Expanding the Atlas of Functional Missense Variation for Human Genes

Abstract

Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon-mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features, and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.

Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry

“…Despite thousands of known common variants that reproducibly associate with disease, the causal variant is rarely understood. Deep mutational scans present one path toward predicting the functional consequences of these variants, with some proposals even envisioning an understanding of the comprehensive human SNP-ome …”

“…Deep mutational scans present one path toward predicting the functional consequences of these variants, with some proposals even envisioning an understanding of the comprehensive human SNP-ome. 77 Deep mutational scanning experiments have begun to outperform other predictive approaches in some cases. For example, a scan of 2000 substitutions in the BRCA1 RING domain enabled a quantitative map of effects on E3 ubiquitin ligase activity and BARD1 RING domain binding activity.…”

CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation

“…They used random codon replacement to generate variants on human CALM1 and they assessed the ability of each variant to rescue a yeast strain carrying a temperature‐sensitive allele of the yeast calmodulin orthologue CMD1 (Sun et al, ). The assay output was scaled between 0 (no growth) and 1 (wild‐type‐like growth) and that score was able to separate pathogenic from nonpathogenic variants (Weile et al, ). Two replicates for each measurement were used to estimate the experimental standard deviation ( SD ).…”

Insights into protein structure, stability and function from saturation mutagenesis

“…Another comprehensive effort to understand and obtain mutational phenotypes for single-site mutants for human proteins, combined random codon-mutagenesis and multiplexed functional variation assays with computational imputation and refinement to produce exhaustive maps for human missense variants [49]. The framework was applied to four proteins: UBE2I, SUMO1, TPK1, and CALM1/2/3.…”