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Leber Congenital Amaurosis Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
AIPL1 81479,81479
CABP4 81479,81479
CEP290 81408,81479
CNGA3 81479,81479
CNGB3 81479,81479
CRB1 81406,81479
CRX 81404,81479
DTHD1 81479,81479
GNAT2 81479,81479
GUCY2D 81479,81479
IMPDH1 81479,81479
INPP5E 81479,81479
IQCB1 81479,81479
KCNJ13 81479,81479
LCA5 81479,81479
LRAT 81479,81479
MERTK 81479,81479
NMNAT1 81479,81479
OTX2 81479,81479
PDE6H 81479,81479
PRPH2 81404,81479
RD3 81479,81479
RDH12 81479,81479
RPE65 81406,81479
RPGRIP1 81479,81479
SNRNP200 81479,81479
SPATA7 81479,81479
TULP1 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
4313Genes x (28)81479 81404(x2), 81406(x2), 81408(x1), 81479(x51) $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


  • Dana Talsness, PhD

Clinical Features and Genetics

Clinical Features

Leber congenital amaurosis (LCA) is the most severe form of inherited retinal degeneration that is usually evident at birth or during the first months of life. LCA is clinically characterized by poor visual function often accompanied by nystagmus, abnormal pupillary responses, photophobia, high hyperopia, markedly diminished electroretinogram (ERG) and keratoconus condition due to oculo-digital signs of Franceschetti such as eye poking, pressing, and rubbing the eyes with a knuckle or finger (Weleber et al. 2013; Perrault et al. 1996). The estimated prevalence of LCA is 2-3 per 100,000 live births and accounts for 10-18% of congenital blindness (Fazzi et al. 2003).


LCA is a genetically heterogeneous disorder and is often inherited in an autosomal recessive manner. To date, over 20 genes have been implicated in the pathogenesis of different types of LCA (Weleber et al. 2013; Chen et al. 2013). Pathogenic variants in AIPL1, CABP4, CEP290, CNGA3, CNGB3, GNAT2, INPP5E, IQCB1, LCA5, LRAT, MERTK, NMNAT1, RD3, RDH12, RPE65, RPGRIP1, SPATA7, and TULP1 cause autosomal recessive (AR) retinal disorder (Chen et al. 2013). Pathogenic variants in IMPDH1, SNRNP200, and OTX2 cause autosomal dominant (AD) retinal disorder (Bowne et al. 2006; Henderson et al. 2009; Swaroop et al. 1999; Zhao et al. 2006). GUCY2D, PDE6H, PRPH2, KCNJ13, CRB1, and CRX are implicated in both AD and AR retinal disorders (Kohl et. 2012; Piri N. 2005; Wang et al. 2013; Weleber et al. 1993; Udar et al. 2003; Hanein et al. 2002; McKay et al. 2005; Abouzeid et al. 2006; Swaroop et al. 1999; Hejtmancik et al. 2008). DTHD1 gene inheritance mode is currently unknown. Together these genes account for 70-75% of the LCA cases (Wang et al. 2015; den Hollander et al. 2008). These genes encode proteins that have a wide range of retinal functions, such as photoreceptor morphogenesis, phototransduction, vitamin A cycling, guanine synthesis, and outer segment phagocytosis (den Hollander et al. 2008). Pathogenic variants in these genes cause not only LCA but also other retinal disorders (Weleber. 2002; Wang et al. 2015; Wang et al. 2013; http://www.omim.org/; Human Gene Mutation Database).See individual gene test descriptions for more information on molecular biology of gene products.

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity for the AIPL1 (4-8%), CEP290 (<20%), CRB1 (10%), CRX (3%), GUCY2D (21%), LCA5 (1-2%), RDH12 (4%), RPE65 (3-16%), RPGRIP1 (5%), TULP1 (1.7%) genes is known (Weleber et al. 2013). However, for other genes, due to the limited number of cases, estimation of clinical sensitivity is difficult (Hanein et al. 2004; Weleber et al. 2013).

A study by Perrault et al. (2000) identified two gross deletions and one duplication in GUCY2D out of 118 patients affected with Leber Congenital Amaurosis (Perrault et al. 2000). Copy number variants have also been reported in CEP290, CRB1, CRX, GUCY2D, LCA5, MERTK, NMNAT1, PRPH2, RDH12, RPE65, RPGRIP1, and TULP1 genes (Human Gene Mutation Database).

Testing Strategy

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

This panel typically provides 99.9% 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 test are all Leber congenital amaurosis patients, family members of patients who have known mutations and carrier testing for at-risk family members.

Related Test



  • Abouzeid H. et al. 2006. Ophthalmic Genetics. 27:15-20. PubMed ID: 16543197
  • Bowne S.J. 2006. Investigative Ophthalmology & Visual Science. 47: 34-42. PubMed ID: 16384941
  • Chen Y. et al. 2013. Investigative Ophthalmology & Visual Science. 54: 4351-7. PubMed ID: 23661368
  • den Hollander A.I. et al. 2008. Progress in Retinal and Eye Research. 27: 391-419. PubMed ID: 18632300
  • Fazzi E. et al. 2003. European Journal of Paediatric Neurology. 7: 13-22. PubMed ID: 12615170
  • Hanein S. et al. 2002. Human Mutation. 20: 322-3. PubMed ID: 12325031
  • Hanein S. et al. 2004. Human Mutation. 23: 306-317. PubMed ID: 15024725
  • Hejtmancik J.F. et a. 2008. American Journal of Human Genetics. 82:174-80. PubMed ID: 18179896
  • Henderson R.H. et al. 2009. Molecular Vision. 15: 2442-7. PubMed ID: 19956411
  • http://www.omim.org/
  • Human Gene Mutation Database (Bio-base).
  • Kohl S. et al. 2012. American Journal of Human Genetics. 91: 527-32. PubMed ID: 22901948
  • McKay G.J. et al. 2005. Investigative Ophthalmology & Visual Science. 46: 322-8. PubMed ID: 15623792
  • Perrault I. et al. 1996. Nature Genetics. 14: 461-4. PubMed ID: 8944027
  • Perrault I. et al. 2000. European Journal of Human Genetics : Ejhg. 8: 578-82. PubMed ID: 10951519
  • Piri N. et al. 2005. Ophthalmology 112: 159-66. PubMed ID: 15629837
  • Swaroop A. et al. 1999. Human Molecular Genetics. 8: 299-305. PubMed ID: 9931337
  • Udar N. et al. 2003. Human Mutation. 21: 170-1. PubMed ID: 12552567
  • Wang H. et al. 2015. Investigative Ophthalmology & Visual Science. 56: 3642-55. PubMed ID: 26047050
  • Wang X. et al. 2013. Journal of Medical Genetics. 50: 674-688. PubMed ID: 23847139
  • Weleber R.G. 2002. Ophthalmic Genetics. 23: 71-97. PubMed ID: 12187427
  • Weleber R.G. et al. 1993. Archives of Ophthalmology. 111: 1531-42. PubMed ID: 8240110
  • Weleber R.G. et al. 2013. Leber Congenital Amaurosis. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301475
  • Zhao C. et al. 2006. Human Genetics. 119: 617-23. PubMed ID: 16612614


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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2) Select Additional Test Options

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