There are several possible causes. Migrating' brain cells may lack the chemical messengers which guide them in the right direction. This can occur because of a genetic disorder. Migrating nerve cells may be prevented from reaching their destination. This can occur because of lack of oxygen , lack of nutrients, toxic chemicals, infection or a metabolic disturbance.
Nobody is certain.
In some individuals with agenesis of the corpus callosum, nothing else abnormal will happen. Maldevelopment of gut and kidneys. Maldevelopment of eyes, nerves, muscle. In some cases it may be the result of a chromosome abnormality. The consequences vary hugely between different individuals.