In the bigger picture: where there's life, there's hope. There are more things in heaven and earth than are dreamt of in your philosophy. Nature's imagination is greater than your imagination.
He's only three. At that age, nobody is "human" in the fullest definition of the word. Full cognitive abilities don't develop for several more years.
The plasticity of the brain, especially young ones, is well documented. It's not surprising to me that functionality could be offloaded to the parts of the brain that are present (although the extremity of this case may be surprising).
I'll be interested to see where he's at when he's 6 years old, and again at puberty.
In my mind, the term you are looking for when you say "human race" is actually homo sapiens. This is a biological term denoting the species.
When I used the word "human", I intended to communicate a more metaphysical idea. Perhaps a better choice of words would be "person", but somehow -- and this seems to be all subjective -- that seemed setting the bar too low. I thought that the word "human" might convey the idea of "person", but also implying a certain level of functioning.
For example, I'd expect more evolved cognitive skills (starting with the persistence of objects, eventually moving through symbolic logic, and so forth) from an entity described as a "human", as well as certain emotional skills, such as empathy.
Back to my original point, none of those attributes I mentioned would be expected at all in a 3-year-old homo sapiens, so this would be a more interesting story in several years when the boy reaches an age at which we'd expect those skills to have developed.
This part of the brain is for X, here is the Y-centre, here is where Z is controlled.
Except, wait, XYZ are missing :-o
Neuroscientists are being descriptive, not proscriptive, when they tell you what areas of the brain are for what. They aren't "deciding" what it means, they are telling you that across a wide range of people, when they see activity X, brain part Y lights up. That the brain might be significantly differently organized if bits of it are missing is hardly a groundbreaking idea, nor even remotely shocking to actual scientists. The brain reconfiguring itself, even in adults, has been repeatedly observed, with vision cortexes replaced by audio processing after becoming blind and so forth. This is interesting, but the "phrenologists" aren't going to be sent into a tizzy because of this one specific case. Your conception of the science might be sent into a tizzy, but that's not the scientist's problem. (Well, at least not directly.)