Microphthalmia/Anophthalmia/Coloboma Panel

Anophthalmia (A; absence of a globe in the orbit), microphthalmia (M; reduced size of the globe) and coloboma (Greek koloboma, meaning ‘‘mutilated’’ or ‘‘curtailed’’) are an interrelated spectrum of congenital, severe, and rare developmental defects of the globe. Microphthalmia, anophthalmia, and coloboma (MAC) account for a significant portion of childhood visual impairment and blindness worldwide (Gregory-Evans et al. 2004. PubMed ID: 15591273; Skalicky et al. 2013. PubMed ID: 24177921). Of note, 3.2-11.2% children with blindness are reported to be presenting with M (Harding and Moosajee. 2019. PubMed ID: 31416264; Verma and Fitzpatrick. 2007. PubMed ID: 18039390). Estimated birth prevalence ranges from 0.6-4.2/100 000 births for A; 2-17/100,000 births for M; and 2-14/100,000 births for coloboma (Skalicky et al. 2013. PubMed ID: 24177921). The overall MAC prevalence is estimated to be two in 10,000 live births (Morrison et al. 2002. PubMed ID: 11826019).

MAC may be unilateral or bilateral. 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. PubMed ID: 15812812), but only 25% of these are part of distinct and well-defined syndromes (Bakrania et al. 2007. PubMed ID: 17522144). Unilateral A/M cases often have developmental anomalies of the other eye; including coloboma, lens, and optic nerve (Ragge et al. 2007. PubMed ID: 17914432). Coloboma is frequently seen in association with other developmental defects, including craniofacial anomalies, skeletal defects, and genitourinary anomalies (Gregory-Evans et al. 2004. PubMed ID: 15591273).

Genetic diagnosis and counselling in managing these conditions is often challenging due to the genetic heterogeneity, incomplete penetrance and possible mosaicism. The risk of recurrence of A/M in the siblings without a clear etiology or family history is 10–15% (Verma and Fitzpatrick. 2007. PubMed ID: 18039390). Early diagnosis and multidisciplinary input impact the overall development of the child and the emotional well-being of the family. Of note, the Microphthalmia, Anophthalmia and Coloboma Support organization offers specialist advice and family support to children born without eyes or with underdeveloped eyes and their families (Ragge et al. 2007. PubMed ID: 17914432).

MAC is genetically heterogeneous. MAC is inherited as an autosomal dominant, autosomal recessive or X-linked trait. MAC has a complex etiology with a wide range of causes, including chromosomal abnormalities, as well as environmental factors (Pedace et al. 2009. PubMed ID: 19254784). Chromosomal duplications, deletions and translocations account for 23–30% of A/M cases (Pedace et al. 2009. PubMed ID: 19254784). Bakrania et al. reported whole SOX2 gene deletions in ~10% of their A/M patient cohort (Bakrania. 2007. PubMed ID: 17522144), which emphasizes the necessity of careful chromosomal analysis (particularly the 3q region that contains the SOX2 gene) (Guichet et al. 2004. PubMed ID: 15503273). 

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. PubMed ID: 20140963; Faivre et al. 2006. PubMed ID: 16470798; Ragge et al. 2005. PubMed ID: 15812812; Williamson and FitzPatrick. 2014. PubMed ID: 24859618). The majority of the causative SOX2 sequence variations occur de novo (Williamson et al. 2020. PubMed ID: 20301477). Occasional cases result from parental gonosomal mosaicism (Faivre et al. 2006. PubMed ID: 16470798; Schneider et al. 2008. PubMed ID: 18831064). Approximately 80% of the severe bilateral MAC cases are due to de novo heterozygous loss-of-function pathogenic variants in in SOX2 or OTX2 (Williamson and FitzPatrick. 2014. PubMed ID: 24859618; Wyatt et al. 2008. PubMed ID: 18781617). The cause of the majority of isolated coloboma cases are unknown (Williamson and FitzPatrick. 2014. PubMed ID: 24859618).

Bi-allelic loss-of-function variants in STRA6 (Gerth-Kahlert et al. 2013. PubMed ID: 24498598) are confirmed as an emerging cause of nonsyndromal eye malformations.

Other genes involved in MAC include ADAMTS18,  ALDH1A3,  ATOH7,  BCOR,  BMP4,  BMP7,  CHD7,  CRYBA4,  FOXE3,  GDF3,  GDF6,  HCCS,  HMGB3,  MAB21L2,  MFRP,  MITF,  NAA10,  NDP,  NHS,  OTX2,  PAX2,  PAX6,  PITX3,  PQBP1,  PRSS56,  RARB,  RAX,  RBP4,  SHH,  SIX6,  SMOC1,  SOX2,  STRA6,  TENM3 (alternatively known as ODZ3),  TFAP2A,  TMEM98,  VAX1, VSX2, YAP1,ABCB6, C12orf57, COL4A1, FNBP4, NDUFB11, PRR12, PXDN, RAB1B, RAB3GAP1, RAB3GAP2, TBC1D20, TMX3 and VSX1 (Wimplinger et al. 2006. PubMed ID: 17033964; Tassabehji et al. 1994. PubMed ID: 7874167; Abouzeid et al. 2012. PubMed ID: 22736936; Aldahmesh et al. 2013. PubMed ID: 23167593; Reis et al. 2011. PubMed ID: 21976963; Aldahmesh et al. 2012. PubMed ID: 22766609; Reis et al. 2010. PubMed ID: 20140963; Asai-Coakwell et al. 2009. PubMed ID: 19129173; Billingsley et al. 2006. PubMed ID: 16960806; Okada et al. 2011. PubMed ID: 21194678; Bardakjian et al. 2013 PubMed ID: 20301552; Williamson and FitzPatrick. 2014. PubMed ID: 24859618; Deml et al. 2014. PubMed ID: 24628545; Liegel et al. 2013. PubMed ID: 24239381; Patel. 2019. PubMed ID: 30653986; van Rahden et al. 2015. PubMed ID: 25772934; Leduc et al. 2018. PubMed ID: 29556724; Choi et al. 2015. PubMed ID: 24939590; Matías-Pérez et al. 2018. PubMed ID: 30181649).

Of note, pathogenic variants in FOXE3 have been reported to have autosomal dominant or autosomal recessive inheritance. Dominant variants are those (e.g., c.958T>C (p.*320Argext*72) and c.942dupG (p.Leu315Alafs*117)), which result in extension of the open reading frame beyond the normal stop codon and are reported to have dominant negative effect (Semina et al. 2001. PubMed ID: 11159941; Iseri et al. 2009. PubMed ID: 19708017). Recessive variants (e.g., missense variants) result in altered protein interactions (Iseri et al. 2009. PubMed ID: 19708017).

Normal intrauterine eye development is controlled by a complex network of diffusible signaling molecules such as transcription factors (encoded by SOX2, OTX2, PAX6, etc.), expression regulators (encoded by YAP1, BCOR, CHD7, etc.), proteins involved in signaling pathways (encoded by BMP4, BMP7, GDF6, etc.) and genes involved in the metabolism of retinoic acid (such as STRA6, ALDH1A3, RARB and RBP4). Disruption of any one of these events has the potential to cause ocular growth and structural defects (Plaisancié et al. 2019. PubMed ID: 30762128; Skalicky et al. 2013. PubMed ID: 24177921).

See individual gene test descriptions for more information on molecular biology of gene products and spectra of pathogenic variants.

SOX2 has been identified as a major causative gene in which copy number variants and heterozygous, loss of function sequence variants account for 15–20% of MAC cases (Reis et al. 2010. PubMed ID: 20140963; Faivre et al. 2006. PubMed ID: 16470798; Ragge et al. 2005. PubMed ID: 15812812; Williamson and FitzPatrick. 2014. PubMed ID: 24859618). Also, BCOR and OTX2 copy number variants (CNVs) have been reported frequently in patients with MAC spectrum (Human Gene Mutation Database; Hilton et al. 2009. PubMed ID: 19367324). Whole-genome copy number variation analysis in patients with A/M identified CNVs in 17% of the cases (Schilter et al. 2013. PubMed ID: 23701296). Together, sequence analysis, gene-targeted deletion/duplication analysis, and chromosomal copy number variant analysis can identify a genetic cause in 80% of individuals with bilateral A/severe M and in up to 20% of all individuals with MAC spectrum (Bardakjian et al. 2013. PubMed ID: 20301552).

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

This panel typically provides 99.7% coverage of all coding exons of the 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).

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).