为了最大限度地发挥精准医学方法的影响，识别疾病背后的遗传变异并准确量化其功能影响至关重要。 von Hippel-Lindautumor 抑制基因（VHL）是体现变异解释挑战的一个基因。 VHL 编码 E3 泛素连接酶，可调节细胞对缺氧的反应。 VHL 种系致病性变异使患者易患肿瘤，包括透明细胞肾细胞癌 (ccRCC) 和嗜铬细胞瘤，并且在散发性肾癌中经常观察到体细胞 VHL 突变。在这里，我们优化并应用饱和基因组编辑来分析 VHL 编码序列中几乎所有可能的单核苷酸变异 (SNV)。为了描述机制，我们量化了 mRNA 剂量效应并比较了同基因细胞系中的功能效应。 2,268 个 VHL SNV 的功能评分以完美的准确性识别出驱动 ccRCC 的一组核心致病等位基因，告知不同肿瘤类型的差异风险，并揭示变异影响功能的新机制。这些结果可直接用于对临床上遇到的 VHL 变异进行分类，并说明精确的功能测量如何解决整个基因的多效性和剂量依赖性基因型-表型关系。© 2024。作者。

To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and to accurately quantify their functional effects. A gene exemplifying the challenge of variant interpretation is the von Hippel-Lindautumor suppressor (VHL). VHL encodes an E3 ubiquitin ligase that regulates the cellular response to hypoxia. Germline pathogenic variants in VHL predispose patients to tumors including clear cell renal cell carcinoma (ccRCC) and pheochromocytoma, and somatic VHL mutations are frequently observed in sporadic renal cancer. Here we optimize and apply saturation genome editing to assay nearly all possible single-nucleotide variants (SNVs) across VHL's coding sequence. To delineate mechanisms, we quantify mRNA dosage effects and compare functional effects in isogenic cell lines. Function scores for 2,268 VHL SNVs identify a core set of pathogenic alleles driving ccRCC with perfect accuracy, inform differential risk across tumor types and reveal new mechanisms by which variants impact function. These results have immediate utility for classifying VHL variants encountered clinically and illustrate how precise functional measurements can resolve pleiotropic and dosage-dependent genotype-phenotype relationships across complete genes.© 2024. The Author(s).