PAX6 rs121913342: Understanding Congenital Aniridia Variants
The rs121913342 variant is a rare genetic change located within the PAX6 gene. It is associated with congenital aniridia, a condition characterized by the underdevelopment or absence of the iris in the eye.
What each genotype means
Typical PAX6 gene function
This genotype represents the common, non-variant form of the PAX6 gene. Individuals with this profile do not carry the specific nonsense mutation associated with congenital aniridia at this location.
This is the most common genotype found in the general population.
PAX6-related ocular risk
This genotype indicates the presence of a heterozygous nonsense mutation in the PAX6 gene, which is known to cause haploinsufficiency and is associated with congenital aniridia. Because PAX6 is a master regulator of eye development, this variant can lead to a spectrum of ocular conditions including iris hypoplasia, foveal hypoplasia, and other developmental eye anomalies. Clinical presentation can be highly variable even within families, and you should consult with an ophthalmologist or genetic counselor to discuss your specific clinical findings.
This specific variant is extremely rare, with a frequency reported at less than 0.00001 in large population databases like gnomAD.
What is the rs121913342 Variant?
The rs121913342 variant is a specific change in the DNA sequence of the PAX6 gene. In genetic terms, this variant is classified as a nonsense mutation. A nonsense mutation introduces a premature stop signal in the genetic instructions, which typically causes the cell to stop building the protein before it is complete. Because the resulting protein is truncated, it is often unstable or nonfunctional. This specific variant is recognized in clinical databases for its role in disrupting the normal production of the PAX6 protein, which is essential for proper ocular development. It sits on the short arm of chromosome 11, a region known to be critical for the regulation of several developmental processes.
The Role of the PAX6 Gene
The PAX6 gene provides the blueprint for a transcription factor, a type of protein that acts like a master switch to control the activity of other genes. During embryonic development, PAX6 is vital for the formation of the eyes, the brain, and the spinal cord. By binding to specific regions of DNA, the PAX6 protein ensures that tissues develop in the correct sequence and structure. When one copy of the PAX6 gene is altered or missing, the body may not produce enough functional protein to support normal development. This state, known as haploinsufficiency, is the primary mechanism behind many PAX6-related conditions, including the development of the iris and other structures within the eye.
Research and Clinical Associations
Scientific research has consistently linked truncating mutations in the PAX6 gene to congenital aniridia. Aniridia is a condition where the iris, the colored part of the eye, is partially or completely missing. Studies indicate that these mutations are often inherited in an autosomal dominant pattern, meaning a single altered copy of the gene is sufficient to cause the condition. While the evidence linking specific nonsense variants like rs121913342 to aniridia is strong in a clinical context, the overall prevalence of this specific variant is extremely low. Researchers use these findings to better understand how gene dosage affects human development, though clinical presentation can vary even among individuals with similar genetic changes.
Population Frequency and Genetic Context
The rs121913342 variant is classified as extremely rare in global population databases such as gnomAD, with a frequency reported at less than 0.00001. Because it is so uncommon, it is not a variant typically found in the general population or through routine ancestry testing. Its presence is usually identified in clinical settings when investigating the cause of congenital eye anomalies. The rarity of this variant underscores that it is not a common polymorphism but rather a rare pathogenic variant. Geneticists emphasize that the presence of such a variant is a significant clinical finding that requires professional interpretation by a genetic counselor or medical geneticist to understand its implications for an individual or their family.
Navigating Genetic Information
If you or a family member have been identified as a carrier of a PAX6 variant, it is important to consult with a healthcare professional, such as an ophthalmologist or a clinical geneticist. Genetic information can be complex, and clinical outcomes are influenced by many factors beyond a single DNA change. This information is for educational purposes and should not be used to diagnose or treat any medical condition. You cannot 'fix' or 'change' a genetic variant, but understanding your genetic status can help you and your doctor make informed decisions about eye health monitoring and long-term care. Always discuss any concerns about genetic test results with a qualified clinician who can provide context specific to your personal and family medical history.
How common is this variant?
The rs121913342 variant is extremely rare in the general population, with a frequency of less than 0.00001 in gnomAD.
Frequently asked questions
What is congenital aniridia?
Congenital aniridia is a condition present from birth where the iris of the eye is underdeveloped or missing. It is often caused by mutations in the PAX6 gene that affect eye development.
Is rs121913342 common?
No, this variant is extremely rare. It is not a common genetic trait found in the general population.
Can I test for this variant?
Clinical genetic testing for PAX6 is typically performed by medical professionals when there is a clinical suspicion of aniridia or related eye conditions. It is not a standard part of recreational ancestry or wellness DNA kits.
What should I do if I have a PAX6 variant?
If you have been informed that you carry a PAX6 variant, you should schedule an appointment with a clinical geneticist or an ophthalmologist. They can provide a proper evaluation and discuss what this means for your health.
Sources & further reading
Educational information only, last refreshed 9/18/2026. Not medical advice — these associations describe population statistics, not individual predictions.
Curious what your genotype is for rs121913342?
Upload a raw DNA file from 23andMe, AncestryDNA, MyHeritage, or FamilyTreeDNA and see this variant — plus thousands more — interpreted in your full report.
Get my report — $29Related variants in PAX6
Pathogenic loss-of-function nonsense variant in PAX6 resulting in congenital absence of the iris (aniridia) and associated anterior segment dysgenesis.
A high-penetrance single nucleotide substitution disrupting PAX6 function and leading to aniridia and congenital anterior segment dysgenesis.
A classic nonsense mutation (p.Arg240Ter) in the PAX6 master regulator of eye development leading to haploinsufficiency and congenital aniridia.
Intronic regulatory polymorphism in the ocular master regulator PAX6 associated with axial length variation and myopia development.
Classical stop-gain variant in PAX6 leading to haploinsufficiency and congenital aniridia with associated foveal hypoplasia and decreased visual acuity.
Pathogenic missense variant in PAX6 causing developmental ocular malformations including aniridia and congenital ocular coloboma.