Can having an infection from chlamydia in the throat untreated for a while be the cause of a brain lesion?

No: It can cause other problems but should not cause a brain lesion. You need to follow up with a neurologist.

Chlamydia: Untreated Oropharyngeal Chlamydia can lead to meningitis or brain infection, but it is extremely rare in an otherwise, young, healthy, asymptomatic individual. I am otherwise not certain as to what you mean by "lesion". Chlamydia is usually easily treated with oral antibiotics; however, if there is intracranial spread, may require IV antibiotics. Intracranial abscess may require surgical drainage