https://news.ycombinator.com/item?id=20511582 (more discussion)

Since this is a prehistoric alteration to the genome, cutting across all humans, it's more than likely a result of natural selection via merciless and deadly contagion. Every early human predecessor with the gene died without offspring, and only the last remaining children of those ancestral origins lacking the gene lived long enough to evade death by the disease.

So, before any or all humans even emerged as a species, something came along and cut down common ancestors, only leaving behind survivors that disused the related genes.