Phantom limb experience and pain is reported by most of the patients with limb amputation and this is also reported by patients with congenital limb loss and spinal cord injuries etc.
There are several hypothesis describing this, and one of them is “neuromas, (peripheral neuromas)” they are the inflamed and long grown nerve endings at the region of residual limb, they may cause pain.
Recent research proposed the adaptive changes in the sensory cortex area in the form of cortical rearrangement and the previous memories of the patients regarding the limb positions may be responsible for this pain.