Clustering of predicted loss-of-function variants in genes linked with monogenic disease can explain incomplete penetrance

Predicted loss-of-function variants (pLoFs) are often associated with disease. For genes linked with monogenic diseases, we hypothesised that pLoFs present in apparently unaffected individuals may cluster in LoF-tolerant regions. We compared the distribution of pLoFs in ClinVar versus 454,773 individuals in UK Biobank and clustered the variants using Gaussian mixture models. We found that genes in which haploinsufficiency causes developmental disorders with incomplete penetrance were less likely to have a uniform pLoF distribution than other genes (P<2.2x10-6). In some cases (e.g., ARID1B and GATA6 ), pLoF variants in the first quarter of the gene could be rescued by an alternative translation start site and should not be reported as pathogenic. In other cases (e.g., ODC1 ), pathogenic pLoFs were clustered only at the end of the gene, consistent with a gain-of-function disease mechanism. Our results support the use of localised constraint metrics when interpreting variants. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the Medical Research Council [MR/T00200X/1] ### 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: The UK Biobank has approval from the North West Multi-centre Research Ethics Committee (21/NW/0157) as a Research Tissue Bank approval. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the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