Evidence for Pathogenicity of Atypical Splice Mutations in Autosomal Dominant Polycystic Kidney Disease

Background and objectives: Mutation-based molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) is complicated by locus and allelic heterogeneity, large multi-exon gene structure and duplication in PKD1, and a high level of unclassified variants. Comprehensive screening of PKD1 and PKD2 by two recent studies have shown that atypical splice mutations account for 3.5% to 5% of ADPKD. We evaluated the role of bioinformatic prediction of atypical splice mutations and determined the pathogenicity of an atypical PKD2 splice variant from a multiplex ADPKD (TOR101) family.Design, setting, participants, & measurements: Using PubMed, we identified 17 atypical PKD1 and PKD2 splice mutations. We found that bioinformatics analysis was often useful for evaluating the pathogenicity of these mutations, although RT-PCR is needed to provide the definitive proof.Results: Sequencing of both PKD1 and PKD2 in an affected subject of TOR101 failed to identify a definite mutation, but revealed several UCVs, including an atypical PKD2 splice variant. Linkage analysis with microsatellite markers indicated that TOR101 was PKD2-linked and IVS8 + 5G→A was shown to cosegregate only with affected subjects. RT-PCR of leukocyte mRNA from an affected subject using primers from exons 7 and 9 revealed six splice variants that resulted from activation of different combinations of donor and acceptor cryptic splice sites, all terminating with premature stop codons.Conclusions: The data provide strong evidence that IVS8 + 5G→A is a pathogenic mutation for PKD2. This case highlights the importance of functional analysis of UCVs.Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disorder worldwide, affecting approximately one in 500 live births. It is characterized by focal development and progressive enlargement of renal cysts, leading to end-stage renal disease (ESRD) in late middle age. Typically, only a few renal cysts are detected in most affected subjects before 30 yr of age. However, by the fifth decade of life, hundreds to thousands of renal cysts are found in most patients. Overall, ADPKD accounts for 5% to 8% of end-stage renal disease (ESRD) in developed countries (1,2). Extrarenal complications of ADPKD are variable and include inguinal hernias, colonic diverticulae, valvular heart disease, and intracranial arterial aneurysms (1).Mutations of two genes, PKD1 (MIM 601313) and PKD2 (MIM 173910), account for approximately 85% and 15% of all cases of ADPKD in linkage-characterized European populations (3,4). Although the clinical manifestations of PKD1 and PKD2 overlap completely, a strong locus effect on renal disease severity is evident with more severe renal disease in PKD1 than PKD2 (median age at ESRD: 54 yr versus 74, respectively) (5). PKD1 is a large gene consisting of 46 exons with an open reading frame of approximately 13 kb and is predicted to encode a protein of 4302 amino acids. Its entire 5′ region up to exon 33 has been duplicated six times proximally on chromosome 16p, and the presence of these highly homologous pseudogenes has made genetic analysis of PKD1 difficult (1,2). Recent availability of protocols for long-range and locus-specific amplification of PKD1 has enabled the complete mutation screening of this complex gene (6–9). In contrast, PKD2 is a single-copy gene consisting of 15 exons with an open reading frame of approximately 3 kb and is predicted to encode a protein of 968 amino acids (1,2).The diagnosis of ADPKD is straightforward in affected subjects with a positive family history and enlarged kidneys with multiple cysts (6). Renal ultrasound is a useful method for this purpose, and age-dependant criteria based on cyst number have been derived for subjects born with 50% risk of PKD1 or PKD2 (6,10). However, ultrasound diagnosis of ADPKD in younger at-risk subjects with equivocal or negative findings and in subjects affected by PKD2 or de novo disease remains a challenge (6). For these reasons, molecular screening is a useful tool in the clinical setting. However, marked allelic heterogeneity is evident, with over 200 different PKD1 and over 50 different PKD2 mutations reported to date (2,6–9,11–13). The majority of these mutations are unique and scattered throughout both genes. Although the majority of these mutations are predicted to be protein truncating (frame-shift deletion/insertion, nonsense or canonical splice changes), a large number of unclassified variants (UCVs; in-frame deletions, mis-sense and atypical splice changes) has also been reported (7–9). Comprehensive screening of both PKD1 and PKD2 by two recent studies identified definitive and probable mutations in 42% to 63% and 26% to 37% of patients, respectively (8,9). These two studies also reported that atypical splice mutations account for approximately 3.5% to 5% of ADPKD (8,9). In the current study, we performed and evaluated the utility of bioinformatics analysis on 17 reported atypical PKD1 and PKD2 splice mutations. We also determine the pathogenicity of an atypical splice variant found in a family affected by PKD2 and highlight the importance of functional analysis of UCVs in molecular diagnostic testing.