Mr Vaughan was primarily responsible for running institutional mandates, which will be passed on to other members of Threadneedle’s UK equity team.
He was also deputy manager, alongside Simon Brazier, on the £1.1bn Threadneedle UK Institutional fund. James Thorne will take on this role.
Mr Vaughan has led the UK smaller companies desk since 2007, and has been with the firm since 2000.