My 6-year-old son has a clicking sound in his knee. Is it due to vitamin D deficiency?

Hi doctor,

My son is 6 years and 4 months old. His height is 45 inches and weight is 19.3 kg. Since the last two years, we noticed that he is not gaining weight and size, and his weight percentile is dropping compared to how he was two years back. He is looking skinny now, and his knee makes multiple clicking sounds most of the time whenever he stands up after sitting in a squat position for the last six months. Now he started complaining of mild pain during that clicking sound. I have seen the knee clicking sound in people aged 50 or above whenever they stand up. He is eating very well. He is physically very active. We did not take him out much in sunlight because of the COVID situation for the last year, and his school is remote. Not sure if vitamin D deficiency is causing this. I have a few questions. Is this sound normal for his age? How to diagnose this? He did not have a fever or feel sick in the last year. Is there any infection like parasites, bacteria, or viral that could cause him to go thin but without fever or sickness? What tests are available for his age?