Autosport understands there is not a problem with the unit but Manor found a potential sequence of events could cause a failure.
So as a precaution, the team opted to change the gearbox ahead of final practice at Suzuka.
As it was his race gearbox, the change puts Wehrlein in breach of the rules that dictate gearboxes must last six consecutive events.
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The only exceptions to these rules, for which a five-place grid penalty applies for a breach, are for non-starters and non-finishers - for technical reasons - of the last race.
Wehrlein was 20th quickest in second practice, 3.042s off the pace but just over a tenth quicker than team-mate Esteban Ocon.
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