Campomelic Dysplasia and Pierre Robin Sequence via the SOX9 Gene

SOX9-related disorders include campomelic dysplasia (CD), acampomelic campomelic dysplasia (ACD), and isolated Pierre Robin Sequence (PRS) (Unger et al. 2013. PubMed ID: 20301724). CD is a severe type of skeletal dysplasia. Clinical features may include shortening and bowing of the long bones, 11 pairs of ribs, hip dislocation, talipes equinovarus, scoliosis or kyphoscoliosis, hypoplastic scapulae, small thoracic cage, pretibial skin dimples, distinctive facies, PRS with cleft palate, laryngotracheomalacia, and respiratory distress (Matsushita et al. 2013. PubMed ID: 24038782; Unger et al. 2013. PubMed ID: 20301724). Approximately 75% of individuals with a 46,XY karyotype have either ambiguous genitalia or normal female external genitalia (Mansour et al. 2002. PubMed ID: 12161603). ACD is similar, but presents without bowing of the long bones. CD is usually lethal in the first year of life due to respiratory failure that results from airway instability (tracheobronchomalacia) or cervical spine instability (Mansour et al. 2002. PubMed ID: 12161603). CD and ACD are frequently identified at birth. In some cases, prenatal diagnosis can be made by ultrasound (Kayhan et al. 2019. PubMed ID: 31234679). In rare instances, mildly affected adults have been diagnosed after the birth of an affected child (Mansour et al. 2002. PubMed ID: 12161603). The exact prevalence of CD is presently unknown, but is suggested to be in the range of 1-in-40,000 to 1-in-80,000, indicating it is very rare (Unger et al. 2013. PubMed ID: 20301724). Genetic testing may aid in establishing a differential diagnosis and may assist reproductive planning.

In rare cases, individuals with large chromosomal rearrangements in the vicinity of the SOX9 gene may present with isolated PRS. PRS refers to a triad of micrognathia, glossoptosis, and upper airway obstruction, which may be accompanied by a U-shaped cleft palate (Izumi et al. 2012. PubMed ID: 22048048; Gangopadhyay et al. 2016. PubMed ID: 23633934). PRS is not a syndrome, but rather a sequential chain of malformations: micrognathia leads to abnormal posterior placement of the tongue (glossoptosis), which results in airway obstruction. PRS is identifiable at birth with an incidence of 1-in-8,500 to 1-in-14,000 live births (Tan et al. 2013. PubMed ID: 24127256). Infants are typically at risk of repeated oxygen desaturations, apnea, cyanosis, feeding difficulties, poor suck, gastroesophageal reflux, aspiration during feeding, and failure to thrive (Gangopadhyay et al. 2016. PubMed ID: 23633934). Genetic testing may aide in establishing a differential diagnosis and may assist reproductive planning.

Pathogenic variants in the SOX9 gene are associated with autosomal dominant CD, ACD, and isolated PRS. Pathogenic variants typically arise de novo due to somatic or germline mosacism, although familial variants have been reported in rare instances (Mansour et al. 2002. PubMed ID: 12161603). SOX9 is the only gene in which pathogenic variants are known to cause CD. Pathogenic variants in the coding region of the SOX9 gene are completely penetrant, however penetrance decreases the further the variant occurs upstream or downstream of the SOX9 gene (Unger et al. 2013. PubMed ID: 20301724). Approximately 90% of cases can be explained by sequence variants within SOX9 coding regions or splice sites (Unger et al. 2013. PubMed ID: 20301724). An additional 5% of cases can be explained by partial or whole gene deletions and by genomic rearrangements identifiable by karyotyping (Unger et al. 2013. PubMed ID: 20301724).

Pathogenic missense and loss of function variants are typically reported with CD. Loss of function variants occur across the entire coding region of SOX9, while missense variants cluster in the high mobility group (HMG) DNA-binding domain (Unger et al. 2013. PubMed ID: 20301724). The most frequent recurrent de novo pathogenic variant in SOX9 is p.Tyr440Ter, which is absent in large population databases (Pop et al. 2005. PubMed ID: 15060123, Lek et al. 2019. PubMed ID: 27535533). Of note, no loss of function variants have been observed in a large population database (https://gnomad.broadinstitute.org/gene/ENSG00000125398). This along with estimates from gene constraint models suggests the SOX9 gene is highly intolerant to loss-of-function variants. Estimates for missense tolerability are difficult to estimate due to the presence of mutation hotspots within the gene.

Pathogenic large chromosomal rearrangements and CNVs are more frequently associated with the milder ACD and isolated PRS phenotypes. These events may involve the coding region of the SOX9 gene or cluster upstream and downstream of the gene (Leipoldt et al. 2007. PubMed ID: 17204049; Jakobsen et al. 2007. PubMed ID: 17551083; Fukami et al. 2012. PubMed ID: 22529047).

SOX9 is a proven key regulator of chondrogenesis, the process in the developing embryo by which cartilage is formed (Wright et al. 1995. PubMed ID: 7704017; Mori-Akiyama et al. 2003 PubMed ID: 12878728; Akiyama and Lefebvre. 2011. PubMed ID: 21594584). Specifically, SOX9 regulates the expression of the collagen genes COL2A1, COL11A2, CD-RAP, and ACAN, all of which are crucial for normal skeletal development. SOX9 heterozygous null mice reproduce the skeletal abnormalities of humans with CD, including cleft palate, hypoplasia and bending of the long bones (Bi et al. 2001. PubMed ID: 11371614). As is observed in humans with severe CD, heterozygous deletion of the SOX9 gene in mice also results in perinatal lethality.

SOX9 is the only gene in which pathogenic variants are known to cause CD. Pathogenic variants, CNVs, and chromosomal rearrangements affecting SOX9 are detected in approximately 95% of affected individuals (Unger et al. 2013. PubMed ID: 20301724).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the SOX9 genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Note that this test does not automatically include coverage of the regions upstream and downstream of the coding region that have been previously reported in ACD and PRS cases harboring large genomic rearrangements or CNV events. However, our exome-wide CNV detection option is available.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).