Yes, you can get Social Security Disability if you’ve been diagnosed with a rare disease. But, a diagnosis alone, even if it’s a rare disease that a lot of doctors and medical providers are not familiar with, is not enough to get Social Security Disability just based on the diagnosis.
Like any other disability, if you have a rare disease, you must show that your symptoms are so severe and not controlled by medication or other treatment to the extent that you are not able to work for at least a year or you’re not expected to be able to work for at least a year. If that is the case, with your condition, then you probably have a good claim for Social Security Disability Benefits.