The study by an international team led by researchers at the Broad Institute and Massachusetts General Hospital (MGH) suggests that if a drug can be developed that mimics the protective effect of these mutations, it could open up new ways of preventing the disease.
Type 2 diabetes affects over 300 million people worldwide and is rising rapidly in prevalence, researchers said.
In the new study, they described the genetic analysis of 150,000 patients showing that rare mutations in a gene called SLC30A8 reduce risk of type 2 diabetes by 65 per cent.
The protein encoded by SLC30A8 had previously been shown to play an important role in the insulin-secreting beta cells of the pancreas, and a common variant in that gene was known to slightly influence the risk of type 2 diabetes.
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However, it was previously unclear whether inhibiting or activating the protein would be the best strategy for reducing disease risk - and how large an effect could be expected.
The study selected people with severe risk factors for diabetes, such as advanced age and obesity, who never developed the disease and had normal blood sugar levels.
Because this particular genetic variation was exceedingly rare outside of Finland, it proved difficult to obtain additional evidence to corroborate the initial discovery.
Then, in 2012, these unpublished results were shared with deCODE genetics, a biopharmaceutical company based in Iceland, who uncovered a second mutation in an Icelandic population that also appeared to abolish function of the gene SLC30A8.
That mutation independently reduced risk for type 2 diabetes and also lowered blood sugar in non-diabetics without any evident negative consequences.
The T2D-GENES Project joined the collaboration, found ten more mutations in the same gene, and again saw a protective effect.
The study was published in the jounal Nature Genetics.