I also have very low vitamin d without supplementation, as dues my daughter who is now developing diabetes.
Low vitamin d is known to be common in people with autoimmune conditions. I saw a rheumatologist a few years back due to joint issues - still unresolved - and one of the first things he tested was vitamin d levels. It is known to be common in multiple sclerosis, and alternative treatment approaches include raising vitamin d levels.
Low vitamin d is implicated in flu illness with incidence highest towards end of winter when d levels are lowest.
It is, implicated in preterm births and other pregnancy complications. Vitamin D Council is leading expert group on this. Certainly interesting works.
There are genetic markers for probable low vitamin d. I have those markers, as does my daughter. Supplementing to be sure our levels are normal is prudent.
Is it implicated in cause, or is it effect? Not known yet.