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If you have been on a gluten-free diet for four years, all of the testing with the exception of the HLA one, was a waste of time. Not sure why your physician would have even considered it.  But that doesn't explain your ongoing celiac-like symptoms. It's beginning to look like they are being caused by some other medical issues unrelated to a gluten disorder. 

Thanks for the insight!  It has been a whirlwind...very overwhelming and frustrating at times.  But what you are saying makes sense to me. I have been on a Gluten Free diet for 4 years now Its been suggested to me to get a second opinion  

@ainsleydale1700, the additional test information you provided is very significant! Here is the important part: "This test detects IgG antibodies to tTG (tissue transglutaminase), and was performed because your IgA level is below normal. The immune response that occurs in celiac disease often leads to IgG antibodies against tTG." It looks to me that you may be a "seronegative" celiac. The frontline diagnostic tests for celiac disease are IGA tests, especially the tTG-IGA. However, another IGA test ("total IGA") was done to check you for IGA deficiency and you were found to be deficient. That means that the usual IGA tests done to diagnose celiac disease, such as the tTG-IGA, would not be reliable. That is why the IGG testing was done "reflexively" (which means in response to the results of a previous test, i.e., the total IGA test.). The IGG tests are not quite as reliable as the IGA tests for diagnosing celiac disease, meaning, there are more "other" possible causes for elevated IGG test scores. The IGG test did give a borderline positive result, however, so the physician ordered the endoscopy with biopsy to check for damage to the small bowel lining that would be caused by untreated (continuing to consume gluten) celiac disease. The biopsy showed no damage so the doc concluded you do not have celiac disease. However, the monkey wrench in the gears of the doc's conclusion is that he gave you permission to proceed with the gluten free diet which would have allowed for healing of the small bowel lining to commence. How long were you gluten free before the biopsy was taken? And how much damage to the small bowel lining was there to begin with? If the damage was minimal, it might have been fully healed by the time the biopsy was done. And the symptoms you describe involving vitamin and mineral deficiencies, tooth enamel loss, cessation of menses, neuropathy, constipation alternating with diarrhea . . . IMO all scream of celiac disease as opposed to NCGS.

Thank you!  I have the classic symptoms while eating gluten-constipation, diarrhea, weight loss, loss of appetite, etc.  My main problems right now are elsewhere in my body.  Dental issues...my teeth started breaking.  I had two teeth break in the past month.  My dentist looked at my teeth with a camera and said I have no enamel left.  Im really struggling with neuropathy, and gynecological conditions.  My periods stopped 6 years ago and Im not in perimenopause or menopause.  When I consume gluten, my resting HR goes up about 30 points, and takes a week or so to normalize.  The list goes on, its very overwhelming Ongoing vitamin D deficiency, magnesium, iron, blood creatinine is always low, dont know if thats relevant. Below is from the Celiac panel, otherwise the results were normal.  Not crazy high, but I wasnt aware the Celiac panel was included in the bloodwork.  So I didnt prepare for it in advance, and Ive been on a gluten-free diet for the past 4 years High t-Transglutaminase (tTG) IgG: 7, Reference Interval: 0-5, Unit: U/mL This test detects IgG antibodies to tTG (tissue transglutaminase), and was performed because your IgA level is below normal. The immune response that occurs in celiac disease often leads to IgG antibodies against tTG.   I know I have a bad reaction to gluten.  But with the low likelihood of Celiac, any guidance on other paths to explore would be greatly appreciated!  Ive been trying to figure this out for years now, and more issues keep coming up.  It has been so overwhelming.  Thanks again.

It’s absolutely worth bringing all of this to your GI appointment. The 2013 CT note about thickening in the second and third portions of the duodenum is especially important, since that area is directly involved in celiac disease and other inflammatory conditions, even if it wasn’t followed up at the time. The weak positive HLA-B27, joint pain, stiffness, numbness, and burning sensations could suggest an autoimmune or inflammatory process, which sometimes overlaps with celiac disease or other gut-related immune conditions. Your periods of neurological symptoms (balance issues, numbness, confusion), low vitamin D, and fluctuating levels despite supplementation are also relevant, as malabsorption can contribute to deficiencies and neurologic complaints. Even “normal” labs are helpful for pattern recognition over time. I’d suggest organizing your records into categories—GI imaging, autoimmune labs, vitamin/mineral levels, neurological evaluations, and symptom timelines—so your GI doctor can see the bigger picture. This kind of long-term pattern can be very useful in connecting dots.