In this passage, it is a bit tricky to tell that there was a removal of Y229A as opposed to an addition unless you know what to look for. However, it all comes down to terminology and notation. First, they refer to Y229A as a variant, which in genetics terms usually refers to a mutation. Therefore, just from that, we know that there is a change from wild-type. Additionally, when you have notation like "Y229A" where there is a letter followed by a number then another letter, this means that the letter corresponding to the first amino acid is replaced with the amino acid corresponding to the second letter. For example, if I were to write "K78A", this would mean lysine (K) was replaced by alanine (A) in that mutation. Therefore, when we look at Y229A, this is a mutation resulting in the replacement of tyrosine (Y) with Alanine (A). Because of this, we know that there was a removal of a tyrosine (aka Y229) and that this adversely affected the protein stability.