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FOXC1-Related Disorders via the FOXC1 Gene

Summary and Pricing

Test Method

Bi-Directional Sanger Sequencing
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
FOXC1 81479 81479 $870
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
1846FOXC181479 81479 $870 Order Options and Pricing

Pricing Comments

CNV detection may be ordered through Test #600.

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

Turnaround Time

4 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

Axenfeld-Rieger syndrome (ARS) is a rare, highly penetrant autosomal dominant disorder characterized by varying degrees of eye anterior segment anomalies with systemic malformations such as dental hypoplasia and a protuberant umbilicus (Hjalt and Semina 2005; Berry et al. 2006; Waldron et al. 2010; Tümer and Bach-Holm 2009; Chang et al. 2012). Dental abnormalities in this syndrome help in the diagnosis and to distinguish ARS from other eye anterior segment abnormalities. Early diagnosis of ARS through its dento-facial and systemic features is essential in treating or preventing the most serious consequence of ARS (O’Dwyer and Jones 2005). The major clinical concern is high risk of developing open-angle glaucoma, which represents the main challenge in terms of treatment. Approximately 50% of the ARS affected patients develop glaucoma (Shields et al. 1985; Alward 2000; Hjalt and Semina 2005; Chang et al. 2012). ARS affected patients also need surveillance and management of sensorineural hearing loss, and cardiac, endocrinological, craniofacial and orthopaedic defects (Chang et al. 2012).

Rieger syndrome (RIEG) and Axenfeld anomaly both are in the anterior chamber cleavage group of anomalies and are considered to be variations of a single developmental disorder and belong to the ARS group (Reese and Ellsworth 1966). RIEG is characterized by malformations of the eyes, teeth, and umbilicus; whereas, Axenfeld anomaly displays only ocular features (Amendt et al. 2000).


Linkage studies mapped four chromosomal loci (4q25, 6p25, 13q14 and 16q24) that are associated with ARS and related or overlapping phenotypes. FOXC1 (the forkhead box C1 gene, also known as FKHL7) is the causative gene at chromosome 6p25 (Alward 2000; Lines et al. 2002; Tümer and Bach-Holm 2009). FOXC1 causative mutations cause autosomal dominant ARS.

FOXC1 encodes a transcription factor that is expressed throughout eye ontogeny (Lines et al. 2002). This factor (FOXC1) is reported to maintain homeostasis in trabecular meshwork (TM) cells by regulating genes that play an important role in stress response (Ito et al. 2014; Paylakhi et al. 2013). TM helps in regulating intraocular pressure by acting as a drainage structure for aqueous humor (Tamm 2009). The mutations in FOXC1 that lead to FOXC1 dysfunction significantly decrease TM cell viability and subsequently contribute to the development of glaucoma. It's been reported that ~75% of ARS patients with FOXC1 mutations develop earlier-onset glaucoma (Ito et al. 2014; Paylakhi et al. 2013). A Genotype-Phenotype correlation study indicated that patients with FOXC1 duplications are at higher risk for development of glaucoma as compared to other FOXC1 mutations. PITX2 is the causative ARS gene at chromosome 4q25. PITX2 also encodes a transcription factor (PITX2). PITX2 and FOXC1 have been reported to interact with each other, which is essential for the regulation of common downstream target genes within specific cell lineages (Berry et al. 2006). Also, coinheritance of PITX2 and FOXC1 mutations has been reported in a family, which segregated with the disease and showed variable phenotypic expression. The most severely affected individual had mutations in both genes, whereas single heterozygous mutations caused milder ARS phenotypes (Kelberman et al. 2011). So far, over 100 mutations have been identified in FOXC1 that are associated with ARS and related phenotypes (Human Gene Mutation Database).

Clinical Sensitivity - Sanger Sequencing

Approximately 25%-60% of Axenfeld-Rieger syndrome cases are due to FOXC1 or PITX2 pathogenic variants (Tümer and Bach-Holm 2009; Reis et al. 2012; Alward 2000). In the remaining ~50% of ARS patients the genetic cause is unknown, which indicates that there are still more genes to be identified (Tümer and Bach-Holm 2009). Several gross deletions, duplications and complex rearrangements have been reported in FOXC1 that are associated with ARS (Human Gene Mutation Database).

Testing Strategy

This test involves bidirectional Sanger sequencing of all coding exons and splice sites of the FOXC1 gene. The full coding sequence of each exon plus ~10 bp of flanking DNA on either side are sequenced. We will also sequence any single exon (Test #100) in family members of patients with a known pathogenic variant or to confirm research results.

Indications for Test

All patients with symptoms suggestive of Axenfeld-Rieger syndrome and related phenotypes are candidates.


Official Gene Symbol OMIM ID
FOXC1 601090
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Alward WL. 2000. American Journal of Ophthalmology. 130: 107-15. PubMed ID: 11004268
  • Amendt BA. et al. 2000. Cellular and Molecular Life Sciences : Cmls. 57: 1652-66. PubMed ID: 11092457
  • Berry FB. et al. 2006. Human Molecular Genetics. 15: 905-19. PubMed ID: 16449236
  • Chang TC. et al. 2012. The British Journal of Ophthalmology. 96: 318-22. PubMed ID: 22199394
  • Hjalt TA., Semina EV. 2005. Expert Reviews in Molecular Medicine. 7: 1-17. PubMed ID: 16274491
  • Human Gene Mutation Database (Bio-base).
  • Ito YA. et al. 2014. Cell Death & Disease. 5: e1069. PubMed ID: 24556684
  • Kelberman D. et al. 2011. Human Mutatation. 32: 1144–52. PubMed ID: 21837767
  • Lines MA. et al. 2002. Human Molecular Genetics. 11: 1177–84. PubMed ID: 12015277
  • O'Dwyer E.M., Jones D.C. 2005. International Journal of Paediatric Dentistry. 15: 459-63. PubMed ID: 16238657
  • Paylakhi SH. et al. 2013. Experimental Eye Research. 111: 112-21. PubMed ID: 23541832
  • Reese AB., Ellsworth RM. 1966. Archives of Ophthalmology. 75: 307-18. PubMed ID: 5948260
  • Reis LM, Tyler RC, Volkmann Kloss BA, Schilter KF, Levin AV, Lowry RB, Zwijnenburg PJG, Stroh E, Broeckel U, Murray JC, Semina EV. 2012. PITX2 and FOXC1 spectrum of mutations in ocular syndromes. Eur. J. Hum. Genet. 20: 1224–1233. PubMed ID: 22569110
  • Shields MB. et al. 1985. Survey of Ophthalmology. 29: 387-409. PubMed ID: 3892740
  • Tamm ER. 2009. Experimental Eye Research. 88: 648-55. PubMed ID: 19239914
  • Tümer Z, Bach-Holm D. 2009. European Journal of Human Genetics : Ejhg. 17: 1527-39. PubMed ID: 19513095
  • Waldron JM. et al. 2010. Special Care in Dentistry : Official Publication of the American Association of Hospital Dentists, the Academy of Dentistry For the Handicapped, and the American Society For Geriatric Dentistry. 30: 218-22. PubMed ID: 20831741


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

Specimen Types

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