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hyperathyroidism or kidney disease?

I'm trying to figure out what is wrong with me, it has been a journey for me to try and rule so many different things out. I constantly feel really cruddy, everything hurts.

I'm 25 Male, 340lbs. history of high cholesterol/triglycerides and high blood pressure.

I have what I describe as visible calcifications in my dip joints from trauma. I have ruled out gout(low uric acid levels), osteoarthritis(herberden nodes), arthritis(13 Rheumatoid factor).  There is no visible sign of herberden nodes under x-ray examination.

My main hunch is that it is pseudogout being caused by elevated pth levels despite being normocalcemic.

I've been tested twice for pth levels along with calcium

1st Test-
PTH 71pg/mL (14-64 range)
Calcium 9.4 mg/dL(8.6-10.3 mg/dL range)
Vitamin D - 25ng/mL  (30-100 range)

The endo requested I go on vitamin D because she believes it is secondary hyperparathyroidism. After 3 months of 50k IU of vitamin D2

The vitamin D supplementation gave me extreme and constant trips to the bathroom, 5-8 bowel movements daily.

2nd Test-
PTH 81
Calcium 9.4
Vitamin D- 27


I also have several other calcium results that range from 9.4-10.1 . Bowel movements normalized after she requested I go on 2000 IU of D3, which I instead opted to buy cod liver oil of 400IU of D3.

I suspect that the reaction to high vitamin D dosages indicates fat soluble vitamins malabsorbtion. One of the possible causes was gallbladder disease.

I have not passed any kidney stones or anything, but after going to the ER with pain in my stomach, I insisted that they check my gallbladder(ultrasound) after reading possible causes of vitamin D malabsorbtion. Indeed I was found to have a fatty liver (Hepatic steatosis)along with multiple gallstones(cholelithasis).

Also something no one mentioned to me was that my kidney walls were thickened.  

The right kidney measures 11.8 x 5.2 x 6.0 cm

the average size of an adult human kidney is about 10 to 13 cm (4 to 5 inches) long, approximately 5 to 7.5 cm (2 to 3 inches) wide and about 2 to 2.5 cm (1 inch) thick.

My main suspicion is that there must be stones in my urinary system also  or nephrotic syndrome, high blood pressure, high triglycerides

I have to meet with a surgeon soon to discuss treatment of my gallbladder, they will probably insist on taking it out.
However, I feel that there is another condition causing the stones(hyperparathyroidism) and would probably seek treatment with ursodeoxycholic acid.
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