If you search for "education ethnicity income Pakistan" in Google Scholar using the following link, you get 4000+ articles from 2015 in which ethnicity is a factor. There is a large variety of causes of variation as you will see. Pick the papers that focus on education for a more relevant read.
From my perspective, what causes variation of education among ethnic groups is their culture. Education of any country is culturally based. ethnicity plays prominent role in education of the people. The differences in language, religion, food etc means a lot in education. So, the education of any group is heavily laden with their culture.