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From the beginning of the first book of 魔法科高校の劣等生 (その refers to 魔法)

当初、その異能は「超能力」と呼ばれていた。純粋に先天的な、突然変異で備わる能力であって、共有・普及可能な技術体系化は不可能と考えられていた。

I might be overthinking but I'm not sure about で after 突然変異. I wonder if「先天的な、突然変異で」is actually modifying 備わる because when I look up this word in a monolingual dictionary, I noticed が is typically used like「冷暖房の備わった部屋」for example. How will the meaning change if「先天的な、突然変異の備わる」is used?

Or maybe, the first part of the sentence is parsed like this way

純粋に (先天的な、突然変異) (備わる能力) あって

Both で goes to あって. I'm not sure if that's case because I think でも should be used instead of で.

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    If you're feeling 備わる is a tricky intransitive verb, thinking of it as "to come/exist (as an equipment or to enhance something)" is not too far. 彼には才能がある = 彼には才能が備わっている = "Talent exists around him"; 冷暖房の備わった部屋 = 冷暖房が備わった部屋 = "a room where an air conditioner has come"; 突然変異備わる能力 = "an ability that comes by/through mutation".
    – naruto
    Jan 6 at 10:02
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    純粋に (先天的な、突然変異で) (備わる能力で) あって ← いや。。 How about parsing it like 「(純粋に先天的な)、(突然変異で備わる)能力であって」?  「純粋に先天的な」 and 「突然変異で備わる」 both modify 能力.
    – Chocolate
    Jan 7 at 3:27
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That last であって is just である in the continuative て form and it acts more or less like です. With this in mind, we can safely assume that the sentence is parsed like this:

(純粋に先天的な、突然変異で備わる能力)である

It's purely an innate ability obtained by mutation.

In that previous sentence, the が is implicit and goes with 能力. The mutation 突然変異 is the means/method by which that ability is acquired, so it needs で. If you change it to 突然変異の備わる能力, this would mean that the ability itself "possess" a mutation (I'm unsure if 備わる can even be used like that in the first place). Assuming we're talking about humans, an example with が for the same context would be:

その能力の備わる人間 [...]

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