Mutations in the PKD1, PKD2, and PKHD1 genes are the primary cause of polycystic kidney disease (PKD). The type of disease is determined by which combination of these genes is affected.
 
Autosomal Dominant Polycystic Kidney Disease
Mutations in the PKD1 and PKD2 genes cause autosomal dominant polycystic kidney disease. The PKD1 gene is located on chromosome 16; the PKD2 gene is located on chromosome 4.
 
The functions of the proteins made by these genes are not fully understood, but it is known that they are involved in transmitting chemical signals from the outside of the cell to the cell's nucleus. Polycystic kidney disease research scientists believe that the two proteins work together to promote normal kidney development and function.
 
Mutations in the PKD1 or PKD2 gene lead to the formation of thousands of cysts, which disrupt the normal functions of the kidneys and other organs. People with mutations in the PKD2 gene typically have a less severe form of the disease than people with PKD1 mutations.
 
In about 90 percent of autosomal dominant PKD cases, an affected person inherits a mutation in the PKD1 or PKD2 gene from one affected parent. The other 10 percent of cases may result from new mutations in one of the genes. These cases occur in people with no history of the disorder in their family.
 
People with autosomal dominant polycystic kidney disease are born with one mutated copy of the PKD1 or PKD2 gene in each cell. Then, during their lifetime, a second mutation occurs in the other copy of the gene in kidney cells (or cells in other organs), triggering cyst formation. The rate at which cysts enlarge and cause a loss of kidney function varies widely; it may be accelerated by a second mutation in PKD1 or PKD2, or by mutations in other important genes.

Autosomal Recessive Polycystic Kidney Disease
The cause of autosomal recessive polycystic kidney disease is a mutation in the PKHD1 gene, located on chromosome number 6. Although the function of this gene is not yet known, it is likely that the protein made by the gene transmits chemical signals from outside the cell to the cell nucleus. Research scientists have not determined how mutations in the PKHD1 gene lead to the formation of numerous cysts and result in the characteristic features of polycystic kidney disease.
 
Acquired Cystic Kidney Disease
Although polycystic kidney disease is usually a genetic disorder, a small percentage of cases are not caused by gene mutations. These nonhereditary cases are called acquired cystic kidney disease. This form of the disorder occurs most often in people who have long-term kidney damage and in those who have been treated with dialysis (a procedure that filters the blood in people with kidney failure).