SHOX Deficiency Disorders, Sequencing and Deletion/Duplication

Content Review: December 2021 Last Update:

Use to detect pathogenic variants in the SHOX gene which cause SHOX deficiency disorders (eg, ISS, LWD, or LMD)

If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information.

Pathogenic variants in the SHOX gene result in a spectrum of disorders due to haploinsufficiency of the SHOX gene. 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 the wrist (Madelung deformity). Variable expressivity results in some individuals only affected with isolated short stature (ISS), whereas others have short stature and additional findings resulting in syndrome disorders (eg, Leri-Weill dyschondrosteosis [LWD] or Langer mesomelic dysplasia [LMD]).

Disease Overview

Epidemiology

The prevalence for SHOX deficiency disorders is at least 1/1,000 

Associated Conditions

Conditiona MIM Number Clinical Information

Isolated/idiopathic short stature

300582

Short stature (below the third percentile) of unknown cause

Usually no mesomelia or Madelung deformity

Highly variable presentation even within the same family

6-22% have one pathogenic SHOX variant 

Leri-Weill dyschondrosteosis

127300

Triad of short stature in early childhood, mesomelia, and Madelung deformity

Madelung deformity typically develops in mid-late childhood

Other features may include high-arched palate, bowing of forearm, hypertrophy of calf muscles, short fourth metacarpals, scoliosis

More common and severe in females

70-90% have one pathogenic SHOX variant 

Langer mesomelic dysplasia

249700

Severe short stature, hypoplasia/aplasia of the ulna and fibula, and thickened/curved radius and tibia

More severe than LWD

Very rare

aIn addition to the conditions listed, Turner syndrome (45,X) and contiguous gene deletion syndromes containing the SHOX region share some features.

Sources: Binder, 2018 ; Marchini, 2016 ; John Hopkins University, 2021 

Genetics

Inheritance

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 a SHOX deficiency disorder 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

Penetrance

High, with variable expressivity and an increased female:male ratio 

Etiology

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

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as NGS) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • Multiplex ligation-dependent probe amplification (MLPA) is performed to call exon-level deletions and duplications.

Clinical Sensitivity

  • At least 90% for SHOX deficiency disorders 
  • About 10% of individuals with LWD do not have a demonstrable SHOX pathogenic variant 

Analytic Sensitivity/Specificity

For massively parallel sequencing:

Variant Class Analytic Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)		 Analytic Specificity (NPA) (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived.

bVariants greater than 10 bp may be detected, but the analytical sensitivity may be reduced.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

MLPA

>99%

Results

Result Variant(s) Detected Clinical Significance

Positive

One pathogenic SHOX variant detected

Confirms a diagnosis of LWD or ISS

Two pathogenic SHOX variants detected

Confirms diagnosis of LMD if located on opposite chromosomes

Negative

No pathogenic SHOX variants detected

Decreases likelihood of, but does not exclude, a diagnosis of a SHOX deficiency disorder

Inconclusive

Variant of uncertain clinical significance detected

Diagnosis of a SHOX deficiency disorder can neither be confirmed nor excluded

Limitations

  • A negative result does not exclude a diagnosis of a SHOX deficiency disorder.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if this patient has had an allogeneic stem cell transplantation.
  • SHOX (NM_006883) exon 6, also known as exon 6b, is not sequenced due to technical limitations of the assay.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of targeted gene(s)
    • Regulatory region and deep intronic variants
    • Breakpoints of large deletions/duplications
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massively parallel sequencing
    • Noncoding transcripts
    • Low-level somatic variants
    • Certain other variants due to technical limitations in the presence of pseudogenes and repetitive/homologous regions
  • MLPA results suggestive of aneuploidy will require further analyses by other methods (eg, chromosome analysis/karyotype, microarray, etc.) for confirmation.

References