Pathogenic paralogous variants can be used to apply the ACMG PS1 and PM5 variant interpretation criteria

Purpose The majority of missense variants in clinical genetic tests are classified as variants of uncertain significance. Broadening the evidence of the PS1 and PM5 criteria has the potential to increase conclusive variant interpretation. Methods We hypothesized that incorporation of pathogenic missense variants in conserved residues across paralogous genes can increase the number of variants where ACMG PS1/PM5 criteria can be applied. We mapped over 2.5 million pathogenic and general population variants from ClinVar, HGMD, and gnomAD databases onto 9,990 genes and aligned these by gene families. Subsequently, we developed a novel framework to extend PS1/PM5 by incorporating pathogenic paralogous variants annotations (para-PS1/PM5). Results We demonstrate that para-PS1/PM5 criteria increase the number of classifiable amino acids 3.6-fold compared to PS1 and PM5. Across all gene families with at least two disease-associated genes, the calculated likelihood ratios suggest moderate evidence for pathogenicity. Moreover, for 36 genes, the extended para-PS1/PM5 criteria reach strong evidence level. Conclusion We show that single pathogenic paralogous variants incorporation at paralogous protein positions increases the applicability of the PS1 and PM5 criteria, likely leading to a reduction of variants of uncertain significance across many monogenic disorders. Future iterations of the ACMG guidelines may consider para-PS1 and para-PM5. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Funding for this work was provided by the German Federal Ministry for Education and Research (BMBF, Treat-ION, 01GM1907D) to D.L., T.B., and P.M., by the BMBF (Treat-Ion2, 01GM2210B) to P.M, the Fonds Nationale de la Recherche in Luxembourg (FNR, Research Unit FOR-2715, INTER/DFG/21/16394868 MechEPI2) to P.M., the Agencia Nacional de Investigacion y Desarrollo de Chile (ANID, Fondecyt 1221464 grant) to E.P., the Familie SCN2A foundation 2020 Action Potential Grant to E.P., the Dravet Syndrome Foundation (grant number, 272016) to D.L, and the NIH NINDS (Channelopathy-Associated Epilepsy Research Center, 5-U54-NS108874) to D.L. ### 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: This study was approved by Cleveland Clinic IRB, approval ID 22-147. Informed consent was waived considering the retrospective nature of the study. 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 is available in the Supplementary Tables.