The most common and most likely answer to this crossword clue is the 6 letter word QUAGGA
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The straight part
We know that "Animal that’s vanished" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case animal that’s vanished = quagga.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does QUAGGA mean?
QUAGGA noun- A southern-African subspecies of zebra, Equus quagga quagga, which went extinct in 1883. The upper parts of the animal were reddish brown, becoming paler behind and beneath, while the face, neck, and fore part of the body were marked by dark stripes.