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SOX2-Related Ocular Disorders via the SOX2 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SOX2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15297SOX281479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Jamie Fox, PhD

Clinical Features and Genetics

Clinical Features

Congenital ocular malformations: 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 tracheooesophageal 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).


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). Of monogenic causes, only SOX2 [Sex determining region Y (SRY)-box 2] has been identified as a major causative gene in which heterozygous, loss of function mutations account for 10–20% of the A/M cases (Reis et al. 2010; Faivre et al. 2006; Ragge et al. 2005; Williamson 2006). Other A/M associated genes include PAX6, SIX6, HESX1, BCOR, SHH, RAX, CHD7, IKBKG, NDP, POMT1, GDF6, VSX2 and SIX3 (Bardakjian et al. 2006; Slavotinek 2011). SOX2-related ocular disorder is inherited in an autosomal dominant manner, and 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).

Sox2 is a member of the Sox family of proteins, which encodes an SRY-like HMG (High Mobility Group) box transcription factor. The HMG domain among Sox proteins is highly conserved and is critical for correct binding to interacting proteins (Williamson 2006). Sox2 plays a key regulatory role in lens development and is reported to interact with Oct-1 and Pax6 to control lens and nasal placode development (Kamachi et al. 2001; Donner et al. 2007).

Clinical Sensitivity - Sequencing with CNV PG-Select

A mutation analysis in a cohort of 120 patients with congenital eye abnormalities, mainly A/M and coloboma, identified pathogenic variations in the coding region of the SOX2 gene in 6 patients and whole gene deletions in 5 patients (Bakrania et al. 2007). Another mutation screening in a cohort of 51 unrelated individuals affected with bilateral (38) or unilateral (13) A/M revealed SOX2 mutations in ten patients (19.6%). Seven of them had novel alterations, while the remaining three individuals had previously reported a recurrent 20-nucleotide deletion designated c.70_89del20. This deletion accounts for 30% of SOX2 mutations in their cohort (Schneider et al. 2009) and ~21% of all SOX2 cases that have been reported to date (Reis et al. 2010).

Testing Strategy

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 SOX2 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.

Indications for Test

Candidates for this test are patients with symptoms consistent with SOX2-related eye disorders and family members of patients who have known mutations.


Official Gene Symbol OMIM ID
SOX2 184429
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Microphthalmia Syndromic 3 AD 206900


  • Bakrania P. et al. 2007. The British Journal of Ophthalmology. 91: 1471-6.  PubMed ID: 17522144
  • Bardakjian et al. 2013. Microphthalmia/Anophthalmia/Coloboma Spectrum. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301552
  • Donner AL, Episkopou V, Maas RL. 2007. Sox2 and Pou2f1 interact to control lens and olfactory placode development. Developmental Biology 303: 784–799. PubMed ID: 17140559
  • Faivre L. et al. 2006. American Journal of Medical Genetics. Part A. 140: 636-9. PubMed ID: 16470798
  • FitzPatrick. 2009. SOX2-Related Eye Disorders. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301477
  • Guichet A. et al. 2004. Prenatal Diagnosis. 24: 828-32. PubMed ID: 15503273
  • Källén B, Tornqvist K. 2005. European Journal of Epidemiology. 20: 345–350. PubMed ID: 15971507
  • Kamachi Y, Uchikawa M, Tanouchi A, Sekido R, Kondoh H. 2001. Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development. Genes & development 15: 1272–1286. PubMed ID: 11358870
  • Pedace et al. 2009. European Journal of Medical Genetics. 52: 273–276. PubMed ID: 19254784
  • Ragge N.K. et al. 2005. American Journal of Medical Genetics. Part A. 135: 1-7; discussion 8.  PubMed ID: 15812812
  • Ragge N.K. et al. 2007. Eye (london, England). 21: 1290-300.  PubMed ID: 17914432
  • Reis L.M. et al. 2010. Molecular Vision 16: 768-73. PubMed ID: 20454695
  • Schneider A, Bardakjian T, Reis LM, Tyler RC, Semina EV. 2009. Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia. American Journal of Medical Genetics Part A 149A: 2706–2715. PubMed ID: 19921648
  • Schneider A. et al. 2008. American Journal of Medical Genetics Part A 146A: 2794-8. PubMed ID: 18831064
  • Slavotinek AM. 2011. Eye development genes and known syndromes. Molecular Genetics and Metabolism 104: 448–456. PubMed ID: 22005280
  • Williamson KA. 2006. Mutations in SOX2 cause anophthalmia-esophageal-genital (AEG) syndrome. Human Molecular Genetics 15: 1413–1422. PubMed ID: 16543359


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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