Differentiation in synaptic pruning is just an example of things that correlate with mental disabilities just as well as they correlate with higher cognition...

There are two more things that easily come to mind:

1) Testosterone levels, specifically fetal testosterone. Apparently when it is high your child will have much better visual spatial abilities and general intelligence
http://www.sciencedirect.com/science/article/pii/S1041608009001083
https://www.sciencedaily.com/releases/2011/03/110311153549.htm

and, just as likely, your child will have ASD traits and introversion.
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.471.4530&rep=rep1&type=pdf

2) Mitochondrial DNA variants. Mitochondria is a symbiotic organism that's been living with us for millions of years, but it isn't human - it has its own DNA. Its basic role is to provide energy to the cells, including the brain. It is been hypothesized that the brain neural efficiency is directly related to the mitochondrial health and its ability to metabolize glucose into ATP.

Some are associated with higher IQ
http://www.davidsongifted.org/db/Articles_id_10032.aspx
some are associated with schizophrenia and ASD:
http://www.ncbi.nlm.nih.gov/pubmed/25446950
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3285768/
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127280
and with attention issues:
http://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1082&context=psych_theses

Since each cell has 1000-2000 of these, you have millions of cells, and each can have its own slightly-different DNA mutations, you really can get any combination you want, different cells working differently, atypical development etc. Unlike the nuclear human DNA, it isn't long - only 37 genes, so they are multi-tasking. One mutates and you have a myriad of issues. Luckily for us, they don't mutate at the same time in all of the cells....

These two specifically are passed maternally - one through prenatal exposure and one through the egg.