# Structure-function analysis of CNGA3-associated achromatopsia patient variants complements clinical genomics in pathogenicity determination

## TL;DR

This study uses 3D protein structure analysis to determine the pathogenicity of CNGA3 gene variants in achromatopsia patients, improving diagnosis and treatment options.

## Contribution

A novel proteoform-based structure-function analysis is introduced to assess the pathogenicity of CNGA3 variants with unknown significance.

## Key findings

- 86.4% of CNGA3 variants of unknown significance showed similar functional consequences to known pathogenic variants.
- Six proteotypic groups were identified based on spatial proximity and functional consequences in the CNGA3 protein structure.
- The analysis supports gene supplementation as a potential therapy for CNGA3-associated achromatopsia.

## Abstract

Achromatopsia is an autosomal recessive genetic disease, and 95% of achromatopsia patients carry pathogenic mutations in the CNGA3 and CNGB3 genes. Once translated, these genes function together by forming a cone photoreceptor CNG channel protein complex.

There are 150 CNGA3 missense variants reported in achromatopsia patients, but the pathogenicity of 103 variants remains unknown due to inconclusive genetic information. Here, we present clinical features of a novel CNGA3 variant in an achromatopsia patient and demonstrate its pathogenicity by a three-dimensional (3D) proteoform-based structure-function analysis. We first identified six proteotypic groups using 47 pathogenic missense variants with distinctive functional consequences by mapping their spatial proximity in a 3D protein structure. This meta-analysis was further applied to 103 missense variants of unknown significance (VUS) found in patients with achromatopsia. Strikingly, 86.4% of VUS had similar/identical functional consequence to nearby pathogenic variants, which suggested their likely pathogenicity and potential molecular pathology. The distinct proteotypic consequence of CNGA3 mutants shown in our analysis strongly supported the notion that gene supplementation may be the most widely applicable therapeutic option for CNGA3-associated achromatopsia patients.

Thus, proteoform-based analysis can be a valuable approach for assessing novel variants and complement clinical genomics in its utilization.

The online version contains supplementary material available at 10.1186/s13023-025-03792-3.