Sox2 is one of the key transcription factors required in induced pluripotent stem cells. As forced Oct4 expression induces pluripotency in Sox2-null cells, a group of researchers concluded that the primary role of Sox2 in induced pluripotent stem cells is controlling Oct4 expression, and they perpetuate their own expression when expressed concurrently.The protein may act as a transcriptional activator after forming a protein complex with other proteins. Mutations in this gene have been associated with bilateral anophthalmia, a severe form of structural eye malformation.

This gene lies within an intron of another gene called SOX2 overlapping transcript (SOX2OT).The ectopic expression of SOX2 may be related to abnormal differentiation of colorectal cancer cells.