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Leber Congenital Amaurosis 4 (LCA4) via the AIPL1 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
AIPL1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8885AIPL181479 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. If the Sanger option is selected, 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.

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


  • Dana Talsness, PhD

Clinical Features and Genetics

Clinical Features

Leber congenital amaurosis (LCA) is an early-onset and most severe form of inherited retinopathy that is typically noticeable in the first year of life (Weleber et al. GeneReviews, 2013). Less severe forms are usually considered juvenile retinitis pigmentosa (Gu et al. Nature Genetics 17(2):194-197, 1997). LCA is clinically heterogeneous. One of the forms, LCA4 (LCA4; OMIM 604393) is characterized by peripheral retinal bone spicule-like pigmentation with prominent maculopathy, optic nerve pallor, profound loss of foveal as well as extrafoveal photoreceptors, which becomes more evident in patients older than 6 years of age, low visual acuity, ranging from 20/600 to no light perception, little or no detectable visual fields, abnormal or flat electroretinogram (ERG) and significant prevalence of bilateral keratoconus associated with cataract (Testa et al. Invest Ophthalmol Vis Sci 52(8):5618-5624, 2011). The estimated prevalence of LCA is 2-3 per 100,000 live births and accounts for 10-18% of congenital blindness (Fazzi et al. Eur J Paediatr Neurol 7(1):13-22, 2003).


LCA is a genetically heterogeneous disorder and is often inherited in an autosomal recessive manner. To date, approximately 19 genes have been implicated in the pathogenesis of different types of LCA (Weleber et al., 2013; Chen et al. Invest Ophthalmol Vis Sci 54(6):4351-4357, 2013). Together, these genes account for 70% of the LCA cases. These genes encode proteins that have a wide variety of retinal functions, such as photoreceptor morphogenesis, phototransduction, vitamin A cycling, guanine synthesis, and outer segment phagocytosis (den Hollander et al. Prog Retin Eye Res 27(4):391-419, 2008). Mutations in these genes cause not only LCA but also early-childhood and even adult-onset retinal degenerations (Weleber et al. Ophthalmic Genet 23(2):71-97, 2002).

Retina and pineal-specific AIPL1, which encodes Aryl hydrocarbon receptor interacting protein like-1, was the fourth gene identified as associated with LCA4 and is located on chromosome 17p13.1 (Sohocki et al. Nat Genet 24(1):79-83, 2000). A high prevalence of severe macular lesions was observed in LCA patients associated with AIPL1 mutations as compared to other genes implicated in LCA. The AIPL1 protein is known to be essential for visual phototransduction and shown to interact with the NUB1 protein (NEDD8 ultimate buster-1). The NUB1 protein stimulates the proteasomal degradation of proteins modified with the ubiquitin-like modifiers (UBLs) NEDD8 and FAT10. The AIPL1 protein is shown to bind the NUB1protein and prevents the NUB1-mediated proteasomal degradation. The amino acid residues 181-330 on AIPL1 are the binding sites for NUB1 and many LCA-associated AIPL1 mutations have been found at this site, indicating that the NUB1 and AIPL1 interaction is altered in LCA4 patients (Kanaya et al. Biochem Biophys Res Commun 317(3):768-773, 2004). These results suggest that the normal functioning of AIPL1 is important for cone and rod photoreceptor development and/or survival following differentiation (Akey et al. Hum Mol Genet 11(22):2723-2733, 2002). AIPL1 mutations are associated with ~7% of the LCA cases worldwide and also dominant retinopathy (Sohocki et al. Mol Genet Metab 70(2):142-150, 2000). Approximately, fifty disease-associated mutations have been identified in AIPL1, where the majority of them are missense/nonsense variants. Splicing, small insertion and deletions have also been reported (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Sohocki et al. (2000) identified causative AIPL1 mutations in ~20% (3/14) of the LCA families (Sohocki et al. Nat Genet 24(1):79-83, 2000). A study done by Li et al. (2011) found AIPL1 mutations in 1.1 % (1/87) of the unrelated Chinese patients with Leber congenital amaurosis, whereas16.1% (14/87) cases had GUCY2D mutations (Li et al. PLoS One 6(5): e19458, 2011). Among all LCA genes, AIPL1 and GUCY2D are known to function in visual phototransduction (den Hollander, et al. Prog Retin Eye Res 27(4): 391-419, 2008).

No gross deletions or duplications have been reported to date in AIPL1 (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the AIPL1 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

Candidates for this test are all LCA patients, in particular patients with symptoms consistent of LCA4, family members of patients who have known mutations and carrier testing for at-risk family members. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in AIPL1.


Official Gene Symbol OMIM ID
AIPL1 604392
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Leber Congenital Amaurosis 4 AR 604393

Related Tests

Leber Congenital Amaurosis 14 (LCA14) or Early Onset Retinal Dystrophy (EORD) and Juvenile Retinitis Pigmentosa via the LRAT Gene
Leber Congenital Amaurosis Panel
Leber Congenital Amaurosis via the CRX Gene
Retinitis Pigmentosa Panel


  • Akey, D.T. (2002).  PubMed ID: 12374762
  • Chen, Y. et al. (2013). PubMed ID: 23661368
  • den Hollander AI, Roepman R, Koenekoop RK, Cremers FPM. 2008. Leber congenital amaurosis: genes, proteins and disease mechanisms. Prog Retin Eye Res 27: 391–419. PubMed ID: 18632300
  • Fazzi, E. et al. (2003). PubMed ID: 12615170
  • Gu, S. M. et.al. (1997). PubMed ID: 9326941
  • Human Gene Mutation Database (Bio-base).
  • Kanaya, K. et al. (2004).  PubMed ID: 15081406
  • Li L, Xiao X, Li S, Jia X, Wang P, Guo X, Jiao X, Zhang Q, Hejtmancik JF. 2011. Detection of Variants in 15 Genes in 87 Unrelated Chinese Patients with Leber Congenital Amaurosis. PLoS ONE 6: e19458. PubMed ID: 21602930
  • Sohocki, M.M. et al. (2000). “Prevalence of AIPL1 mutations in inherited retinal degenerative disease.” Mol Genet Metab 70(2):142-150. PubMed ID: 10873396
  • Sohocki, M.M. et al. (2000).  PubMed ID: 10615133
  • Testa, F. et al. (2011). PubMed ID: 21474771
  • Weleber RG. 2002. Infantile and childhood retinal blindness: a molecular perspective (The Franceschetti Lecture). Ophthalmic Genet. 23: 71–97. PubMed ID: 12187427
  • Weleber, RG et.al. (2013). PubMed ID: 20301475


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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