There are many types of connective tissue diseases (about 200, I read). Some of the better known are rheumatoid arthritis, lupus (SLE), and scleroderma. These are the ones for which the anti-nuclear antibodies are used for diagnosis. Rheumatoid arthritis can lead to craniocervical instability in adulthood, caused by inflammatory arthritic changes in the C0(skull)-C1 joint. Although not well known, joint hypermobility and antlanto-axial subluxation (C1-C2) can occur in SLE (as described in this article).
There's a different kind of connective tissue disorder more typically associated with widespread abnormalities of collagen, including the Ehlers Danlos Syndromes (EDS), Marfan Syndrome and others.
Marfan Syndrome is usually diagnosed by clinical presentation, as shown on this web page. Loewy-Dietz Syndrome diagnosis uses a mixture of clinical criteria and genetic testing. Shprintzen Goldberg Syndrome is a rare connective tissue disorder in which patients may resemble Marfan's patients and in which craniosynostosis (premature fusion of the skull bones in infants) is common, and it is also diagnosed with a combination of clinical features and genetic testing.
As for non-hereditary connective tissue disorders, according to a webpage on the Cleveland Clinic's site, the following are potential causes of such:
Connective tissue diseases can also be caused by things that exist in the environment. Non-inherited causes of autoimmune types of connective tissue disease may include:
Exposure to toxic chemicals, such as those found in air pollution and cigarette smoke.
Exposure to ultraviolet light.
Inadequate nutrition, including lack of vitamins D and C.
Exposure to solvents is thought by some to be a risk factor for scleroderma in particular. There are some studies indicating that cigarette smoking by mothers may increase the risk of RA and SLE. Silicone breast implants have been associated with an increased incidence of some autoimmune diseases, including scleroderma, RA and SLE (see the study from 2018 discussed here).
Emphysema, which is a breakdown of lung connective tissue, appears to result from exposure to chemicals that cause release of metalloproteases in the lung. Metalloproteases are collagen degrading enzymes that are now suspect for causing inherited connective tissue problems, such as CCI/AA after infections (at present mainly suspected only by intrepid patient thinkers/researchers). Search on this forum for discussions of Matrix Metalloproteases (MMPs).
Infections are a possible causes of MMP-related issues, including by coxsackie viruses and Borellia (Lyme disease causing and related bacteria). To my knowledge the hypothesis that MMPs are the cause of non-hereditary collagen breakdown leading to CCI/AAI has hardly been studied. I did find this nice little article in the journal Spine that established an association between MMP activity in RA and progression of lesions at the antlantoaxial joint: Predictors for the Progression of Cervical Lesion in Rheumatoid Arthritis Under the Treatment of Biological Agents.I hope that this becomes a topic of intense investigation soon!