I always figured Marvel started calling Namor "Marvel's First and Mightiest Mutant" as a marketing ploy to sell him as X-Men-related somehow, but here they are calling Namor "The first known mutant of our time" in Fantastic Four Annual # 1 in July, 1963. X-Men # 1 was published in Sept, 1963.

I recall a letter in the back of a 90s Namor comic where someone said he should be called Marvel's first hybrid, and the response was that the little wings on his feet are what make him a mutant.