SHOX-Related Disorders

  • Most comprehensive test for molecular confirmation of SHOX-related disorders
  • Deletion/duplication analysis is performed first; sequencing will then be performed based on clinical information/suspected diagnosis provided and result of deletion/duplication analysis
Related Tests

Useful if there is suspicion for a large, contiguous gene deletion/duplication that includes the SHOX gene

May be helpful to determine mechanism of SHOX deletions (eg, translocations, Turner syndrome)

  • Useful for confirming a diagnosis when a pathogenic sequence variant has been identified in family member
  • A copy of the family member’s lab report documenting the familial variant is REQUIRED
  • Useful for confirming a diagnosis when a pathogenic deletion/duplication variant has been identified in family member
  • A copy of the family member’s lab report documenting the familial variant is REQUIRED

Pathogenic variants in the SHOX gene result in a spectrum of disorders due to haploinsufficiency of the SHOX gene/protein. Clinical features often include short stature, mesomelia (shortening of the lower portion of arm and leg), and abnormal alignment of the radius, ulna, and carpal bones at wrist (Madelung deformity). Variable expressivity results in some individuals affected only with isolated short stature (ISS), while others have short stature and additional findings resulting in syndrome disorders (eg, Leri-Weill dyschondrosteosis [LWD] or Langer mesomelic dysplasia [LMD]).

Disease Overview


At least 1/1,000 for a SHOX deficiency-related disorder

  • Isolated/idiopathic short stature (ISS); MIM 300582
    • Stature (below the third percentile)
    • Usually no mesomelia or Madelung deformity
    • 6-15% have one pathogenic SHOX variant
    • Highly variable presentation even within the same family
  • Leri-Weill dyschondrosteosis (LWD); MIM 127300
    • Symptoms: triad of short stature in early childhood, mesomelia, and Madelung deformity
    • Madelung deformity typically develops in mid-late childhood; more common and severe in females
    • Other features may include high-arched palate, bowing of forearm, hypertrophy of calf muscles, short fourth metacarpals, scoliosis
    • 70-90% have one pathogenic SHOX variant
  • Langer mesomelic dysplasia (LMD); MIM 249700
    • Symptoms: more severe than LWD; severe short stature, hypoplasia/aplasia of the ulna and fibula and thickened/curved radius and tibia; very rare
    • Typically do not have Madelung deformity
    • Most patients have two pathogenic SHOX variants on opposite chromosomes leading to complete absence of functional SHOX protein
  • Others: Turner syndrome (45,X) and contiguous gene deletion syndromes containing the SHOX region share some features


Short Stature Homeobox-Containing SHOX Gene

  • Composed of 6 exons; 35 kb
  • Produces a transcription factor for skeletal development, especially growth and maturation of long bones in arms/legs
  • Located in pseudoautosomal region 1 (PAR1) on short arms of X and Y chromosomes
  • Gene does not undergo X-inactivation; males and females typically have two functional/expressed copies of SHOX gene
  • Enhancer elements located upstream and downstream of the gene regulate SHOX expression


Pseudoautosomal inheritance

  • Homologous SHOX genes are located on the X chromosome and Y chromosome and follow autosomal inheritance instead of sex-linked inheritance.
  • A SHOX pathogenic variant causing SHOX deficiency can be located on either of the X chromosomes in a female or on either the X or Y chromosome in a male.
  • Pseudoautosomal dominant for LWD and ISS
    • Haploinsufficiency caused by only one functional/expressed copy of SHOX gene
  • Pseudoautosomal recessive for LMD
    • Complete loss of SHOX function/expression due to biallelic inactivation
  • Some cases may be caused by a de novo pathogenic variant but the specific proportion of such cases is unknown
  • Germline mosaicism is possible, but not reported to date



  • Variable expressivity
  • Increased female:male ratio


  • Most pathogenic SHOX variants are deletions (80-90%)
    • Range from single exon deletions to >2.5 Mb or larger
    • Intragenic and enhancer elements deletions are reported
  • Sequence variants account for 10-20% of pathogenic variants

Test Interpretation

Clinical Sensitivity

  • Deletion/duplication analysis: 80-90%
  • Sanger sequencing: 10-20%

Analytical Sensitivity/Specificity



Possible Results by Deletion/Duplication Analysis
SHOX copy number Interpretation


Homozygous deletiona


Heterozygous deletiona




Heterozygous duplicationb


Homozygous duplication or heterozygous triplicationb

aTypically diagnostic for SHOX-related disorders (ISS, LWD, LMD)

bMay or may not be associated with SHOX-related disorders; could be associated with chromosomal aneuploidy

Possible Results by Sanger Sequencing

  • One pathogenic SHOX variant detected
    • Confirms a diagnosis of LWD or ISS
  • Two pathogenic SHOX variants detected
    • Confirms diagnosis of LMD

Negative Result

No pathogenic SHOX variants detected

  • Decreases likelihood of, but does not exclude, a diagnosis of a SHOX-related disorder

Inconclusive Result

Variant of uncertain clinical significance detected

  • Diagnosis of a SHOX-related disorder can neither be confirmed nor excluded


  • Not all copy number changes will affect gene function and result in disease
  • Not detected:
    • Breakpoints of deletions
    • Deep intronic and some regulatory variants
    • Most chromosomal inversions or translocations
  • Diagnostic errors can occur due to rare sequence variants or repeat element insertions
  • MLPA results suggestive of aneuploidy will require further analyses by other methods (chromosome analysis/karyotype, microarray, etc.) for confirmation.
Additional Resources