Comprehensively Testing the Function of Missense Variation in the STK11 Tumour Suppressor

Abstract The tumor suppressor gene STK11 encoding Serine/Threonine Kinase 11 (STK11) is associated with Peutz-Jeghers Syndrome (PJS), a heritable gastrointestinal disease that increases lifetime cancer risk, and with somatic variation that contributes to ∼30% of lung and 20% of cervical cancers. Although identifying pathogenic variants is clinically actionable, over 94% of STK11 missense variants that have been observed clinically lack a definitive classification. We therefore measured the impact of STK11 variants at scale in a mammalian cell-based assay, scoring 6,026 (73% of all possible) amino acid substitutions across the full-length gene. Functional scores—which were consistent with biochemical properties, smaller-scale assays, and pathogenicity annotations—identified a subset of PJS patients with germline STK11 variants diagnosed later in life, as well as somatic STK11 variants found in cancer patients that had comparable overall survival estimates to wild-type STK11. Our scores provided new evidence for 350 annotated VUS STK11 missense variants and ∼80% of missense variants that have not yet been reported clinically, but we might expect to observe in the future. Thus, our effect map provides a proactive resource for gaining sequence-structure-function insights and evidence for actionable interpretation of clinical missense variants. Competing Interest Statement Unrelated to this work, F.P.R. is an investor in Ranomics Inc. and an investor in and advisor for SeqWell Inc. and BioSymetrics Inc, and has accepted grant funding from Alnylam Inc., Biogen Inc., Deep Genomics Inc. and Beam Therapeutics. He is also an investor and advisor in Constantiam Biosciences Inc. which provides related services. A.P.L.M, F.H., and M.E.R. are employed by Ambry Genetics. S.R.M., H.W., S.F., L.A., and T.T. are employed by and invested in Tango Therapeutics.