Shoto’s facial mark wasn’t inborn. Unfortunately, he got it when he was just five years old. His mother, Rei, threw hot water on his fiery side out of frustration with his dad. Half of his face resembles his father's face since he has a bifurcated appearance. This constantly reminded Rei of Enji’s physical, mental, and emotional abuses. She lashed out and poured her anger and resentment on Shoto.  This scene is in the twenty-third episode of the anime (S2, Episode 10), entitled Shoto Todoroki: Origin. You can find this upsetting panel of Rei and Shoto in tears after the incident in Chapter 39 of the manga.