Germline missense variants in FBXW11 differentially affect its subcellular localization and protein interactome

The neurodevelopmental, jaw, eye, and digital syndrome shows high clinical variability and is caused by heterozygous FBXW11 missense variants. FBXW11 encodes an F-box protein containing a WD40 domain that forms a seven-bladed β-propeller. FBXW11 is part of the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex, which mediates the ubiquitination and proteasomal degradation of numerous substrates, thereby regulating diverse cellular processes and pathways. Here, we report a de novo FBXW11 missense variant, NM_033644.3:c.1100 C > T; p.(Ser367Phe), in an infant with developmental delay and severe skeletal phenotype characterized by multisuture craniosynostosis with turricephaly and postaxial polysyndactyly. We studied the functional consequences of the reported FBXW11 variants p.(Gly229Arg), p.(Arg350Trp), and p.(Glu431Lys), as well as p.(Ser367Phe), all located within the WD40 substrate-binding domain, by ectopic expression of HA-tagged wild-type and variant FBXW11 β-isoforms. Subcellular localization studies revealed FBXW11 WT mainly in the nucleus. HA-FBXW11 E431K showed either nuclear or nucleo-cytoplasmic distribution, whereas FBXW11 G229R and FBXW11 S367F were excluded from the nucleus. Using liquid chromatography-tandem mass spectrometry and independent co-immunoprecipitations, we identified variant-specific and shared alterations in FBXW11 interaction networks. Decreased complex formation with the SCF components was observed for FBXW11 G229R . Both FBXW11 G229R and FBXW11 S367F showed reduced binding to the nuclear substrate SUN2. Enriched complex formation of FBXW11 G229R and FBXW11 S367F with the chaperonin-containing TCP-1 (CCT) subunits suggests that both FBXW11 protein variants are trapped by CCT, potentially delaying or arresting folding of FBXW11’s β-propeller. Together, our data show that FBXW11 missense variants differentially affect binding to specific substrates and/or interaction partners, providing a molecular explanation for the clinical variability.