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Cataract Type 11 via the PITX3 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PITX3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8847PITX381479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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

Cataracts are described as opacification of the crystalline lens of the eye that result in abnormal refraction index and light scattering. Congenital cataracts (CC) are a serious and leading cause of reversible blindness in childhood. They account for about one-tenth of the cases of childhood blindness (Francis and Moore 2004). Estimated prevalence rate is 1.2 - 6.0 per 10,000 live births. Early diagnosis and surgery and optical correction have resulted in an improved outcome for infants with either unilateral or bilateral cataracts (Lambert and Drack 1996).

PITX3- associated posterior polar type is a clinically distinct opacity and appears as 2- to 3-mm disks of dense whitish material in the center of the posterior lens capsule (Bidinost et al. 2006; Berry et al. 2004).


Currently, isolated or primary cataracts have been mapped to about 39 genetic loci, and over 25 of those are connected to pathogenic variants in specific genes. However, this number is constantly increasing. Among the candidate genes, the majority of the identified pathogenic variants (about half) are in crystallins (CRYAA, CRYAB, CRYBA1, CRYBB1, CRYBB2, CRYBB3, CRYBA4, CRYGS, CRYGC, CRYGD), followed by (about a quarter) lens-specific connexins (GJA3, GJA8). The remainder are divided among growth and Transcription Factors (HSF4, MAF, PITX3), Membrane Proteins aquaporin-0 ((AQP0,also known as MIP), cytoskeletal structural proteins (beaded filament structural proteins BFSP1 and BFSP2) and others (FYCO1, GCNT2, HSF4, LIM2, SIL1, TDRD7, FOXE3, CHMP4B, EPHA2, SLC33A1, AGK) (Hejtmancik 2008).

Heterozygous pathogenic variants in PITX3 are shown to be causative for autosomal dominant posterior polar cataract and variable anterior segment mesenchymal dysgenesis (Bidinost et al. 2006; Berry et al. 2004). Two siblings from a consanguineous marriage with a causative variant in the homozygous state showed a severe phenotype (Bidinost et al. 2006). Missense, small deletions and insertions have been shown to be causative (Human Gene Mutation Database). PITX3 encodes a homeobox bicoidlike transcription factor and plays an important role in lens and anterior segment development (Bidinost et al. 2006; Addison et al. 2005).

Clinical Sensitivity - Sequencing with CNV PGxome

Predicting clinical sensitivity for the PITX3 gene is challenging due to the limited number of cases. However, all the reported causative variants are detectable by this method. Gross deletions or duplications have not been reported in this gene that are associated with cataracts. However, a deletion involving PITX3, along with 7 other genes, has been reported in Smith-Magenis-like syndrome (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the PITX3 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).

Indications for Test

Patients with posterior polar type cataract are good candidates.


Official Gene Symbol OMIM ID
PITX3 602669
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Anterior Segment Mesenchymal Dysgenesis AD 107250
Cataract 11 AD 610623

Related Tests

Anterior Segment Dysgenesis via the FOXE3 Gene
Congenital Cataracts and Ayme-Gripp Syndrome via the MAF Gene
Congenital Cataracts Panel


  • Addison P.K. et al. 2005. The British Journal of Ophthalmology. 89: 138-41.  PubMed ID: 15665340
  • Berry V. et al. 2004. Journal of Medical Genetics. 41: e109.  PubMed ID: 15286169
  • Bidinost C. et al. 2006. Investigative Ophthalmology & Visual Science. 47: 1274-80.  PubMed ID: 16565358
  • Francis P.J., Moore A.T. 2004. Current opinion in ophthalmology. 15: 10-5. PubMed ID: 14743013
  • Hejtmancik J.F. 2008. Seminars in cell & developmental biology. 19: 134-49. PubMed ID: 18035564
  • Human Gene Mutation Database (Bio-base).
  • Lambert S.R., Drack A.V. 1996. Survey of ophthalmology. 40: 427-58. PubMed ID: 8724637


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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