Cleft palates and similar facial conditions, immune system and calcium deficiencies can all be associated with problems in the same genes, said John Burn, professor of clinical genetics, Newcastle University at the British Association Festival of Science.
The university has carried out a study of almost 600 children which is helping for the first time to build up a picture of what causes heart defects and why some defects run in the family.
The walls of the heart, facial tissue and the glands governing immunity and calcium levels are all formed from the same group of cells. Normally, the cells - which are "left over" after the formation of the spinal cord - migrate from the back of the neck early in pregnancy to form the heart, face and glands. But in babies who lack the suspect group of genes, the cells fail to migrate properly.
Around one in 200 babies is born with a significant heart defect and one in 40 of these is missing the crucial group of 17 genes. A higher proportion is found among those born with severe heart problems.
The discovery of the faulty genes may help the diagnosis of heart defects and other linked conditions. It will particularly help parents who already have one child with heart problems and want a second child.