Aniridia: genes and variants

Genes linked to Aniridia

• PAX6: Paired box protein Pax-6

  It orchestrates developmental gene programs in the eye, forebrain, and pancreatic endocrine system. Haploinsufficiency most classically causes aniridia and can also produce broader ocular, endocrine, and neurodevelopmental abnormalities.

  60 disease-causing and 96 uncertain variants in PAX6 are linked to Aniridia.

Weakly linked (only a few uncertain records): SOX2.

Where Aniridia variants cluster

• PAX6 Paired (positions 4–130): 46 of 60 disease-causing changes, 2.5× more than its size predicts.

Known disease-causing variants in Aniridia

Uncertain variants in Aniridia that look disease-causing

Which prediction tools work for Aniridia

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• CATVariant: 97 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• MetaLR: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 92 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 74 out of 100

Same protein, different disease

• Coloboma, ocular, autosomal dominant is also caused by PAX6 variants; they fall in the same places as the Aniridia variants (5 disease-causing).

Diseases related to Aniridia

• Irido-corneo-trabecular dysgenesis, also linked to PAX6
• Coloboma, ocular, autosomal dominant, also linked to PAX6
• Foveal hypoplasia 1, also linked to PAX6
• Coloboma of optic nerve, also linked to PAX6

Frequently asked questions

Which genes are linked to Aniridia?

In CATVariant, Aniridia is linked to 1 analyzed protein: PAX6 (Paired box protein Pax-6).

How many genetic variants are linked to Aniridia?

162 variants: 60 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 97 are of uncertain significance or have conflicting reports.

Which uncertain variants in Aniridia look disease-causing?

6 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example PAX6 G72R, PAX6 Q47H, PAX6 G13D, PAX6 G51E and PAX6 L32R. These are leads for expert review, not diagnoses.

Which variant effect predictor works best for Aniridia?

Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.74, based on 46 disease-causing and 17 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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