Quantifying prion disease penetrance using large population control cohorts

Abstract

More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. We assess the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. We show that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.

Figure 1. Reportedly pathogenic PRNP variants are >30 times more common in controls than expected based on disease incidence

Reported prion disease incidence varies with the intensity of surveillance efforts (13), with an apparent upper bound of ~2 cases per million population per year (Materials and Methods). In our surveillance cohorts, 65% of cases underwent PRNP open reading frame sequencing, with 12% of all cases, or 18% of sequenced cases, possessing a rare variant (Table S1), consistent with an oft-cited estimate that 15% of cases of Creutzfeldt-Jakob disease are familial (31). Genetic prion diseases typically strike in midlife, with mean age of onset for different variants ranging from 28 to 77 (22, 32) (Table S10); we accepted 80, a typical human life expectancy, as an upper bound for mean age of onset, and to be additionally conservative, we assumed that all individuals in ExAC and 23andMe were below any age of onset, even though both contain elderly individuals (33) (Figure S1). Thus, no more than ~29 people per million in the general population should harbor high-penetrance prion disease-causing variants. Therefore at most ~1.7 people in ExAC (A) and ~15 people in 23andMe would be expected to harbor such variants. In fact, reportedly pathogenic variants are seen in 52 ExAC individuals (B) and on 141 alleles in the 23andMe database.

Figure 2. Reportedly pathogenic PRNP variants include Mendelian, benign, and intermediate variants

Prior evidence of pathogenicity is extremely strong for four missense variants - P102L, A117V, D178N and E200K - each of which has been observed to segregate with disease in multiple multigenerational families (–, –48) and to cause spontaneous disease in mouse models (–54). These account for >50% of genetic prion disease cases (Table S1), yet are absent from ExAC (Table S3), and collectively appear on ≤5 alleles in 23andMe’s cohort (Table S5), indicating allele frequencies sufficiently low to be consistent with the prevalence of genetic prion disease (Figure 1). Conversely, the variants most common in controls and rare in cases had categorically weak prior evidence for pathogenicity. R208C (8 alleles in 23andMe) and P39L were observed in patients presenting clinically with other dementias, with prion disease suggested as an alternative diagnosis solely on the basis of finding a novel PRNP variant (55, 56). E196A was originally reported in a single patient, with a sporadic Creutzfeldt-Jakob disease phenotype and no family history (37), and appeared in only 2 of 790 Chinese prion disease patients in a recent case series (57), consistent with the ~0.1% allele frequency among Chinese individuals in ExAC (Tables S5 and S8). At least three variants (M232R, V180I, and V210I) occupy a space inconsistent with either neutrality or with complete penetrance (see main text and Figure 3). R148H, T188R, V203I, R208H and additional variants are discussed in Supplementary Discussion.

Figure 3. Certain variants confer intermediate amounts of lifetime risk

M232R, V180I, and V210I show varying degrees of enrichment in cases over controls, indicating a weak to moderate increase in risk. Best estimates of lifetime risk in heterozygotes (Materials and Methods) range from ~0.08% for M232R to ~7.8% for V210I, and correlate with the proportion of patients with a positive family history. Allele frequencies for P102L, A117V, D178N and E200K are consistent with up to 100% penetrance, with confidence intervals including all reported estimates of E200K penetrance based on survival analysis, which range from ~60% to ~90% (, –26). Rates of family history of neurodegenerative disease in Japanese cases are from (Table S10) and in European populations are from Kovacs et al (21), with Wilson binomial 95% confidence intervals shown. *Based on allele counts rounded for privacy (Materials and Methods). †GSS, Gerstmann Straussler Scheinker disease associated with variants P102L, A117V and G131V. ‡FFI: fatal familial insomnia associated with a D178N cis 129M haplotype.

Figure 4. Effects of truncating variants in the human prion protein are position-dependent

Truncating variants reported in prion disease cases in the literature (Table S2) and in our cohorts (Table S1) cluster exclusively in the C-terminal region (residue ≥145), while truncating variants in ExAC are more N-terminal (residue ≤131). The ortholog of each residue from 23–94 is deleted in at least one prion-susceptible transgenic mouse line (70). C-terminal truncations abolish PrP’s glycosylphosphatidylinositol anchor but leave most of the protein intact, a combination that mediates gain of function through mislocalization, causing this normally cell-surface-anchored protein to be secreted. Consistent with this model of pathogenicity, mice expressing full-length secreted PrP develop fatal and transmissible prion disease (71, 72). By contrast, the N-terminal truncating variants that we observe retain only residues dispensable for prion propagation, and are likely to cause a total loss of protein function.