Cardinal Henry Beaufort was the son of John of Gaunt by his third wife. He was a first cousin to Richard II and the half-brother of Henry IV. In about 1420 he assisted with the completion of the tower and the rebuilding of the south transept. 

Under the influence of Cardinal Beaufort, who was a powerful political figure, St Mary Overie was used for many important ceremonies such as the marriage of Edmund, Earl of Kent, to the daughter of the Duke of Milan in 1406, and the marriage of James I, King of Scotland, to Joan Beaufort (the Cardinal's niece) in 1424. The Cardinal's coat of arms can be seen on the east wall of the south transept.

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