BACKGROUND For the majority of rare clinical missense variants, pathogenicity status cannot currently be classified. Classical homocystinuria, characterized by elevated homocysteine in plasma and urine, is caused by variants in the cystathionine beta-synthase (CBS) gene, most of which are rare. With early detection, existing therapies are highly effective. METHODS Damaging CBS variants can be detected based on their failure to restore growth in yeast cells lacking the yeast ortholog CYS4. This assay has only been applied reactively, after first observing a variant in patients. Using saturation codon-mutagenesis, en masse growth selection, and sequencing, we generated a comprehensive, proactive map of CBS missense variant function. RESULTS Our CBS variant effect map far exceeds the performance of computational predictors of disease variants. Map scores correlated strongly with both disease severity (Spearman's ϱ = 0.9) and human clinical response to vitamin B6 (ϱ = 0.93). CONCLUSIONS We demonstrate that highly multiplexed cell-based assays can yield proactive maps of variant function and patient response to therapy, even for rare variants not previously seen in the clinic.

中文翻译：

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胱硫醚β-合酶的主动基因型到患者表型图谱。

背景 对于大多数罕见的临床错义变异，目前无法对致病性状态进行分类。经典同型半胱氨酸尿症的特征是血浆和尿液中同型半胱氨酸升高，是由胱硫醚β-合酶（CBS）基因变异引起的，其中大多数是罕见的。通过早期发现，现有疗法非常有效。方法 破坏性 CBS 变体可以根据其在缺乏酵母直系同源物 CYS4 的酵母细胞中无法恢复生长来检测。在首次观察到患者的变异后，该检测仅被反应性地应用。使用饱和密码子诱变、整体生长选择和测序，我们生成了 CBS 错义变异功能的全面、主动的图谱。结果我们的 CBS 变异效应图远远超过了疾病变异的计算预测因子的性能。地图评分与疾病严重程度 (Spearman's ϱ = 0.9) 和人类对维生素 B6 的临床反应 (ϱ = 0.93) 密切相关。结论我们证明，高度多重的基于细胞的检测可以产生变异功能和患者对治疗反应的主动图谱，即使对于以前在临床中未见过的罕见变异也是如此。