The gene mutation, found in the population of Greenland, will give clues to the different causes of the condition, said Danish scientists.
The new mutation is present in almost one in five of Greenlanders and raises the risk of type 2 diabetes by up to ten times, researchers said.
However, it was not found in other European, Chinese or African-American populations, suggesting type 2 diabetes has multiple causes, Professor Torben Hansen, of the University of Copenhagen told 'BBC News'.
The team analysed blood samples from 5,000 people for 250,000 gene variants which play a role in metabolic diseases such as diabetes, obesity and cardiovascular disease.
"Our attention was quite soon caught by a particular variant of the TBC1D4 gene which controls glucose uptake in muscle cells," said Assistant Professor Niels Grarup from the Novo Nordisk Foundation Center for Basic Metabolic Research at the University of Copenhagen.
"Roughly speaking, this means that in carriers of this particular gene variant, the uptake of glucose by the muscles is hampered, for example after a meal which results in raised blood glucose levels.
"However, this particular gene variant is primarily found in Greenlanders, and about 23 per cent of the Greenlandic population are carriers of the variant which prevents the optimum functioning of the glucose transporters in the cells," he said.
Sixty per cent of the test individuals aged above 40 who had inherited the gene variant from both their mother and their father had type 2 diabetes. For the group aged above 60, the figure was 80 per cent.
"If you have inherited the gene variant from both your parents, the risk of developing diabetes is, of course, extremely high. This was the case for 4 per cent of the Greenlanders we examined," said Grarup.
"We already know of a number of gene variants in European populations which slightly raise the risk of developing diabetes, but this new gene variant has a much more pronounced effect than we have ever seen before," he added.