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Sorry to hear about your vitamin B roller coaster ride! I think many people here can relate.
Did your functional medicine doc ever ask you to take folate or methyl-folate? It seems rather unusual for someone who knows a lot about methylation to advise taking B12 and B6/P5P, but not folate...
So the plan was that I was to start 250mg methyl-folate 2x per week 3 weeks after I had started the others but there was a delay in delivery and I received the methyl-folate the same day I decided I needed to stop all Bs. I took a dose of methyl-folate that morning and after talking to my husband that afternoon about all the strange symptoms I'd been having decided to stop the Bs. She based this protocol on my genetic profile, my labs over the last year, and my symptoms. I am taking other supplements as well and I'm awaiting the results of an extensive stool test and Magnesium labs.