Aniridia via The PAX6 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits


Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1483 PAX6$910.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

The overall PAX6 mutation detection rate by sequencing in different populations varied from 30-90% (Zhang et al. 2011; Villarroel et al. 2008; Park et al. 2012).

See More

See Less

Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 PAX6$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price













Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features

Aniridia (AN) is a rare congenital bilateral panocular disorder defined as iris aplasia or hypoplasia resulting in reduced visual acuity and nystagmus (Nelson et al.1984). It can be isolated or, in rare cases, associated with multiple ocular abnormalities such as cataracts, glaucoma (Mihelec et al. 2008), Peter’s anomaly (Hanson et al. 1994), neurodevelopmental abnormalities (Dansault et al. 2007) and WAGR syndrome(Wilms Tumor-Aniridia-Genitourinary Anomalies-Mental Retardation). The estimated prevalence of AN is about 1 in 40,000 to 100,000 (Hingorani et al. 2008) and is unknown for WAGR syndrome.


Approximately two-thirds of AN cases are familial with autosomal dominant inheritance and the remaining one third are sporadic with no previous family history (Nelson et al. 1984; Ton et al. 1991). PAX6 (paired box gene 6; OMIM 607108), which is located on chromosome band 11p13, has been identified as the major candidate gene, if not the only gene, for AN. PAX6 encodes a highly conserved transcription factor that comprises a paired domain, a homeodomain, and a serine/threonine-rich C-terminal domain, and plays an essential role in eye development (Kokotas and Petersen 2010). Mutation frequency is higher in the paired domain as compared to the rest of the gene. Transitions (C>T) at four CpG dinucleotides in exons 8, 9, 10 and 11 are major mutation hotspots and account for ~50% of PAX6 nonsense mutations (Tzoulaki et al. 2005). So far, the vast majority of PAX6 mutations (94%) introduce a premature termination codon (PTC) into the PAX6 coding region and causing haploinsufficiency, which has been the major pathomechanism for AN (Tzoulaki et al. 2005 ; Kokotas and Petersen 2010). PAX6 overexpression is also implicated in severe eye abnormalities (Schedl et al. 1996). Over 330 causative mutations have been identified in PAX6 (Brown et al. 1998). Neonates with sporadic AN carry a risk of developing Wilms' tumor (WT) as part of WAGR syndrome (Nelson et al. 1984), due to the contiguous deletion of WT susceptibility gene (WT1) and PAX6, which are 700kb apart (Nelson et al. 1984 ; Fischbach et al. 2005). A high frequency of chromosomal rearrangements have been associated with both sporadic and familial AN (Crolla and van Heyningen 2002 ; Lim et al. 2012).

Testing Strategy

This test involves bidirectional DNA Sanger sequencing of all coding exons of the PAX6 gene. The full coding region of each exon plus ~10 bp of flanking non-coding DNA on either side are sequenced. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.

Indications for Test

Patients with symptoms suggestive of Aniridia, Coloboma of optic nerve,  Foveal hypoplasia and presenile cataract syndrome, Optic nerve hypoplasia and aplasia are candidates.


Official Gene Symbol OMIM ID
PAX6 607108
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Genetic Counselors
  • Brown A, McKie M, Heyningen V Van, Prosser J. 1998. The human PAX6 mutation database. Nucleic acids research 26: 259–264. PubMed ID: 9399848
  • Crolla JA, Heyningen V van. 2002. Frequent chromosome aberrations revealed by molecular cytogenetic studies in patients with aniridia. The American Journal of Human Genetics 71: 1138–1149. PubMed ID: 12386836
  • Dansault A, David G, Schwartz C, Jaliffa C, Vieira V, Houssaye G de la, Bigot K, Catin F, Tattu L, Chopin C. 2007. Three new PAX6 mutations including one causing an unusual ophthalmic phenotype associated with neurodevelopmental abnormalities. Molecular vision 13: 511. PubMed ID: 17417613
  • Fischbach BV. 2005. WAGR Syndrome: A Clinical Review of 54 Cases. PEDIATRICS 116: 984–988. PubMed ID: 16199712
  • Hanson IM. et al. 1994. Nature Genetics. 6: 168-73. PubMed ID: 8162071
  • Hingorani M, Williamson KA, Moore AT, Heyningen V van. 2009. Detailed ophthalmologic evaluation of 43 individuals with PAX6 mutations. Investigative ophthalmology & visual science 50: 2581–2590. PubMed ID: 19218613
  • Kokotas H, Petersen MB. 2010. Clinical and molecular aspects of aniridia. Clin. Genet. 77: 409–420.
    PubMed ID: 20132240
  • Lim HT, Seo E-J, Kim G-H, Ahn H, Lee H, Shin KH, Lee J-K, Yoo H-W. 2012. Comparison between aniridia with and without PAX6 mutations: clinical and molecular analysis in 14 Korean patients with aniridia. Ophthalmology 119: 1258–1264. PubMed ID: 22361317
  • Mihelec M, St Heaps L, Flaherty M, Billson F, Rudduck C, Tam PPL, Grigg JR, Peters GB, Jamieson RV. 2008. Chromosomal rearrangements and novel genes in disorders of eye development, cataract and glaucoma. Twin Res Hum Genet 11: 412–421. PubMed ID: 18637741
  • Nelson LB, Spaeth GL, Nowinski TS, Margo CE, Jackson L. 1984. Aniridia. A review. Surv Ophthalmol 28: 621–642. PubMed ID: 6330922
  • Park SH, Kim MS, Chae H, Kim Y, Kim M. 2012. Molecular analysis of the PAX6 gene for congenital aniridia in the Korean population: Identification of four novel mutations. Molecular vision 18: 488. PubMed ID: 22393275
  • Schedl A, Ross A, Lee M, Engelkamp D, Rashbass P, Heyningen V van, Hastie ND. 1996. Influence of PAX6 gene dosage on development: overexpression causes severe eye abnormalities. Cell 86: 71–82. PubMed ID: 8689689
  • Ton CC, Hirvonen H, Miwa H, Weil MM, Monaghan P, Jordan T, Heyningen V van, Hastie ND, Meijers-Heijboer H, Drechsler M. 1991. Positional cloning and characterization of a paired box- and homeobox-containing gene from the aniridia region. Cell 67: 1059–1074. PubMed ID: 1684738
  • Tzoulaki I. et al. 2005. Bmc Genetics. 6: 27. PubMed ID: 15918896
  • Villarroel CE, Villanueva-Mendoza C, Orozco L, Alcántara-Ortigoza MA, Jiménez DF, Ordaz JC, González-del Angel A. 2008. Molecular analysis of the PAX6 gene in Mexican patients with congenital aniridia: report of four novel mutations. Molecular vision 14: 1650. PubMed ID: 18776953
  • Zhang X, Wang P, Li S, Xiao X, Guo X, Zhang Q. 2011. Mutation spectrum of PAX6 in Chinese patients with aniridia. Molecular vision 17: 2139. PubMed ID: 21850189
Order Kits

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options

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.
  • 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.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
loading Loading... ×