Professor Bernard Keavney, from Newcastle University and The University of Manchester, led the research which included investigators from Newcastle, Nottingham, Oxford and Leicester universities in the UK, and colleagues in Europe, Australia and Canada.
Congenital heart disease (CHD) is the most common form of congenital malformation, occurring in seven in 1000 babies born and is one of the major causes of childhood death and illness.
Most patients born with CHD now survive to adulthood, so identifying the responsible genes is important as experts attempt to provide individual-specific genetic counselling for these people.
The genetic markers in the patients were compared to the markers of over 5,600 people in good health who acted as a control group.
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The researchers found a relationship between a particular region of the human genome and risk of atrial septal defect (ASD) - a "hole" between the heart's blood-collecting chambers, which they went on to confirm in additional cases of atrial septal defect and healthy controls.
"We found that a common genetic variation near a gene called Msx1 was strongly associated with the risk of a particular type of CHD called atrial septal defect or hole in the heart," Keavney said.
Researchers looked at all the major types of congenial heart disease (CHD), but they did not find a genetic marker common in all types of CHD.
"Our work also suggests that if we conduct larger studies we will be able to find genes that cause other types of CHD. Although we are not there yet, further studies may enable us to give better genetic counselling to high risk families," Keavney said.
"Such an understanding is fundamental to any attempt to treat people with heart disease at any age - for example those suffering from heart failure - using regenerative medicine," Keavney said.
The study was published in journal Nature Genetics.