Gajardo Macarena, Guerrero José Luis, Poblete Bárbara, Bayyad Esperanza, Castro Ignacio, Maturana Jorge, Tobar Jaime, Faúndes Víctor, Krall Paola
Facultad de Medicina, Universidad de Chile, Santiago, Chile.
Servicio de Nefrología, Hospital Luis Calvo Mackenna, Santiago, Chile.
Front Mol Biosci. 2025 Apr 23;12:1561380. doi: 10.3389/fmolb.2025.1561380. eCollection 2025.
Advanced genetic strategies have transformed our understanding of the genetic basis and diagnosis of many phenotypes, including rare diseases. However, missense variants (MVs) are frequently identified and often classified as variants of uncertain significance (VUS). Although changes in protein free energy (ΔΔG) were recently proposed as a tool for VUS classification, no objective cut-offs exist to distinguish between benign and pathogenic variants.
We utilized the computational tool mCSM to calculate ΔΔG and predict the impact of MVs on protein stability. Specifically, we systematically analyzed the ΔΔG of MVs in IFT140 to identify those potentially pathogenic and associated with Mainzer-Saldino syndrome (MSS). To this end, we evaluated ΔΔG in IFT140 MVs sourced from ClinVar, gnomAD, and MSS patients, aiming to resolve the diagnosis of MSS in a child with a novel homozygous IFT140 variant, initially reported as a VUS.
IFT140 MVs from MSS patients showed lower ΔΔG values than those reported in gnomAD individuals (-1.389 vs. -0.681 kcal/mol; p = 0.0031). A ROC curve demonstrated strong discriminative ability (AUC = 0.8488; p = 0.0002), and a ΔΔG cut-off of -1.3 kcal/mol achieving 50% sensibility and 90% specificity. The analysis of ClinVar IFT140 variants classified as VUS, showed that 75/323 (23%) presented ΔΔG values below the cut-off. In the child clinically suspicious of MSS, this cut-off allowed the reclassification of the VUS (IFT140:p.W80C; ΔΔG = -1.745 kcal/mol) as likely pathogenic, which confirmed the diagnosis molecularly.
Our findings demonstrate that ΔΔG analysis can effectively distinguish potentially pathogenic variants in IFT140, enabling confirmation of MSS. The established cut-off of -1.3 kcal/mol showed strong discriminative power, aiding in the reclassification of VUS identified in IFT140. This approach highlights the utility of protein stability predictions in resolving diagnostic uncertainty in rare diseases.
先进的基因策略改变了我们对包括罕见病在内的许多表型的遗传基础和诊断的理解。然而，错义变异（MVs）经常被发现，且常常被归类为意义未明的变异（VUS）。尽管最近有人提出蛋白质自由能变化（ΔΔG）可作为VUS分类的工具，但目前尚无区分良性和致病性变异的客观临界值。
我们利用计算工具mCSM来计算ΔΔG，并预测MVs对蛋白质稳定性的影响。具体而言，我们系统分析了IFT140中MVs的ΔΔG，以识别那些可能致病并与梅恩泽尔 - 萨尔迪诺综合征（MSS）相关的变异。为此，我们评估了来自ClinVar、gnomAD和MSS患者的IFT140 MVs中的ΔΔG，旨在对一名患有新型纯合IFT140变异（最初报告为VUS）的儿童进行MSS诊断。
来自MSS患者的IFT140 MVs的ΔΔG值低于gnomAD个体报告的值（-1.389对-0.681千卡/摩尔；p = 0.0031）。ROC曲线显示出很强的判别能力（AUC = 0.8488；p = 0.0002），且ΔΔG临界值为-1.3千卡/摩尔时，敏感性达到50%，特异性达到90%。对ClinVar中分类为VUS的IFT140变异进行分析发现，75/323（23%）的ΔΔG值低于临界值。在临床上怀疑患有MSS的儿童中，该临界值使得VUS（IFT140:p.W80C；ΔΔG = -1.745千卡/摩尔）被重新分类为可能致病，从而在分子水平上确诊。
我们的研究结果表明，ΔΔG分析能够有效区分IFT140中潜在的致病性变异，从而确诊MSS。所确定的-1.3千卡/摩尔的临界值显示出很强的判别能力，有助于对IFT140中鉴定出的VUS进行重新分类。这种方法突出了蛋白质稳定性预测在解决罕见病诊断不确定性方面的实用性。
