Make your own free website on

Some SCID Learning Resources

2.  PNP Deficiency

Adriana van der Merwe is a 6 year old girl, living in Johannesburg, South Africa. On September 9th, 2002 Adriana was diagnosed as having SCID - severe combined immunodeficiency caused by purine nucleoside phosphorylase (PNP) deficiency .

SCID (PNP) deficiency is a very rare genetic disease, initially described in 1975; since then 32 other patients with the disorder have been documented. Since this disease is very rare, not much is known about it.

Adriana's doctor, Dr. Michael Loubser, (011 462-5580) stated the following in his assessment: "Long-term outlook and management:   This is a very rare disease, less than 40 cases have been reported in the literature. Adriana is the 3rd patient with PNP deficiency that I have treated in the past 10 years. Unfortunately this disease carries a poor prognosis. Twenty nine of the 34 informative cases have died. Sixteen deaths were due to infections including three to chicken pox. Five were due to tumors (four lymphoma and one lymphosarcoma) and three died of GvHD following bone marrow transplantation."

Click here to read Dr Loubser's full assessment:

Purine nucleoside phosphorylase (PNP) deficiency
by Jody L. Duke

Purine nucleoside phosphorylase (PNP) deficiency is a very rare genetic disease. It is an autosomal recessive disorder, so both the father and the mother must pass a defective allele on to their child. PNP is an enzyme encoded by a gene on chromosome 14 that is 9000 bases long. This gene has 6 exons and 5 introns. When PNP is assembled, three PNP subunits join together to form a trimer. Each subunit has its own bonding site, so they can work independently even while joined together. Consequently, a person heterozygous for this disorder can still function normally because they have a normal allele to code for an active protein. PNP is supposed to free the base guanine from its sugar and phosphate so that it can be used again. When PNP is defective, the guanines with phosphate and sugar still attached (called dGTP) build up and inhibit another enzyme, called ribonucleotide reductase, from working. When ribonucleotide reductase is inactive, DNA synthesis can't occur and cells can't replicate.

The lack of cell replication is especially critical in the immune system. T-cells in the immune system are needed to fight infections, and B-cells, when activated by T-cells, engulf and destroy pathogens. When PNP is defective, T-cells can't replicate and therefore can't activate B-cells or combat infections, causing a condition known as SCID (severe combined immune deficiency). Children with PNP deficiency are highly prone to infections, autoimmune disorders, neurological impairment, and cancer. They are more susceptible to cancer because they don't have T-cells to secrete biochemicals to kill the cancer cells. These children usually die in their teens or earlier of infection or cancer. However, if PNP deficient children are protected from infections and carcinogens, their chances of surviving longer will be increased.

PNP deficiency was initially described in 1975, and since then 32 other patients with the disorder have been documented. Since this disease is very rare, not much is known about it. We are just beginning to learn the genetic basis of PNP deficiency.

In the gene for PNP that is 9000 bases long, four point mutations are known to be linked to the disorder. These mutations have been described in papers by Lucy Andrews and several colleagues. In an allele of one PNP deficient patient, a missense mutation in exon 2 at amino acid position 51 changed the sequence AGT to GGT, which changed the amino acid from serine to glycine. These two amino acids are similar in size and shape, so this mutation doesn't affect the enzyme. This may be a mutation that occurs throughout the population but it doesn't have a visibly different phenotype. Another mutation was shown in exon 4 at amino acid position 128. GAT is switched to GGT, causing aspartic acid to change to glycine. This mutation affects the charge of the molecule and therefore renders the protein inactive. A third mutation was found at amino acid position 234 when CGA was changed to CCA, exchanging a proline for an arginine. These two amino acids are differently charged and position 234 is in a very tight turn. Proline changes the entire structure of the protein so it is now inactive.

These three mutations were described in a patient in 1992. A fourth mutation was described in a patient in 1995, yet this mutation was not describe in the patient studied earlier. This mutation is a switch from G to T in the very last base of exon 2. When the intron between exons 2 and 3 was spliced, the splicing machinery did not stop at exon 2. Instead is followed all the way through to intron 1. This means that exon 2 was mistakingly spliced out and now the PNP protein is lacking that exon. Also, a more serious problem is created. The G to T switch occurs at the first base in a codon. This first base is indeed part of exon 2, but the remaining two bases of the codon were in exon 3. With exon 2 gone and that first base of the codon missing, the rest of the gene is frameshifted, rendering it ineffective.

Most of these discoveries of mutations leading to PNP deficiency occurred using standard genetic techniques. The DNA of the PNP deficient patients, the patient's parents, and a normal subject were isolated. Then the DNA was cut with restriction enzymes, denatured into single strands, and amplified using PCR. The amplified DNA was sequenced by gel electrophoresis and blotting techniques. Several methods, like the Bethesda Research Laboratories dsDNA sequencing kit, were used to accomplish the sequencing.

The discovery of these different mutations has a very important implication. PNP deficiency is clearly caused by different defects in the gene. It may be difficult to detect with genetic testing because it is unclear how many and which kind of mutations we are searching for. Surely, even more causes of PNP deficiency will be documented in the future, making detection even more difficult.


Andrews, Lucy G., Michelle R. Aust, and Michael Barrett. "Molecular Analysis of Mutations in a Patient with Purine Nucleoside Phosphorylase Deficiency." American Journal of Human Genetics 51 (1992): 763-72.

Andrews, Lucy G., and Louise M. Markert. "Exon Skipping in Purine Nucleoside Phosphorylase Deficiency mRNA Processing Leading to Severe Immunodeficiency." The Journal of Biological Chemistry 267 (1992): 7834-8.

Klug, William S., and Michael R. Cummings. Concepts of Genetics. New Jersey: Prentice Hall, 1994.


Forward to:

3. X-linked SCID
4. Autosomal SCID
Back to:
1. ADA-Deficiency SCID
2. PNP-Deficiency SCID