The pain can be because of multiple causes like caries, gingivitis, sensitive teeth or nerve pain. The gum growing over the molar is found when the molar tries to erupt and the eruption are not complete. Eventually the molar will cut through the gums but if this is very painful then the gum tissue can be cut by your Doctor to help the molar to erupt. Consult your Doctor.
The answer is based on information provided. Exact advice is not possible without a proper examination and investigations. You are requested to consult your Doctor. Take care and keep us posted.
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