A gene is basically a segment of DNA that encodes the blueprint for a specific protein. Each protein has a specific function. There are many different possible functions for proteins. Some proteins encode enzymes that digest a particular kind of food substance. Some proteins carry important things from one place to another, such as oxygen being carried through the blood. Some proteins are involved in the synthesis of the different components of our tissues: they make copies of the DNA and other parts of each cell when it divides into two cells. Some proteins are themselves structural and the most important group of these are the collagens. There are many different kinds of collagen that are involved in different structures of the body, such as bone, cartilage and muscle. In nearly all cases, they have a structural role. Alport syndrome is caused by damage in any one of three genes that encode a form of collagen that is important in the kidney. A large part of the molecular genetic study of Alport involves checking for whether individuals with a disease that may be Alport have mutations in these particular collagen genes.
There are many families in the Alport study, so we have tried to develop efficient methods for collagen gene mutation screening. The following table summarizes year by year accumulation of independently ascertained kindreds who actively participate in the University of Utah study, by providing medical information and blood or other specimens.
The period marked <'90 covers the years 1949-1990. "Non-Alp HN" refers to seven families with an unknown form of hereditary nephritis that is almost certainly not Alport syndrome. About 7 families have left the study, mainly when the only affected family members declined to participate, so that the total of participating Alport families at the end of 1998 was roughly 253.
Mutation detection
Although we have used various other methods in the past, the most rapid means that we currently have available for molecular diagnosis is mutation detection. By this approach, we attempt to find the specific molecular genetic defect that causes the disease in a particular family. This approach would not be possible unless we knew the specific genes that cause most forms of Alport Syndrome. Since there are 100,000 genes in the human genome and there are thousands of "parts" to each gene that might be defective, it is not now possible to perform a test of ALL of the genes in any single individual. In fact, it is still rather difficult to test even ONE gene in a single individual. Genes vary in size and small genes are easier to "scan" for mutations than big ones. The X-linked Alport gene, COL4A5, happens to be a very large gene.
Because COL4A5 is so large, most methods that are used to identify mutations involve breaking the gene down into smaller sub-segments and examining each of these sub-segments for some change that would destroy the normal function of the gene. Since different families almost always have different mutations, the entire gene must be examined in every new family.
There are various methods of mutation detection. What they all have in common is some means of comparing a particular DNA segment from many individuals and looking for ones that show an unusual pattern. Many times these unusual patterns indicate the presence of a change in the DNA that has damaged the gene where it occurs. There are different types of genetic damage that may occur. The "code" may be altered so that a protein with a different structure is produced. This almost always results in a protein that does not work as well. Other kinds of mutations damage the expression of the gene without actually altering the code.
At the present time, the COL4A5 mutations for 137 of 253 Alport families in the Utah study have been identified. Once the specific damaging change has been identified in one individual from a family, other members of the same family can be tested. Since the specific change has been defined for that family, it is generally straightforward to test other family members for it.
