Comment by dekhn

What's an allele? There is no real answer to that question. Or rather, the concept of allele is highly abstract and does not correspond well to actual genomic sequences.

Predicting phenotypes is not a linear function of the genome. It's a highly nonlinear function, affected by complex generative processes, feedback control, homeostasis, and many other active control mechanisms. With that said, you could come up with a proxy score that was a function of the genome and had predictive value for autism (ideally better than binary, with a description of the predicted autistic traits somebody showed).

Biology is the only field I've worked in where both "necessary but not sufficient" and "sufficient but not necessary" can both be the case at the same time.