Yes, genetic C1q deficiency can lead on to a lupus-type illness with low C3 and or C4, I am fairly sure. It is not common to test all complement component levels and genes. Traditionally the functional tests have been C3, C4 and something called CH50. Genetic tests have been available more recently mostly on a research basis but things have probably moved on quite a lot since I retired.
Thought I would post what I ended up finding out about my low C3.
I saw an immunologist at the University of Washington (Seattle) last month. He ran C3, C4, CH50 and AH50 tests. He also ran a Pneumococcal Titer test and a T-Cell Subset Panel.
My C3 came back exactly the same as it has 2 other times (30% of normal) and CH50 is also low (11 points below normal range). C4 still normal and AH50 was normal. Pneumococcal titers normal, CD4/CD8 Ratio inverted due to elevated CD8.
He said he considers my inverted CD4/CD8 Ratio to be normal and that my elevated CD8 is normal and means my immune system is working well. He also did not think that my low NK Cell Function test (this was run by ME/CFS specialist) result of 4% was of much clinical significance or that it was anything to worry about.
As for my low C3 and CH50 he said it's his opinion that it's most likely a partial genetic deficiency of C3 itself, but that he is not aware of any further testing that can establish this with 100% certainty (ie: genetic testing). I still feel a genetic Factor H or Factor I deficiency need to be ruled out at a deficiency of either one causes low C3 and CH50 as a result. My 23andme results do show that I am homozygous for at least 2 C3 gene variants, both of which aren't all that common, and I also have at least 1 homozygous CFH (factor H) variant.
As for health effects of a partial C3 deficiency. The immunologist says he does not consider me to have a primary immune deficiency because of it, but that I should inform my doctors that I have low complement, and any time there is suspicion that I may have a bacterial infection to always err on the side of caution and take antibiotics. This seems smart to me as I do seem to have a slightly higher susceptibility to bacterial infections than most people.
He has referred me to a colleague of his who specializes in both immunodeficiency and rheumatology as he does think it's within the realm of possibilities that my low C3 could be causing me to experience autoimmune or autoimmune-like symptoms (ex: lupus-like illness). He said he already discussed my case with this colleague, and he had some suggestions for further testing that could be done. I'm hoping this other doctor will be great and will be able to help me sort this low C3 thing out a bit more in relation to my symptoms. Plus hopefully agree to check my Factor H and Factor I, and C2 levels also which has yet to be done. If it is indeed an isolated partial C3 deficiency then it is within the realm of possibility that it could cause autoimmune symptoms. I've found cases in medical journals in which someone with a partial C3 deficiency (with levels similar to mine) who developed autoimmune/autoimmune like symptoms. I've also read that it's thought that the potential for C3 deficiency to cause autoimmune problems is subestimated.
UPDATE: I've secured an appointment with the immunodeficiency/rheumatology specialist for the beginning of November. Which is great seeing as this doctor only sees patients 1 day a week for half a day. I should also be getting the results of my skin nerve biopsies my neurologist had done on my left hip and leg to look for evidence of Small Fiber Peripheral Neuropathy as I have had the classic symptoms of it in my my feet for many years now (I'm in my late 30's) and in the past year it seems to have spread to one side of my face and my hands as well.