The simple view of the bonding in methane You will be familiar with drawing methane using dots and crosses diagrams, but it is worth looking at its structure a bit more closely. There is a serious mis-match between this structure and the modern electronic structure of carbon, 1s 2 2s 2 2p x 1 2p y 1.
The second reason for a low vitamin D is that you have primary hyperparathyroidism due to a small tumor in your neck and the body converts all the vitamin D-25 (that your doctor is measuring) to the active Vitamin D-1-25 (that doctors do not measure). This is the blue blob on the graph.
They think that the low vitamin D levels cause too little calcium to be absorbed in the intestines. They think that this low amount of calcium is sensed by normal parathyroid glands which causes the normal parathyroid glands to appropriately increase their production... causing a high PTH level.