Confused about my results

[AllyJR]

Both the doctor and I are baffled by my test results. Wondering if anyone could shed some light on this situation! I've had celiac-like GI symptoms for years. I have a family history of celiac (great-grandma), Addison's (mom), and every other autoimmune disease you can think of with my aunts and cousins. I myself have hashimotos. Because of the strong family history of autoimmune disease my doctor ordered the full celiac panel of blood tests - all of which came back negative! (I was not gluten free fyi.) So the doctor did an endoscopy and took biopsies. Biopsies showed "villous blunting and lymphocytes greater than 30". Because it was indicative of "weak celiac disease" they sent me to get a genetic test. The test came back saying I'm only positive for HLA DQ A1*05 (half of the HLA DQ2 haplotype). The doctor said I could try going gluten free if I want to, but it likely isn't celiac disease.

I have been gluten free for a month now and I feel like a new person! I've been suffering for so long and I feel amazing! No more diarrhea, stomach aches, reflux etc! My symptoms had been extremely severe and they are almost completely gone. I'm so thankful but... I'm so confused! Celiac? The doctor says it's probably NCGS but I keep reading that the first criteria for that diagnosis is a negative biopsy and mine very much showed damage. 

[Russ H]

Sorry but I have to dash for an appointment so little time just now. Your signs and symptoms and response to a gluten-free diet sound like seronegative coeliac disease.

Seronegative coeliac disease, Coeliac UK.

[trents]

Exactly what component was indicative of "weak celiac disease"? Is that a reference to the endoscopy results or the whole picture of the results of the blood test combined with the endoscopy results? Villous blunting is the hallmark of celiac disease.

Edited May 28 by trents

[AllyJR]

The biopsy results were what said indicative of "weak or partially treated celiac disease".

[trents]

8 minutes ago, AllyJR said:

The biopsy results were what said indicative of "weak or partially treated celiac disease".

That's how I took it but I was confused because in your previous post you said of your biopsy, "and mine very much showed damage". 

In the celiac antibody panel that was ordered, was there a test for total IGA included, aka, "Immunoglobulin A (IgA)"? This one checks for IGA deficiency. IGA deficiency can result in false negatives for the IGA celiac antibody tests such as the TTG-IGA and the DGP-IGA.

[AllyJR]

Celiac panel was 

IgA 106

tTG IgA AB <2

Gliadin Deamidated IgA Ab 4

Gliadin Deamidated IgG Ab 2

Endomysial IgA Antibody Negative 

Tissue Transglutaminase IgG Ab Test not performed 

[trents]

With regard to the Iga 106, is there a reference range given for that one?

[AllyJR]

Thank you for looking at these for me! The reference range for IgA was: Normal range: 87 - 352 mg/dL

[trents]

So, you are not IGA deficient. But as Russ H suggested, it looks like you may be a seronegative celiac.

[Scott Adams]

6 hours ago, AllyJR said:

Both the doctor and I are baffled by my test results. Wondering if anyone could shed some light on this situation! I've had celiac-like GI symptoms for years. I have a family history of celiac (great-grandma), Addison's (mom), and every other autoimmune disease you can think of with my aunts and cousins. I myself have hashimotos. Because of the strong family history of autoimmune disease my doctor ordered the full celiac panel of blood tests - all of which came back negative! (I was not gluten free fyi.) So the doctor did an endoscopy and took biopsies. Biopsies showed "villous blunting and lymphocytes greater than 30". Because it was indicative of "weak celiac disease" they sent me to get a genetic test. The test came back saying I'm only positive for HLA DQ A1*05 (half of the HLA DQ2 haplotype). The doctor said I could try going gluten free if I want to, but it likely isn't celiac disease.

I have been gluten free for a month now and I feel like a new person! I've been suffering for so long and I feel amazing! No more diarrhea, stomach aches, reflux etc! My symptoms had been extremely severe and they are almost completely gone. I'm so thankful but... I'm so confused! Celiac? The doctor says it's probably NCGS but I keep reading that the first criteria for that diagnosis is a negative biopsy and mine very much showed damage. 

Your situation is actually more common than many realize, and while confusing, there are logical explanations for your test results. The key points are that your biopsy showing villous blunting and increased lymphocytes does indicate intestinal damage typically seen in celiac disease, despite your negative blood tests. This phenomenon is known as seronegative celiac disease, which affects about 10% of celiac patients. Your partial HLA-DQ2 genetic result doesn't rule out celiac either, as a small percentage of celiac patients don't have the complete genetic markers. The fact that you've responded so dramatically to a gluten-free diet is another strong indicator that this is likely celiac disease rather than NCGS, since NCGS doesn't usually cause intestinal damage. Your doctor might consider ordering additional tests like IgG-based celiac tests (tTG-IgG or DGP-IgG), or repeating the endoscopy after you've been gluten-free for a longer period to check for healing. Many celiac specialists would actually diagnose you with celiac disease based on your biopsy results combined with your positive response to the gluten-free diet, regardless of the blood test results. It may be worth consulting with a gastroenterologist who specializes in celiac disease for further evaluation. Your experience highlights why celiac disease can be so challenging to diagnose and why doctors need to look at the whole clinical picture rather than relying on any single test.

[Russ H]

There is a good paper here on causes of seronegative villous blunting. The most common is seronegative coeliac disease.

Not All That Flattens Villi Is Celiac Disease: A Review of Enteropathies

[knitty kitty]

Do get checked for all kinds anemia, iron deficiency anemia, B12 deficiency anemia, pernicious anemia, B6 deficiency anemia.  Anemia is very common in Hashimoto's!  

Anemia, Diabetes and thiamine deficiency are known causes of seronegative Celiac Disease.  

You only need one gene for Celiac.  Welcome to the tribe!

Keep us posted on your progress.  

Edited June 6 by knitty kitty
Typo correction

[AllyJR]

Thank you! I saw a different provider this week who took one look at all my medical information and declared it was celiac in the first 5 minutes of the appointment. I am still a bit in shock but so very thankful to have an official diagnosis. The doctor told me to have my children tested and one of them came back with a "weak positive" TTG IgA! Not sure what to think about that! This week has been a wild ride. Thankfully this website has such great information! I've been going through all the do's and don't's of cross contact etc. 

[knitty kitty]

Hurrah for an official diagnosis!  

You may want to put the whole family on gluten free, as a preventative measure for the ones not testing positive right now.  Remember, exposure to gluten triggers the Celiac genes your kids have inherited from you.  Keeping them gluten free now, even though they don't test positive right now, can delay triggering Celiac Disease development in them. 

[trents]

@AllyJR, older studies placed the likelihood of the first degree relatives of those with celiac disease also developing celiac disease at about 10%. Two more recent and large sample studies place it at almost 50%. There are likely multiple epigenetic factors involved in the development of active celiac disease, one of which may be the consumption of modern cultivars of wheat which, through genetic manipulation, contain multiple times the gluten content of ancient wheat. You will have to decide whether or not it is prudent and necessary to require your children who have not yet developed active celiac disease (and who may not ever develop it) to eat gluten free. There certainly will be a social cost for them if you do. If you do decide to go that direction, it would certainly make it easier for you to be consistent in avoiding gluten in the home and so, to keep yourself safe.

 

[AllyJR]

Very interesting! My whole family is full of autoimmune disease. Celiac, Lupus, Addison's, Graves and Hashimotos. My great grandmother who had celiac passed away due to digestive complications and my grandmother (her daughter) is 88 and is struggling with severe life-threatening digestive issues. She was never diagnosed but I am suspicious she may have celiac. My mom has Schmidt's (combo of Addison's and Hashimotos). Now that I have 2 autoimmune conditions I am definitely concerned that my kids have a very high risk of developing an autoimmune disease. 

[knitty kitty]

@AllyJR,

Similar to my family having a variety of health problems related to undiagnosed Celiac Disease.  Not only does one inherit the autoimmune disease genes, we also learn poor eating habits from our families.  

Look into the Autoimmune Protocol Diet which reduces inflammation and promotes healing.  This diet cuts out foods that can be inflammatory while intestines heal.  I highly recommend it.  

Nutritional deficiencies can affect gene expression.  There's some research that shows thiamine deficiency can affect gene expression, causing autoimmune genes to switch on.  Taking a B Complex and additional Thiamine in the form Benfotiamine can be beneficial in that respect.  Vitamin D can help regulate the immune system and is important in growth of bones in children.  Focus on nutrition to promote growth and development in children.  

Keep us posted on your progress!

[AllyJR]

Thank you! Definitely sounds like something I need to read about!

[Russ H]

On 6/6/2025 at 5:16 PM, trents said:

@AllyJR, older studies placed the likelihood of the first degree relatives of those with celiac disease also developing celiac disease at about 10%. Two more recent and large sample studies place it at almost 50%. 

 

There is a predictive model for children on this link. Depends on sex, HLA genes and number of affected close relatives.  The model only goes up to age 12 so it would be interesting to know what the lifetime risk is.

https://hputter.shinyapps.io/preventcd/