Contribution of a common single-nucleotide polymorphism to the genetic predisposition for erythropoietic protoporphyria

Abstract

Erythropoietic protoporphyria (EPP) is an inherited disorder of heme biosynthesis that results from a partial deficiency of ferrochelatase (FECH). Recently, we have shown that the inheritance of the common hypomorphic IVS3-48C allele trans to a deleterious mutation reduces FECH activity to below a critical threshold and accounts for the photosensitivity seen in patients. Rare cases of autosomal recessive inheritance have been reported. We studied a cohort of 173 white French EPP families and a group of 360 unrelated healthy subjects from four ethnic groups. The prevalences of the recessive and dominant autosomal forms of EPP are 4% (95% confidence interval 1-8) and 95% (95% confidence interval 91-99), respectively. In 97.9% of dominant cases, an IVS3-48C allele is co-inherited with the deleterious mutation. The frequency of the IVS3-48C allele differs widely in the Japanese (43%), southeast Asian (31%), white French (11%), North African (2.7%), and black West African (<1%) populations. These differences can be related to the prevalence of EPP in these populations and could account for the absence of EPP in black subjects. The phylogenic origin of the IVS3-48C haplotypes strongly suggests that the IVS3-48C allele arose from a single recent mutational event. Estimation of the age of the IVS3-48C allele from haplotype data in white and Asian populations yields an estimated age three to four times younger in the Japanese than in the white population, and this difference may be attributable either to differing demographic histories or to positive selection for the IVS3-48C allele in the Asian population. Finally, by calculating the KA/KS ratio in humans and chimpanzees, we show that the FECH protein sequence is subject to strong negative pressure. Overall, EPP looks like a Mendelian disorder, in which the prevalence of overt disease depends mainly on the frequency of a single common single-nucleotide polymorphism resulting from a unique mutational event that occurred 60,000 years ago.

Figure 1

A, Exon/intron organization of the human FECH gene and reported mutations responsible for EPP. Previously unreported mutations are shown in bold. B, Differences between human and chimpanzee cDNA. Bold vertical lines denote exons, and unbroken lines denote introns. c = cDNA Sequence (human [GenBank accession number NM000140]; chimpanzee [GenBank accession number DQ149645]). p = Protein sequence (GenBank accession number NP000131). g = FECH Gene sequence (GenBank accession number AJ250235).

Figure 2

Schematic representation of the clinical, enzymatic, and molecular data of the 95 EPP families for which both FECH enzyme activity and gene defect were available. Wt = Wild-type allele; M =FECH-Mutated allele.

Figure 3

Peripheral lymphocyte FECH activity (nanomoles of mesozinc/hour/milligram of protein at 37°C) in six different groups are represented as box plots showing the median, the quartiles, and the 90th and the 10th percentiles. Additionally, the mean ± SD values are as follows: control group, 4.83 ± 0.91; IVS3-48T/T healthy relative group, 5.03 ± 0.66; IVS3-48T/C healthy relative group, 4.20 ± 0.60; asymptomatic carrier group, 2.42 ± 0.41; symptomatic patient group with the dominant form, 1.45 ± 0.32; and symptomatic patient group with the recessive form, 0.375 ± 0.15.

Figure 4

Phylogeny of the IVS3-48C haplotypes presenting the more parsimonious combination of single-site mutations and recombination events. Each haplotype is represented by a circle, the area of which represents the relative frequency of that haplotype amongst the overall IVS3-48C haplotypes. Each circle is subdivided to show the proportion of the individual haplotype frequency in each of the WF, SEA, and WA population groups. The solid lines connect haplotypes by single-site difference with precision of the position directly on the line. Dashed lines denote recombination events. The root haplotype (RH) is where the IVS3-48C mutation probably occurs. With a frequency of 9%, RH is the second most frequent WA FECH haplotype. The haplotype names are the same as in table 3.