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Septo-optic Dysplasia Spectrum Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
GLI2 81479,81479
HESX1 81479,81479
HK1 81479,81479
OTX2 81479,81479
PAX6 81479,81479
PROP1 81404,81479
SOX2 81479,81479
SOX3 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10211Genes x (8)81479 81404(x1), 81479(x15) $990 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

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


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Septo-optic dysplasia spectrum (SOD) is a rare congenital developmental abnormality characterized by two or more features of the classical triad: hypoplasia of the optic nerves (unilateral or bilateral), pituitary hypoplasia and midline defects of brain. The majority of patients (96%) have optic nerve hypoplasia on MRI imaging (Cemeroglu et al. 2015. PubMed ID: 25879316). Hormonal dysfunction such as combined hypopituitarism and precocious puberty is present in 78% of cases. Other less frequent symptoms include developmental delay, seizures, visual impairment, sleep disturbance, obesity, anosmia, sensorineural hearing loss and cardiac anomalies. MRI imaging can reveal hypoplasia of the optic nerves and optic chiasm, agenesis of the septum pellucidum, abnormalities of the corpus callosum and hypothalamopituitary axis. The incidence is approximately 1 in 10,000 live births. Onset of the disorder can be at birth or later when growth failure occurs in a child (Webb and Dattani. 2010. PubMed ID: 19623216; Koizumi et al. 2017. PubMed ID: 28458461; Ganau et al. 2019. PubMed ID: 31695544).

SOD can be caused by defects in several genes with variable and overlapping presentations. It can be difficult to diagnose by clinical manifestations, laboratory findings and image studies alone. An accurate molecular diagnosis is critical for treatment, prognosis, prediction of recurrence risk, as well as future family plans. Of note, hormonal insufficiencies should be treated as early as possible, as untreated hormonal abnormalities affect neurodevelopment, and increase the risk for visual impairment, hypoglycaemia, adrenal crises and consequent death (Webb and Dattani. 2010. PubMed ID: 19623216).


This panel for SOD spectrum contains 7 genes: GLI2, HESX1, PAX6, PROP1, OTX2, SOX2 and SOX3. SOD is inherited in an autosomal recessive manner in PROP1, an autosomal dominant manner in four genes (GLI2, PAX6, OTX2 and SOX2), and an X-linked manner in SOX3. HESX1 pathogenic variants can be inherited in either an autosomal dominant or recessive manner.

Pathogenic variants are detected more commonly in HESX1, SOX2, SOX3, and OTX2 compared to the other genes (Ganau et al. 2019. PubMed ID: 31695544). A wide variety of causative variants in these genes have been reported including missense, nonsense, splicing, small insertions/deletions and large deletions/duplications (Human Gene Mutation Database). De novo pathogenic variants are common in SOX2 (Dennert et al. 2017. PubMed ID: 27862890).

HESX1 is a homeobox gene expressed in ES cells. It encodes a transcriptional repressor involved in the development of forebrain and pituitary.

PAX6 encodes paired box gene 6, a transcriptional regulator involved in oculogenesis and other development.

PROP1 encodes prop paired-like homeobox 1, a paired-like homeodomain transcription factor required for normal pituitary development.

OTX2 codes for orthodenticle Drosophila, homolog of. This protein is a transcriptional factor involved in brain, craniofacial and sensory organ development.

SOX2 and SOX3 encode SRY-box 2 and SRY-box 3 respectively. Both are members of the SOX family of transcription factors involved in the regulation of embryonic development and determination of cell fate.

GLI2 encodes GLI-KRUPPEL family member 2, a transcription factor involved in SHH signal transduction.

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity is about 4% for SOD and 10% for defects in pituitary development (Cerbone et al. 2020. PubMed ID: 32140665).

Testing Strategy

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

This panel provides 100% 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).

Indications for Test

Candidates for this panel include patients with symptoms of Septo-optic dysplasia spectrum.


Official Gene Symbol OMIM ID
GLI2 165230
HESX1 601802
HK1 142600
OTX2 600037
PAX6 607108
PROP1 601538
SOX2 184429
SOX3 313430
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test



  • Cemeroglu et al. 2015. PubMed ID: 25879316
  • Cerbone et al. 2020. PubMed ID: 32140665
  • Dennert et al. 2017. PubMed ID: 27862890
  • Ganau et al. 2019. PubMed ID: 31695544
  • Human Gene Mutation Database (Bio-base).
  • Koizumi et al. 2017. PubMed ID: 28458461
  • Webb and Dattani. 2010. PubMed ID: 19623216


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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