Functional assessment enables the reclassification of CNGA3 gene variants related to achromatopsia based on ACMG/AMP criteria

Today, in the era of high-throughput genetic sequencing, and the number of gene therapy trials still increasing, standardized variant classification has become indispensible. It is important to ensure that the disease in a given patient is truly caused by the variants in the target gene of gene therapy. Guidelines for variant interpretation have been developed (i.e., ACMG/AMP classification) and are further standardized on a subject-, gene- or variant-specific basis. In this context, functional assessment of variants has become increasingly important. In our recently published study in Genetics in Medicine, we have further developed and applied a medium-throughput, luminescence bioassay based on the calcium-sensitive photoprotein aequorin to functionally evaluate 150 yet uncharacterized CNGA3 missense variants.

Biallelic variants in CNGA3 are a common cause of autosomal recessive achromatopsia, and CNGA3 encodes for the channel-forming A-subunit of the cone photoreceptor cyclic nucleotide gated channel. Variants were compiled from our own achromtopsia-related data set, as well as public databases (i.e., HGMD, LOVD, ClinVar).

The functional read-out of mutant versus wild-type homomeric CNGA3 channels allowed to define 125 variants as functionally abnormal and 25 variants as functionally normal. Adding this important information to the ACMG/AMP-classification, resulted in re-classification of 52/55 variants of uncertain significance (VUS) as either benign, likely benign or likely pathogenic, hereby reaching a VUS re-classification rate of 94.5%.

This allows for the first time to ultimately support the clinical variant interpretation in the majority of CNGA3-associated achromatopsia cases.

The project is part of the DFG-SPP2127 and funded by the German Research Council (Deutsche Forschungsgemeinschaft).

Link to the original publication: Functional evaluation allows ACMG/AMP-based re-classification of CNGA3 variants associated with achromatopsia.

^{In the picture from left top to bottom right: Solaki M., Reuter P., Kohl S., Wissinger B.}