Something like whatever mechanisms decode structure from the genome are faulty and produce slightly wrong structures throughout the brain and body.
Anecdotally, I see a higher rate of general illness and physical birth defects in autistic people.
https://www.nature.com/articles/mp2010136
> Most ASD/MD cases (79%) were not associated with genetic abnormalities, raising the possibility of secondary mitochondrial dysfunction. Treatment studies for ASD/MD were limited, although improvements were noted in some studies with carnitine, co-enzyme Q10 and B-vitamins. Many studies suffered from limitations, including small sample sizes, referral or publication biases, and variability in protocols for selecting children for MD workup, collecting mitochondrial biomarkers and defining MD. Overall, this evidence supports the notion that mitochondrial dysfunction is associated with ASD. Additional studies are needed to further define the role of mitochondrial dysfunction in ASD.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711487/
It makes a certain amount of sense that a collagen / connective tissue disorder is going to have wide-ranging effects, including the nervous system
In this setting, it's not unreasonable that any genetic syndrome would be more associated with autism; indeed, it's more interesting to find lesions that have a lower proportion of autistic carriers compared to the general population.
There's too many correlations that aren't common enough, I really think we've got the causality backwards. But then again I don't know anything