The variant, a twelve-letter deletion in the ASGR1 gene on chromosome 17, was discovered by analyzing the entire genome and clinical information from across the population of Iceland.
It was also confirmed in data from some 300,000 people in other countries such as the UK, the US, Germany, and others.
Individuals have significantly reduced non-HDL cholesterol levels and the study also demonstrated a 35% lower than average risk of heart disease.
Amgen said the variation presents better protection against coronary heart disease than can easily be accounted for by the reduction in cholesterol alone.
The development of therapeutic compounds to inhibit the protein made by the gene is expected to provide the similar positive effect on cholesterol and heart disease in broad populations.
The similar rare variant/common disease paradigm has contributed to the development of PCSK9 inhibitors.
deCODE genetics founder and CEO Kari Stefansson said: "We know we have put our finger on something fundamental when we find a single variant that confers on carriers an average one year of extra lifespan.
"Our unrivalled population resources and knowledge of genetics in Iceland put us in a privileged position to systematically discover such low-frequency variants. As our model expands to different corners of the globe, we expect to accelerate our discovery and validation efforts to many populations and all continental ancestries."
deCODE has discovered important genetic risk factors for several common diseases ranging from cardiovascular disease to cancer.
Image: deCODE genetics’ study demonstrated a 35% lower than average risk of heart disease. Photo: courtesy of dream designs/FreeDigitalPhotos.net.