Autism spectrum disorder, schizophrenia, bipolar disorder, etc are related disorders. There is no single gene associated with the disorder, but a few genes are associated with them. Most people with ASD or related disorders have a combination of these gene varients. Most of the genes are really close to eachother on the same chromosome.

The severity of the disorders or which features one has seems to be predicted by different combinations of these gene variants.

The genes themselves are important in brain development, they're not necessarily associated with sex development despite being on sex chromosomes.

The genes themselves (at least some of them) are used in pruning branches of neurons as they develop, so they don't have too many, or not enough connections in the brain. In layman's terms, they control how the brain is wired.

No two austic, schizophrenic or bipolar person is going to have the exact same varients in these genes, but a group of schizophrenic people will be more similar to eachother than they would be to autistic people.

In this study all the varients they found in transgender individuals are of the same genes associated with ASD, schizophrenia, etc and other neurological developmental disorders. But the researchers came to a different conclusion because the genes are on an sex chromosome.