Humans have 46 chromosomes, so...?

Yes. The functional definition of species involves ability to reproduce not by chromosome number. A person with downs syndrome is still capable of reproducing (technically at least). Same with a person who has an extra sex chromosome or one too few. A person missing a sex chromosome (although most are sterile) might still have 50% normal sex cells (gametes) and 50% lacking the chromosome. (remember gametes only have 1/2 of the chromosomes anyway). Therefore they still count as Homo sapian. It should be noted that this definition of species cannot account for all organisms (crosses that actually work... like zebroids or other successful hybrids) but it is still the most common (and most accurate) way to define a species. Although still classified as separate species, Canis familaris (dogs) and Canis lupus (wolves) are capable of having successful offspring. Biologists are trying to decide on whether to incorporate them as one species despite their physical differences. Then there is also a definition based on shared physical characteristics: They still have the traits of humans (minus genetic disorder) therefore they are human.

I do not think it matters really, a human is a human... genetic disorder or not.