Functional characterisation guides classification of novel BAP1 germline variants

We have identified six patients harbouring distinct germline BAP1 mutations. In this study, we functionally characterise known BAP1 pathogenic and likely benign germline variants out of these six patients to aid in the evaluation and classification of unknown BAP1 germline variants. We found that pathogenic germline variants tend to encode truncated proteins, show diminished expression of epithelial-mesenchymal transition (EMT) markers, are localised in the cytosol and have reduced deubiquitinase capabilities. We show that these functional assays are useful for BAP1 variant curation and may be added in the American College of Medical Genetics and Genomics (ACMG) criteria for BAP1 variant classification. This will allow clinicians to distinguish between BAP1 pathogenic and likely benign variants reliably and may aid to quickly benchmark newly identified BAP1 germline variants. Classification of novel BAP1 germline variants allows clinicians to inform predisposed patients and relevant family members regarding potential cancer risks, with appropriate clinical interventions implemented if required. Ministry of Health (MOH) National Medical Research Council (NMRC) National Research Foundation (NRF) Published version We would like to thank the patients and research participants for their contribution to the study. This work was supported by the Khoo Postdoctoral Fellowship Award (Duke-NUS-KPFA/2019/0034 to J.H.H), the National Medical Research Council Open Fund—Young Individual Research Grant (MOH-000232 to J.H.H), the National Medical Research Council Open Fund—Individual Research Grant (MOH-000144 to B.T.T), the National Medical Research Council Singapore Translational Research Investigator Award (MOH-000248 to B.T.T.), the NRF-NSFC Joint Research Grant (Data Science) (NRF2016NRF-NSFC001–057 to B.T.T), the LKC Startup Grant (LKC MOE to J.N.), the National Research Foundation Singapore under its Clinical Scientist Award (NMRC/CSA-INV/0017/2017) and administered by the Singapore Ministry of Health’s National Medical Research Council (to J.N.). This work is also partially funded by NCC Research Fund, NCC Cancer Fund, Terry Fox and Lee Foundation supporting funds to J.N.