Incompletely penetrant PKD1 alleles suggest a role for gene dosage in cyst initiation in polycystic kidney disease

Abstract

Autosomal dominant polycystic kidney disease (ADPKD) caused by mutations in PKD1 is significantly more severe than PKD2. Typically, ADPKD presents in adulthood but is rarely diagnosed in utero with enlarged, echogenic kidneys. Somatic mutations are thought crucial for cyst development, but gene dosage is also important since animal models with hypomorphic alleles develop cysts, but are viable as homozygotes. We screened for mutations in PKD1 and PKD2 in two consanguineous families and found PKD1 missense variants predicted to be pathogenic. In one family, two siblings homozygous for R3277C developed end stage renal disease at ages 75 and 62 years, while six heterozygotes had few cysts. In the other family, the father and two children with moderate to severe disease were homozygous for N3188S. In both families homozygous disease was associated with small cysts of relatively uniform size while marked cyst heterogeneity is typical of ADPKD. In another family, one patient diagnosed in childhood was found to be a compound heterozygote for the PKD1 variants R3105W and R2765C. All three families had evidence of developmental defects of the collecting system. Three additional ADPKD families with in utero onset had a truncating mutation in trans with either R3277C or R2765C. These cases suggest the presence of incompletely penetrant PKD1 alleles. The alleles alone may result in mild cystic disease; two such alleles cause typical to severe disease; and, in combination with an inactivating allele, are associated with early onset disease. Our study indicates that the dosage of functional PKD1 protein may be critical for cyst initiation.

Figure 1. Homozygous inheritance of PKD1: R3277C in a consanguineous family

(a) Pedigree of family M34 showed inheritance of PKD through four generations, but only II2 and II3 (black shading) have renal impairment; age at ESRD is shown. Individuals with mild disease are shaded and total cyst number detected by CT or magnetic resonance imaging at the indicated age are shown, including multiple cysts (MC) in I1 at autopsy. Segregation of the R3277C alleles (R or C) is indicated below each patient where information is available, parenthesis indicate inferred genotypes. (b) (II2) Unenhanced coronal MR image (top) and axial MR image (bottom) following administration of gadolinium and (II3) unenhanced CT analysis shows bilaterally enlarged kidneys with numerous small and uniform cysts. Following the administration of gadolinium, there is layering of the contrast (white arrows) in dilated calyces (II2). Single cysts are indicated with arrowheads on CT (III1 and III2) or magnetic resonance imaging (III4) of mildly affected individuals. (c) Wild-type (wt), heterozygous (het), and homozygous (hom) sequence of R3277C showing the normal and variant DNA and amino-acid sequence. (d) Multisequence alignment of PC1 orthologues as indicated shows R3277 is invariant. PC1-like human sequences, as indicated, illustrate a high level of conservation of R3277.

Figure 2. Homozygous inheritance of PKD1: N3188S in a consanguineous Pakistani family

(a) Pedigree showing renal phenotype; multiple cysts (MC), in utero (IU) PKD, or negative ultrasound (–ve U/S) and the genotype of N3188S (N or S). (b) Sequence of N3188S showing the wild-type (wt), heterozygous (het), and homozygous (hom) DNA and amino-acid sequence. The position of IVS27 is also indicated. (c) Sequence alignment of PC1 orthologues and human PC1-like proteins as indicated. N3188 is completely conserved in the orthologues and well conserved in homologues, but is serine in PC1L1.

Figure 3. Family M390-inherited PKD1 variants: R2765C and R3105W

(a) Pedigree of M390 showing the proband II5, who has multiple cysts (MC) in the kidney, and mildly affected individuals (II2 and II3) with single cysts; negative imaging data and age are illustrated. The R2765C (R or C) and R3105W (R or W) genotypes are shown below. Only II5 is a compound heterozygote. (b) CT images of II5 kidney (top and middle) showing multiple renal cysts and (bottom) a single liver cyst (arrowheads). (c) CT of II2 showing a single large cyst. (d) Sequence data illustrating the two variants showing the nucleotide and amino-acid changes. (e) Sequence alignment of PC1 orthologues and human PC1-like homologous proteins. R3105 is highly conserved as a basic residue in all homologues. (f) Multisequence alignment of PC1 orthologues shows that R2765 is a basic residue in all species.

Figure 4. Pedigrees of three families with in utero ADPKD presentations that have inherited a truncating and a hypomorphic ADPKD allele

Each family has an in utero (IU) case, and renal phenotypes of other family members are shown: multiple cysts (MC); negative ultrasound (–ve U/S), or ESRD. Genotypes of the PKD1 variants: a, Q2158X and R3227C; b, Y3819X and R2765C; and c, 7915dup20 and R2765C, are shown below each pedigree. The etiology of cysts in P118 I1 is unclear but could potentially represent a low level of mosaicism not detected by sequence analysis.