Xiao Binghe, Zhang Shaohua, Ainiwaer Maierdanjiang, Liu Houyi, Ning Li, Hong Yingying, Sun Yang, Ji Yinghong
Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.
Key laboratory of Myopia and Related Eye Diseases, NHC, Shanghai, China.
BMJ Open Ophthalmol. 2025 Jan 14;10(1):e001906. doi: 10.1136/bmjophth-2024-001906.
We compared the protein structure and pathogenicity of clinically relevant variants of the gene with AlphaFold2 (AF2), Alpha Missense (AM), and ThermoMPNN for the first time.
The sequences of clinically relevant Cog4 missense variants (one novel identified p.Y714F and three pre-existing p.G512R, p.R729W and p.L769R from Uniprot Q9H9E3) were imported into AF2 for protein structural prediction, and the pathogenicity was estimated using AM and ThermoMPNN. Different pathogenicity metrics were aggregated with principal component analysis (PCA) and further analysed at three levels (amino acid position, substitution and post-translation) based on all possible Cog4 missense variants (n=14 915).
Localised protein structural impact including change of conformation and amino acid polarity, breakage of hydrogen bond and salt-bridge, and formation of alpha-helix were identified among clinically relevant Cog4 variants. The global structural comparison with multidimensional scaling demonstrated variants with similar protein structures (AF2) tended to exhibit similar clinical and biological phenotypes. The Cog4 p.Y714F variant exhibited greater protein structural similarity to mutated Cog4 found in Saul‒Wilson syndrome (p.G512R) and shared similar clinical phenotype (congenital cataract and psychomotor retardation). PCA of included pathogenic metrics demonstrated p.Y714F occurred at a critical position in Cog4 amino acid sequence with disrupted post-translational phosphorylation.
Deep learning algorithms, including AF2, AM and ThermoMPNN, can be useful for evaluating variant of uncertain significance (VUS) by structural and pathogenicity prediction. Despite classified as VUS (American College of Medical Genetics and Genomics criteria: PM1, PP4), the pathogenicity in this Cog4 variant cannot be ruled out and warrants further investigation.
我们首次使用AlphaFold2（AF2）、Alpha Missense（AM）和ThermoMPNN比较了该基因临床相关变体的蛋白质结构和致病性。
将临床相关的Cog4错义变体序列（一个新鉴定的p.Y714F以及来自Uniprot Q9H9E3的三个已有的p.G512R、p.R729W和p.L769R）导入AF2进行蛋白质结构预测，并使用AM和ThermoMPNN评估致病性。基于所有可能的Cog4错义变体（n = 14915），通过主成分分析（PCA）汇总不同的致病性指标，并在三个水平（氨基酸位置、取代和翻译后）进行进一步分析。
在临床相关的Cog4变体中发现了局部蛋白质结构影响，包括构象和氨基酸极性的变化、氢键和盐桥的断裂以及α-螺旋的形成。与多维尺度分析的全局结构比较表明，具有相似蛋白质结构（AF2）的变体往往表现出相似的临床和生物学表型。Cog4 p.Y714F变体与在索尔-威尔逊综合征中发现的突变Cog4（p.G512R）表现出更大的蛋白质结构相似性，并具有相似的临床表型（先天性白内障和精神运动发育迟缓）。纳入的致病性指标的PCA表明，p.Y714F发生在Cog4氨基酸序列的关键位置，翻译后磷酸化受到破坏。
包括AF2、AM和ThermoMPNN在内的深度学习算法可用于通过结构和致病性预测来评估意义未明的变体（VUS）。尽管根据美国医学遗传学与基因组学学会标准被分类为VUS（PM1，PP4），但该Cog4变体的致病性不能排除，值得进一步研究。
