When your immune system comes into contact with a cell that has an HLA marker that is different than the markers on your cells your immune system will target the foreign cells for destruction.
Each of your cells presents a combination of more than 200 HLA markers. However, some of these markers are more important than others in terms of immune system recognition. There are 6 main HLA markers that the immune system uses to target foreign cells. These HLA markers are called HLA-A, HLA-B, HLA-C, HLA-DR, HLA-DP, and HLA-DQ. These HLA markers are coded for by genes on chromosome 6.
Genes code for proteins. The gene for HLA-A codes for an HLA-A protein. What makes this more complicated is that there are different versions of the HLA-A gene that code for different versions of the HLA-A protein. This is what makes it so that one person's HLA-A marker might be different than another person's HLA-A marker.
There are 59 known versions of the HLA-A gene, 118 versions of the HLA-B gene, and 124 versions of the HLA-C gene. With this much variation in just these three markers it can be very difficult to find a perfect match.
Inheritance of HLA markers
Mother's markers for all 6 HLA genes. Notice that she has two markers for each gene (because she has two copies of each chromosome) so there are 12 markers total.
A person with the markers shown below would be an 11/12 match to the mother as they have 11 markers that are identical and one marker (HLA-B12) different.