Aug 2026· Gene· Vol 1011, pp.
150340
· 0 citations· 50 references
Medicine
TL;DR
A novel missense variant is characterized that causes aberrant splicing of PKHD1 in CD and underscores the necessity of functional analysis for evaluating the pathogenicity of missense variants, especially those at the last nucleotide of an exon.
Abstract
Background
Caroli disease (CD) is a rare inherited disorder characterized by dilatation of intrahepatic bile ducts, and prenatal diagnosis of this disease is extremely rare. PKHD1 is the only known causative gene, yet the pathogenicity of most missense variants remains unclear.
Methods
Exome sequencing (ES) was performed on a fetus with clinical features of CD. Candidate variants were validated by Sanger sequencing in the family. The impact of the novel missense variant on pre-mRNA splicing was assessed using minigene assays, and structural modeling of the PKHD1 protein was conducted with AlphaFold 3.
Results
At 23 weeks of gestation, the fetus showed hepatic cysts on ultrasound and a "central dot" sign on MRI, suggesting a diagnosis of CD. The fetus also exhibited features of autosomal recessive polycystic kidney disease and oligohydramnios. ES identified and Sanger sequencing confirmed three PKHD1 variants: a paternal nonsense variant c.5323C>T; p.(Arg1775*), and two maternal missense variants c.6682G>C; p.(Glu2228Gln) and c.8012G>T; p.(Arg2671Leu). The variant c.6682G>C is novel and minigene assays demonstrated that it caused exon 40 skipping, leading to an in‑frame deletion (c.6491_6682del; p.(Gly2164_Arg2227del)). Structural modeling predicts that this deletion lies within a large β‑barrel domain and may compromise its structural stability. Conclusion We characterize a novel missense variant that causes aberrant splicing of PKHD1 in CD. This finding underscores the necessity of functional analysis for evaluating the pathogenicity of missense variants, especially those at the last nucleotide of an exon. Our study expands the mutation spectrum of PKHD1 and provides insights into genotype‑phenotype correlations.
In this study, pathogenic FBN1 variants were identified in three patients, thereby confirming the clinical diagnosis of MFS and contributing two novel variants to the FBN1 variant repository, and provide a comparative assessment of genotype-phenotype correlations.
Xing Zhao, L. Yuan, Yan Sun et al.· Clinica chimica acta; intern...· 0 citations
Background Congenital pulmonary airway malformation type IV (CPAM IV) and pleuropulmonary blastoma (PPB) exhibit significant radiographic and histopathological overlap, making their differentiation challenging. While DICER1 mutations are known to predispose individuals to the PPB spectrum, the molecular association between CPAM IV and early-stage PPB remains controversial. Case presentation We report a girl pathologically diagnosed with CPAM IV. Whole-exome sequencing (WES) of the lesion tissue identified a heterozygous splicing variant in the DICER1 gene (c.4206 + 1G > T). Sanger sequencing subsequently confirmed this variant to be germline, inherited from her asymptomatic father. Bioinformatic analysis predicted that this variant disrupts the highly conserved donor splice site of intron 22. Functional validation by RT-PCR demonstrated that the c.4206 + 1G > T variant results in exon fragment deletion. According to the ACMG/AMP guidelines, this variant was classified as likely pathogenic. Additionally, a somatic DICER1 hotspot mutation (c.5438A > G p.E1813G) was detected in the tissue, consistent with the two-hit tumorigenesis model. At the 22-month postoperative follow-up, although chest CT revealed a small cystic lucency with surrounding calcification, the patient remained clinically stable, without evidence of malignant progression or extrapulmonary involvement. Conclusion This article reports a case of CPAM IV carrying a pathogenic germline variant and a somatic hotspot mutation in the DICER1 gene. Our findings support the view that DICER1-associated CPAM IV may represent an early stage within the PPB disease spectrum. Given the incomplete penetrance of DICER1 syndrome and an approximately 50% risk of transmission to offspring, we propose that DICER1 genetic testing could be considered for selected pediatric patients diagnosed with CPAM IV, regardless of family history. This approach may aid in early and accurate differentiation, inform surgical management, and guide the development of appropriate long-term surveillance strategies.
Ya Dao, Shan Pei, Xichen Zhang et al.· Frontiers in Pediatrics· 0 citations
Background Autosomal dominant polycystic kidney disease (ADPKD) is most commonly caused by pathogenic variants in PKD1. Here, we reported the functional characterization of an intronic PKD1 variant identified in an ADPKD-affected family and its subsequent application in preimplantation genetic testing for monogenic disorders (PGT-M). Case presentation A three-generation ADPKD family was enrolled. Whole-exome sequencing revealed a heterozygous PKD1 c.7489 + 5G>A variant, which co-segregated with the disease and was initially classified as a variant of uncertain significance. A minigene assay demonstrated that the variant induced skipping of exon 18, leading to a frameshift (p.Arg2404Valfs*123), supporting its reclassification as pathogenic. The couple underwent PGT-M using trophectoderm biopsy, haplotype linkage analysis, and direct mutation detection. An unaffected pregnancy was achieved, and subsequent prenatal diagnosis confirmed the absence of the variant and a normal chromosomal karyotype. Conclusion We validated a pathogenic splicing variant in PKD1 and successfully applied PGT-M to prevent disease transmission, resulting in an unaffected pregnancy.
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