Autoimmune Encephalitis and Genes

I was involuntarily hospitalized for the first time in the psych ward in October 2015, in June 2016 I was diagnosed with Hashimoto’s thyroiditis, and then in April 2017 I was diagnosed with autoimmune encephalitis (specifically Hashimoto’s encephalitis). I was diagnosed also with coeliac disease, which is a permanent autoimmune disorder. That is a lot of diagnoses, all autoimmune related, and they all came in a short period of time (it’s not surprising though, because often people with an autoimmune disease tend to have more than one – this fact points to the genetic cause of a faulty immune system).

Since then I have done a lot of research on my condition, but in 2015/2016 I was probably still in denial. I remember being certain that my depression was due to only external circumstances such as my job, not having kids, small apartment, etc. I kept thinking  – I know it’s the bachelor apartment that is making me feel claustrophobic and trapped, I have never lived in such a small space, this is not how people should live, this is causing my depressive state. I was living in a small bachelor apartment together with my boyfriend and it was not enough space for two people, you start to irritate each other, and that could have been contributing to stress. But I also know that I was not accepting that something was also biologically wrong with me, that I needed to investigate medical causes. At that point I was already seeing a correlation between eating wheat and brain fog, but then I would go again to buy a chicken wrap and when my thoughts would become less clear, I still kept repeating – it cannot be the wrap, this seems very unlikely, it must be something else – probably I am allergic to mold in the apartment. It’s also very difficult to analyze the situation when your brain is getting worse daily and you don’t realize it.

The correlation between eating wheat and brain fog, based on my observations, was very strong though, and I did finally start eating gluten-free. Then I received my test results for antibodies associated with coeliac disease and the values were right at the threshold. To me this was a clear indication of disease, since even though I had been not eating gluten for a while, the antibodies were still present and the value was right at the point of making a positive diagnosis.

What also helped me understand and accept why I was hit with a number of autoimmune disorders. Several years ago I sent my saliva to 23andme and got back results telling me that I was mostly Eastern European (obvious to me) and Balkan (was a surprise). Also that I had increased risk of developing age-related macular degeneration. I thought this was irrelevant to my symptoms and I did not open 23andme again for a while. I logged in a few months ago and the website had been updated, there was a new result – Celiac Disease.


From 23andme – the variant tested is a change from a C to a T in the DNA sequence of the HLA-DQA1 gene. The rs2187668 marker is a tag SNP for the HLA-DQ2.5 haplotype.

From Wiki: DQ2.5 and the linked DR3 are associated with probably the greatest frequency of autoimmune occurrence relative to any other haplotypes. The haplotype is positively associated with coeliac disease, dermatitis herpetiformis, juvenile diabetes, Lambert-Eaton myasthenic syndrome (LEMS), Sjögren’s syndrome, and autoimmune hepatitis (although significant proportion of the risk is secondary to coeliac disease). DR3 and/or DQ2.5 are linked to the following diseases: Moreen’s ulceration, “bout onset” multiple sclerosis, Grave’s disease and systemic lupus erythematosus.

I can’t say that I felt great when I read this, but I was able to say to myself – “now I understand”. I was not unlucky to have an onset of autoimmune encephalitis, a very rare disease, I am unlucky to carry this genetic mutation, but given this mutation, coeliac disease and encephalitis are not so unlikely. How to use this information? I printed out my test results and handed them to my family doctor and my neuropsychiatrist. There is a difference between a one in a lifetime occurrence of brain inflammation after some virus and being genetically predisposed to multiple autoimmune diseases. Unfortunately it is the second case for me and I want to make sure that doctors are aware of this.

Another genetic mutation listed in my 23andme results is Gene: CFH. The variant tested is a change from a T to a C in the DNA sequence of the CFH gene. It results in a version of the complement factor H protein that may not be able to regulate the immune system as well. I have read about this mutation and did not find that much information, but it does mention that it also affects immune system regulation. Perhaps it is the combination of the two mutations – in the HLA and CFH genes that for me lead to development of several autoimmune diseases. Research and time will tell us more.

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Neuropsych Amateur

Misdiagnosed with schizophrenia for a year. Later on received the correct diagnosis of autoimmune encephalitis (Hashimoto's Encephalitis) in April 2017. This is me trying to understand this autoimmune disease, what led to it, and why it took so long to diagnose.

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