A. Chromosomal anomalies and genetic syndromes are often suspected when children are born with multiple problems or congenital anomalies, especially if they include mental retardation and developmental delays.
In the case of your son, the only real congenital anomaly is his horseshoe kidney, which is not that uncommon, occurring in about 1 in 400 persons. And mitral valve prolapse is also very common, affecting about five to ten percent of people.
Turner syndrome is a condition that can include all of your son's problems, including Grave's disease, mitral valve prolapse, scoliosis, and a horseshoe kidney, however, Turner syndrome only affects girls.
Another condition, Noonan Syndrome, also has similar symptoms, including scoliosis, heart defects, and renal anomalies. However, these children also have distinctive facial features (triangular shaped face, wide set eyes, down slanting eyes) and are usually short.
And kids with chromosome 22q11.2 deletions can have many of the conditions you mention, including Graves' disease. They do seem to have other findings though, like cleft lip and palate and more serious heart defects, so this condition may not really fit.
Marfan syndrome should also be suspected in tall kids with heart murmurs and scoliosis, but they don't usually have Graves' disease though.
When doing research, the National Organization of Rare Diseases can be helpful. Simply enter one or more symptoms or findings and see what diseases are commonly associated with them.
Jablonski's Multiple Congenital Anomaly/Mental Retardation (MCA/MR) Syndromes Database is another good resource. You can enter multiple congenital anomalies and see what conditions or syndromes match them.
As you can see, diagnosing a genetic condition can be difficult. And it is not always as simple as ordering a chromosome test, as some genetic conditions need more detailed FISH analysis to be detected.
At this point, an evaluation by a Pediatric Genetics Specialist would be the most helpful next step to see if there is a genetic condition linking your child's multiple problems.
The Rare Diseases site might also be helpful.

