Poster Presentation GENEMAPPERS 2026

Evaluating functional assay data and its value in the curation of CYP1B1 variants (#73)

Johanna Hadler 1 , Patricia Graham 1 2 , Stuart W Tompson 3 , Francesca Pasutto 4 , Kristina Whisenhunt 3 , Owen Siggs 5 , Subhabrata Chakrabarti 6 , Terri L Young 3 , David A Mackey 7 , Andrew Dubowsky 8 , Emmanuelle Souzeau 1 , Kathryn P Burdon 2
  1. Department of Ophthalmology, Flinders University, Bedford Park, SA, Australia
  2. Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
  3. Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
  4. Institute of Human Genetics, Friedrich-Alexander-Universitätsklinikum Erlangen-Nürnberg, Erlangen, Bavaria, Germany
  5. Garvan Institute of Medical Research, Sydney, NSW, Australia
  6. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, India
  7. Centre for Ophthalmology and Vision Sciences, Lions Eye Institute, University of Western Australia, Perth, WA, Australia
  8. SA Pathology, Adelaide, SA, Australia

Biallelic variants in the CYP1B1 gene are the main cause for Primary Congenital Glaucoma (PCG). Onset is usually in the first 3 years of life, resulting in irreversible vision loss.

The Clinical Genome Resource (ClinGen) Glaucoma Variant Curation Expert Panel (VCEP) have recently developed specifications for the clinical classification of CYP1B1 variants modelled on the widely used ACMG/AMP variant classification guidelines. Functional assays can be an important source of evidence when determining pathogenicity of variants.

Here we present our evaluation of functional evidence for CYP1B1 variants. We reviewed the literature for published assays and determined whether the relevant mechanism of disease was tested. We decided that application of benign functional evidence was not appropriate for this gene based on incomplete understanding of disease mechanism. We used 28 control variants (classified as benign or pathogenic without the application of functional evidence) to establish assay thresholds for functional evidence application and calculate OddsPaths for evidence strength, combining assays where possible after comparing characteristics.

We have reviewed 17 reports of which 3 were found to discriminate between pathogenic and benign variants and we were able to apply supporting pathogenic evidence to the appropriate variants. For the other assays we were unable to reach a significant OddsPath or establish an appropriate threshold for pathogenic impact. The VCEP recommends the use of suitable pathogenic and benign controls when planning assays to ensure the ability to use the results in variant curation.

The VCEP has now completed preliminary curation of 59 CYP1B1 variants using the refined specifications and confirmed the classification of 46 previously recorded on ClinVar, reclassified 4 variants and added 9 new variants to ClinVar.

The remaining published variants are now being curated and will be published on ClinVar to help standardise variant classification and benefit management of patients in a clinical setting.