Coupling of metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and resulting traits and diseases

Abstract

Genetic studies of the metabolome can uncover enzymatic and transport processes shaping human metabolism. Using WES-based rare variant aggregation testing to detect genes associated with levels of 1,294 plasma and 1,396 urine metabolites, we discovered 235 gene-metabolite associations, many previously unreported. Validation through genetic and new computational approaches (in silico gene knockouts in whole-body models of human metabolism) provided orthogonal evidence that population-based studies of rare, damaging variants in the heterozygous state permit inferences usually obtained from inborn errors of metabolism. Allelic series of functional variants in transporters responsible for transcellular sulfate reabsorption (SLC13A1, SLC26A1) exhibited graded effects on plasma sulfate and human height, and pinpointed alleles that strongly increased risk for dozens of musculoskeletal traits and diseases in the population. We present a powerful approach to identify new players in incompletely characterized human metabolic reactions, and to reveal metabolic readouts of disease risk to inform disease prevention and treatment.