1000 calories per day is not near enough to sustain your body's needs. You should be aiming for twice that much. You are in a borderline starvation mode and even apart from celiac disease that explains a lot of your medical issues. And you should be aiming for 75-100 gm of protein per day. Do you have access to eggs? Protein powders are good for supplementing protein should not become the main source of dietary protein as they lack any supporting necessary nutrients. Eggs are a nearly complete food, being an excellent source of protein, vitamins and healthy fats. 

Basically I don't eat lots of protein from so I bought protein powder I Don't know how much but I just make 2 scoops of it and mix it with dates and milk .and I just calculated the things I eat in the day and I am surprised that I get less than 1000 calories 😬.

How many grams of protein per day would you say you are getting and how many calories per day? I did some research on causes for low creatin and low urea.

Oh, lovely, another knitter!  What are your favorite things to knit?  I love knitting lace.  Lace doileys and shawls.  And socks, not necessarily lacy though. Low Vitamin D has an impact on the thyroid. The Role of Vitamin D in Autoimmune Thyroid Diseases: A Narrative Review  https://pmc.ncbi.nlm.nih.gov/articles/PMC9966459/ Impact of Vitamin D on Immunopathology of Hashimoto's Thyroiditis: From Theory to Practice https://pubmed.ncbi.nlm.nih.gov/37513592/ P.S. if you're low in one vitamin, you're probably low in others as well.  Have you had other vitamins checked for deficiencies?  

Vitamin D acts as a hormone and influences other hormones if the Vitamin D level is at eighty nmol/l or above.   I had a lot of hormone problems when my Vitamin D was in single digits prior to diagnosis of celiac disease.  Vitamin D is needed to keep bones strong and helps regulate the immune system, lowering inflammation.   I used high dose Vitamin D 3 to correct my deficiency quickly.  It's very safe and recommended by doctors.  Take Vitamin D 3, not the D 2 form prescribed frequently.  D2 is not utilized as well as D 3.  Thiamine is needed to activate Vitamin D in the body.   Interesting Reading: Safety of High-Dose Vitamin D Supplementation: Secondary Analysis of a Randomized Controlled Trial https://pubmed.ncbi.nlm.nih.gov/31746327/ High-Dose Vitamin D Supplementation Can Correct Hypovitaminosis D Prior to Total Knee Arthroplasty https://pubmed.ncbi.nlm.nih.gov/34737019/ The short-term effect of high dose vitamin D3 supplementation in improving hypovitaminosis in patients with type 2 diabetes - A randomized clinical trial https://pubmed.ncbi.nlm.nih.gov/35470105/ The role of vitamin D in menopausal women’s health https://pmc.ncbi.nlm.nih.gov/articles/PMC10291614/#:~:text=Vitamin D (VD) is known,menopause are also increasingly prominent.