Pratap was born in Thiruvananthapuram. His father Kolathinkal Pothen was a well known business man of Thiruvananthapuram. He has two brothers and two sisters. He did his schooling at Lawrence School, Lovedale, in Ooty. He finished Schooling in 1968. His elder brother Hari Pothen was also a film producer was married to then famous actress Jayabharathi for a short while. His father died when he was 18. The youngest of five children, he grew up in a household where art, politics, entertainment and business co-existed, allowing him to experience a large cross-section of life from his ancestral home in Trivandrum in Kerala. He was married twice. His first marriage was with leading actress Raadhika in 1985 and subsequently they divorced in 1986. His second marriage was with Amala Satyanath in 1990, a senior corporate professional and they have a daughter Keya born in 1991. Later they got separated and divorced in 2012. He left MCC with a B.A in economics in 1969.
He also directed a Telugu film – Chaithanya. Seevalapperi Pandi, Jeeva, Lucky Man and Vetrivizha are some of the popular films he directed in Tamil.