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Patom Crater is the modern (ca 500 years old) volcano-like geological edifice comprised of Proterozoic limestone lumps and situated in southern folded rim of Siberian platform. From its discovery in 1949, the crater’s origin remains unclear. Impact factor, volcanic and cryogenic models were proposed. As result of present investigations the geological interpretation of magnetotelluric soundings along 5 km profile across of the Patom crater has been performed. The Patom tectonic zone with the mark of Devonian fluid-metasomatic process has been discovered. The zone breaks the layers of carbonaceous shale of sedimentary host rocks. Absence of records of relatively young and considerable geological processes, as well as other geophysical and geochemical data, leading us to the suggestion about the cryogenic model of the Patom Crater origin, like unusual hydrolaccolith