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So, the new mutate abilty reads :

As a mutating creature spell resolves, instead of entering the battlefield, it merges with its target into one creature. Its controller chooses to put the resolving mutating creature spell on top of its target or underneath it. You'll end up with a pile of cards that all represents a single creature. That creature will have all the characteristics of the top card, and it will also have the abilities of every card underneath.

If my commander is on the top of the pile I'm pretty sure the pile will be my commander (and will be able to deal commander damages) but that happen if it's not on the top?

The closest think I can think of is meld, but I'm not sure it applied to mutate.

903.3bIf a player’s commander is a meld card and it’s melded with the other member of its meld pair, the resulting melded permanent is that player’s commander.

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Eli Shiffrin's response to this question in a Reddit AMA:

If any card in the merged permanent is your commander, the whole thing is your commander.

(Eli Shiffrin is the MTG Rules Manager)

Link to the answer

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    As far as 903.3b goes, it doesn't apply, since the permanent isn't melded. however there will probably be a new rule for mutated cards outlining the same thing. You won't get actual CR entries covering this until Ikoria releases. – vaasa Apr 4 at 12:17

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