is associated with a spectrum of phenotypes ranging from normal stature to Léri-Weill dyschondrosteosis characterized by mesomelia and short stature or the more severe Langer mesomelic dysplasia in case of biallelic SHOX deficiency. Little is known about the interactions and phenotypic consequences of achondroplasia in combination with SHOX deficiency, as the literature on this subject is scarce, and no genetically confirmed clinical reports exist. We present the clinical findings in an infant girl with concurrent achondroplasia and SHOX deficiency. We conclude that the clinical findings in infancy are phenotypically compatible with achondroplasia, with no features of the SHOX deficiency evident. This may change over time, as some features of SHOX deficiency only become evident later in life.

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. 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. 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.