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

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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The work of N.S., M.S., O.B., M.W., M.K., Pe.S., and A.K. was funded by German Research Foundation (DFG) project ID 431984000 (SFB 1453). N.S. and Y.L. were supported by DFG KO 3598/4-2 (to A.K.). Germany's Excellence Strategy (CIBSS, EXC-2189, project ID 390939984) supported the work of M.K., M.S., and A.K.. The work of J.H., D.F., and A.K. was supported by DFG project ID 499552394 (SFB 1597/1). S.P. was funded by H2020 MSCA-ITN-2019 ID:860977 (TrainCKDis). Pe.S. was supported by DFG SE 2407/3-1. The work of U.T.S. was supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant 01ZX1912B). The work of Pa.S. was supported by DFG Project-ID 1050086601 (SCHL 2292/2-1). I.T. was funded by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (#757922), the Science Foundation Ireland under Grant number 12/RC/2273-P2, and a Horizon Europe grant (#101080997). Genotyping and urine metabolomics in the GCKD study were supported by Bayer Pharma. Plasma metabolomics has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement no. 115974. The JU receives support from the European Union's Horizon 2020 research and innovation program and the EFPIA and the JDRF. Any dissemination of results reflects only the authors' view; the JU is not responsible for any use that may be made of the information it contains. The GCKD study was and is supported by the BMBF (FKZ 01ER 0804, 01ER 0818, 01ER 0819, 01ER 0820 and 01ER 0821) and the KfH Foundation for Preventive Medicine. Unregistered grants to support the study were provided by corporate sponsors (listed at https://gckd.org). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All ethics committees of the participating centers listed below gave ethical approval for the GCKD study and this work: Universities or Medical Faculties of Aachen, Berlin, Erlangen, Freiburg, Hannover, Heidelberg, Jena, München, Würzburg I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript.