The protein encoded by this gene is a homeodomain containing transcription factor.

[6] Mutations disrupting the function of this gene are associated with spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD).

[8] Two small bones in the middle ear, the malleus and incus, are homologous to the articular and quadrate, the bones of the proximal jaw joint in fish and other non-mammalian jawed vertebrates.

NKX3-2 expression is required to pattern the articulated joint between these jaw bones, as knockdowns or knockouts of this gene result in the loss of the jaw joint in zebrafish,[9] chicken,[10] and amphibians.

[11] Overexpression of this gene results in the development of ectopic mandibular cartilages in zebrafish [12] and amphibians.