Microphthalmia and Anophthalmia via the RAX Gene

Anophthalmia (A; absence of a globe in the orbit) and microphthalmia (M; reduced size of the globe) are severe and rare developmental defects of the globe with an estimated incidence of 0.2–0.4/10 000 and ~1.5/10 000 live births, respectively (Källén and Tornqvist 2005). Both A/M may be unilateral or bilateral, and over 50% of A/M affected individuals have systemic abnormalities such as hypothalamic–pituitary disorder, mild dysmorphic facial features and short stature, urogenital anomalies, cryptorchidism and/or micropenis in males, developmental delay, seizures, oesophageal atresia or tracheoesophageal fistula and hearing loss (Ragge et al. 2005), but only 25% of these are part of distinct and well-defined syndromes (Bakrania et al. 2007). Unilateral A/M cases often have developmental anomalies of the other eye; including coloboma, lens, and optic nerve (Ragge et al. 2007).

Anophthalmia/Microphthalmia (A/M) may be inherited as an autosomal dominant, autosomal recessive, or X-linked trait. A/M has a complex aetiology with a wide range of causes, including chromosomal abnormalities, as well as environmental factors (Pedace et al. 2009). Chromosomal duplications, deletions and translocations account for 23–30% of A/M cases. Bakrania et al. reported whole SOX2 gene deletions in ~10% of their A/M patients cohort (Bakrania et al. 2007), which emphasizes the necessity of careful chromosomal analysis (particularly the 3q region that comprises the SOX2 gene) (Guichet et al. 2004). SOX2 has been identified as a major causative gene in which heterozygous, loss of function variants account for 15–20% of the A/M cases (Reis et al. 2010; Faivre et al. 2006; Ragge et al. 2005; Williamson and Fitzpatrick 2014). The majority of the causative SOX2 sequence variations are de novo (FitzPatrick 2009). Occasional cases result from parental gonosomal mosaicism (Faivre et al. 2006; Schneider et al. 2008). Heterozygous loss-of-function variants in SOX2 and OTX2 (Wyatt A. et al. 2008) are the most common genetic pathologies associated with severe eye malformations. Bi-allelic loss-of-function variants in STRA6 (Gerth-Kahlert et al. 2013) are confirmed as an emerging cause of nonsyndromal eye malformations.

Pathogenic variants in RAX (retina and anterior neural fold homeobox) cause recessive microophthalmia and anophthalmia (Chassaing et al. 2014). The RAX gene (also known as Rx) is expressed very early in retinal development. Members of the Rx/Rax (retinal homeobox) gene family are shown to be essential for vertebrate eye development. Abnormal expression has been shown to have profound effects on eye development (Pan et al. 2010; Mathers et al. 1997; Bailey et al. 2004). Over ten pathogenic variants (Missense, nonsense, splicing, small and one gross deletion) have been documented causative to date (Human Gene Mutation Database).

Heterozygous loss-of-function variants in SOX2 and OTX2 (Wyatt et al. 2008) are the most common genetic pathologies associated with severe eye malformations. It has been reported that RAX causative variants account for ~1.3 to 3% of all anophthalmia/microphthalmia patients) (Chassaing et al. 2014; Voronina et al. 2004).

This test provides full coverage of all coding exons of the RAX gene 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 full 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).

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).