Protein-lysine methyltransferase that selectively trimethylates the flavoprotein ETFB in mitochondria (PubMed:25023281, PubMed:25416781). Thereby, may negatively regulate the function of ETFB in electron transfer from Acyl-CoA dehydrogenases to the main respiratory chain (PubMed:25416781). Interacts with HSPD1; this protein may possibly be a methylation substrate. Concentrated in cytoplasmic granular foci. Belongs to the methyltransferase superfamily. ETFBKMT family.