Mesoproterozoic period included several global tectonic events like break-up of Nuna and formation of Rodinia. However, although Siberia is a significant piece of both supercontinents, Mesoproterozoic time is marked by quiescence of magmatic and tectonic activity in it. We report here a mafic dyke (named Gornostakh dyke) in the southeastern Siberian Craton dated at 1419 ± 32 Ma by LA-ICPMS U–Pb geochronology of apatite. The dyke has tholeiitic compositions with high MgO and alkaline content, low-Ti, and arc-like trace element pattern. Due to the absence of subduction tectonics in the study area, geochemical data could be attributed to a significant contribution from metasomatically enriched subcontinental lithospheric mantle previously modified by subduction processes. That kind of composition is common for low-Ti dykes of intraplate flood basalt provinces similar to, for example, Permian–Triassic Siberian large igneous province (LIP). Paleogeographic reconstructions suggest that Siberia was connected to Laurentia and Baltica and their reconfiguration interrupts a prolonged tectonic quiescence in the Siberian Craton from ca. 1.88 Ga reflecting a transition from Nuna to Rodinia configuration. The mafic magmatism on 1419 Ma on the southeastern margin of the Siberian Craton together with coeval extensional tectonics observed in the structure of the Sette-Daban ridge proposes a hypothetical LIP which may be a direct consequence of the beginning of this transition.