The encoded protein has 313 amino acids with a predicted molecular weight of 33.845 kDa.

The protein is a synaptic vesicle glycoprotein with four transmembrane domains weighing 38 kDa.

It is present in neuroendocrine cells and in virtually all neurons in the brain and spinal cord that participate in synaptic transmission.

[8] Recent research has shown, however, that elimination of synaptophysin in mice creates behavioral changes such as increased exploratory behavior, impaired object novelty recognition, and reduced spatial learning.

[10] Using immunohistochemistry, synaptophysin can be demonstrated in a range of neural and neuroendocrine tissues,[11] including cells of the adrenal medulla and pancreatic islets.