Effect of Low Vitamine B12 on Class 1 Medical
I am not a doctor, really the best way to get definitive answers is by talking to an AME. 

Vitamin B12 deficiency isn't by itself any sort of issue, lots of people get less than they need because of diet, especially vegetarians and vegans. Vitamin B12 deficiency can lead to a form of anemia, which is potentially disqualifying, unless it can be kept below a certain level. 

So, if your doctor hasn't found any sort of anemia or other condition due to lack of B12 then there's no consideration on your medical. Work on getting more in your diet or keep up on the supplements. However, if you have anemia or some other condition due to the deficiency then it is a consideration on a medical.