Polycystic kidney disease (PKD) is a genetic disease that can be inherited in two different ways: autosomal dominant inheritance and autosomal recessive inheritance. Autosomal dominant polycystic kidney disease (ADPKD) is the most common single-gene hereditary kidney disease, with an incidence rate of about 1/1000-1/2500 (1, 2). ADPKD is classified into two types, polycystic kidney disease type 1 (OMIM173900) and polycystic kidney disease type 2 (OMIM613095). The discovery and cloning of the PKD1 and PKD2 genes have facilitated the development of molecular diagnostics based on DNA sequencing (3). About 78% of ADPKD cases are caused by PKD1 gene mutations on chromosome 16, and about 15% of cases are caused by PKD2 gene mutations on chromosome 4 (4, 5). The PKD1 and PKD2 genes encode polycystin 1 (PC1) and polycystin 2 (PC2), respectively, which are primarily located in the primary cilium of renal tubular epithelial cells. In addition to mutations in the PKD1 and PKD2 genes, other mutations have been found in some ADPKD patients, including GANAB, DNAJB11, IFT140 and other gene mutations that can cause atypical ADPKD (6–8). Mutations in genes related to autosomal dominant polycystic liver disease (PRKCSH, SEC63, LRP5, ALG8, and SEC61B) may also cause mild kidney phenotypes (9). Clinical manifestations of ADPKD include hypertension, hematuria, proteinuria, and decreased kidney function. Patients with ADPKD may also experience other complications involving multiple organs or tissues, such as liver cysts, pancreatic cysts, spleen cysts, and intracranial aneurysms.

About 50% of ADPKD patients usually progress to end-stage kidney disease (ESKD) by the age of 60 (10, 11). Evidence shows that about 5−10% of patients receiving kidney replacement therapy (KRT) worldwide have ADPKD, and it accounts for about 5% of ESKD patients in China, affecting about 1.25 million people (12). ADPKD is the fourth most common cause of ESKD, and it brings a heavy burden to society and families (3).

Currently, there have been significant advancements in understanding the pathogenesis of ADPKD in the fields of cell biology and molecular mechanisms. Mutations in the main genes PKD1 and PKD2 lead to various abnormalities in downstream cell signal transduction, including intracellular calcium disorders, abnormalities in cAMP and mTOR signaling pathways, and classical and non-classical Wnt pathway signal activation. These abnormalities partially explain the pathogenesis and progression of kidney cysts. In addition to the genetically abnormal PKD genes, several studies have shown that the formation of cysts requires the normal haplotype of secondary acquired somatic cell loss, known as the “second hit” hypothesis. Additionally, a “threshold” model for cyst formation has been proposed, suggesting that cyst formation may be triggered when the level of polycystin protein in renal tubular epithelial cells falls below a critical threshold (13). Despite significant progress in understanding the pathogenesis of ADPKD, several issues remain unresolved. For instance, while PC2 is known to function as a TRP-like calcium channel and interact with PC1 to regulate primary cilia signaling pathways, the exact role of calcium ions in the pathogenesis of ADPKD is still not fully understood. Moreover, the mechanism by which decreased polycystin signaling in cilia leads to the formation of cystic lesions remains unclear, highlighting the need for further basic and clinical research to expand our understanding of ADPKD’s pathogenesis (13, 14).

Early diagnosis of PKD patients, identification of pathogenic mutations in ADPKD families, regular monitoring of clinical indicators, and timely symptomatic treatment can help delay the progression of ADPKD. Genetic diagnosis is increasingly being used to provide information for the clinical management of PKD nephropathy patients. This approach can result in a more accurate diagnosis, targeted disease monitoring, treatment, and family genetic counseling (15). Studies have shown a high correlation between the phenotype and genotype of ADPKD patients, with pathogenic gene mutations being the primary determinant of disease progression (16). Several studies have shown that the type of mutation is closely related to the severity of ADPKD. Patients with PKD2 mutations generally have a milder form of kidney disease compared to those with PKD1 mutations (17). Additionally, frameshift mutations, nonsense mutations, and splice site changes in PKD1 truncated mutations are associated with more severe disease than non-truncated mutations, such as missense mutations and in-frame insertion/deletion (18–20). Furthermore, mutations in non-PKD1 or PKD2 genes can also result in the development of renal cysts. For example, the deletion of the tuberous sclerosis complex 2 (TSC2) gene adjacent to the PKD1 gene can cause a rare and severe form of polycystic kidney disease that often leads to ESKD in childhood (21).

In some cases of ADPKD, mutations in PKD1 or PKD2 genes are not detected, and somatic mosaicism may be present (22). These mutations are not concentrated in any specific location of the gene. Identifying gene mutations associated with ADPKD can aid in diagnosis and predicting disease progression. Ultrasound, the most commonly used diagnostic method, may have low sensitivity, particularly in high-risk individuals under 40 years of age, hindering early or presymptomatic diagnosis (23). With the advancements in precision medicine and increased understanding of cystic diseases, whole-exome sequencing (WES) using next-generation sequencing may become a vital tool in screening for ADPKD and providing accurate diagnoses and effective treatments.

This study involved the use of whole-exome sequencing (WES) to screen eight Chinese patients who had been diagnosed with ADPKD and then verified the results with Sanger sequencing in their family members. We also analyzed the pathogenicity of the mutations to identify the specific pathogenic mutation gene responsible for the disease in each patient and their family. Some of the gene mutations identified in this study have not been previously reported, which has important implications for both clinical practice and further research on ADPKD.

In this study, we aimed to analyze the gene mutations in 8 Chinese families with ADPKD. This investigation is crucial to expand the genetic diversity data of different ethnic groups, improve the ADPKD mutation database, and explore its underlying pathogenesis. Due to the differences in genetic backgrounds and environmental factors, there is considerable phenotypic variability among ADPKD patients. Key factors that determine the progression of ADPKD include age, PKD genotype (including mutation gene, mutation type, gene mutation location, and the presence of multiple gene mutations), urine protein, estimated glomerular filtration rate (eGFR), and highly adjusted total kidney volume (HtTKV) (30).

Two variants of the PKD1 gene were found in Pedigree A: c.8447T > C (p.Leu2816Pro) and c.4247T > G (p.Phe1416Cys). The first variant is known to cause ADPKD in several patients and families (26, 27). The pathogenicity of the second variant is unknown, and no information on its frequency in the population was found in the GnomAD databases. The proband and their father had ADPKD, with the father having the pathogenic mutation. The proband’s son is a carrier of the second variant with a normal phenotype. Further study is needed to determine the role of the second variant in ADPKD.

Pedigree B’s proband was diagnosed with ADPKD and has a frameshift mutation c.3298_3301delGAGT (p.Glu1100Thrfs*3) in PKD1 gene. The mutation is not reported in relevant databases, and leads to a truncated PC1 protein affecting its function (31). No information on its frequency in the population was found in the GnomAD databases. The mutation is suspected to be pathogenic based on ACMG guidelines and is inherited from the proband’s mother who died of ADPKD. The proband’s sister also has ADPKD and PL. The proband’s nephew carries the mutation but is currently asymptomatic. Further follow-up is ongoing.

In pedigree C, two variants were found in the PKD1 gene. One of the variants, c.6406C > T, has been reported as pathogenic (28). The other variant, c.4798A > G, is new and its pathogenicity is uncertain. The population frequency in the GnomAD is 0.000016. The variants may work together to cause the disease in the family. Family members with the variants show co-segregation of genotype and phenotype, with early onset of ADPKD and kidney failure. The role of the new variant in ADPKD needs further confirmation.

A new PKD1 gene mutation c.7567G > A (p.Glu2523Lys) was detected in pedigree D, with the proband, father, and son carrying it. The proband has ADPKD and CKD3, while the father was diagnosed with ADPKD in middle age and has normal kidney function. The mutation is predicted to have harmful effects on the gene and is considered pathogenic in this family, although its significance is uncertain according to ACMG guidelines. The population frequency of this mutation in the GnomAD is 0.000051. The proband’s son is a carrier and is being closely monitored. Further research is needed to determine the mutation’s role in ADPKD.

The proband in pedigree E have PKD1 gene mutations, including a harmful c.11215C > T(p.Gln3739*) nonsense mutation in exon 39 and a newly discovered c.11717G > C(p.Cys3906Ser) missense mutation in exon 43, which is of uncertain significance. The mutation frequency of c.11717G > C in the GnomAD databases is 0.000011. The proband’s sister is an ADPKD patient. Their father had ADPKD, suggesting inheritance. The proband’s daughter and nephew did not inherit the mutations. Both proband and his sister developed ESKD at an early age, and the two mutations are considered pathogenic when present together.

In pedigree F, the PKD1 gene of the proband and his younger brother with the disease was found to have a novel intron variation c.7703 + 5G > C. However, the proband’s daughter did not inherit these mutations. No reports on the mutation frequency of the population at this locus in the GnomAD databases. The mutation frequency of the population at this locus is unknown. Predictive analysis indicates harmful effects on the gene and mRNA splicing. The mutation is predicted to be pathogenic based on genetic characteristics and clinical manifestations. However, it is still uncertain based on ACMG guidelines. The proband and his siblings may have inherited the mutation from their father who had PKD. Further observation and follow-up are needed.

Pedigree G has a proband who developed ADPKD in their youth and entered ESKD 30 years later. The proband’s daughter has ADPKD but normal kidney function. One of the mutations, c.8312A > T (p.Glu2771Val), has been reported previously (29), while the other mutation, c.3296G > A, is likely a new mutation, the mutation frequency in the GnomAD databases is 0.000061. Both mutations are predicted to be harmful and affect PKD1 mRNA splicing. According to ACMG guidelines, the mutations are classified as of uncertain significance. The proband’s son is negative for the mutations and apparently normal. The mutations are considered pathogenic and require further follow-up observation.

In pedigree H, the proband and his son have two mutations in PKD1: a frameshift mutation and a missense mutation, which are likely new mutations. The frameshift mutation is predicted to be harmful and classified as pathogenic, no reports on the mutation frequency of the population at this locus in the GnomAD databases. The missense mutation is predicted to be harmful by one software tool (SpliceAI) and polymorphic/neutral by others, with uncertain significance, the mutation frequency in the GnomAD databases is 0.000006 in the GnomAD databases. The proband’s father had ADPKD, suggesting inheritance of the mutations. The proband has early onset ADPKD and his son has a single renal cyst with normal liver and kidney functions, currently under monitoring.

In this study, 13 mutation sites were identified in the PKD1 gene, including 9 new mutations not previously reported, from 8 ADPKD probands (Figure 9). Among the 8 probands, 4 had progressed to ESKD, with ages ranging from 38 to 58 years old, and all had chosen hemodialysis as their kidney replacement therapy. Hypertension is a common occurrence in ADPKD patients, with about 60% diagnosed before kidney function decline (32, 33). The average age of hypertension diagnosis in PKD1 mutation patients is around 39 years old (26). Seven of our 8 probands had hypertension, except for probands E and D, who were diagnosed at the same time or after the ADPKD diagnosis. It remains uncertain whether hypertension in ADPKD is caused by the primary angiopathy of polycystic protein gene mutation or the activation of a renal renin-angiotensin-aldosterone system (RAAS) due to cyst expansion, and further research is needed. Therefore, gene detection can offer valuable insights for the diagnosis and treatment of ADPKD with hypertension. ADPKD typically occurs after the age of 40 and 100% by age 80, making it a late-onset disease (34). In this study, PKD1-related mutations were also found in family members who appeared clinically normal and were younger than 21 years old. The absence of related clinical manifestations in these family members can be explained by the age-dependent delayed dominance of ADPKD, which requires further follow-up and observation.

The human PKD1 gene is made up of 46 exons with complex structures. However, the presence of six pseudogenes, which are highly homologous to exons 1 to 33 of PKD1, poses a challenge to the molecular diagnosis of ADPKD (35). Second-generation sequencing technology has revolutionized genetic analysis, enabling disease group screening, WES, and even whole genome analysis, replacing single gene analysis based on Sanger sequencing. To date, the ADPKD mutation database has recorded 2,322 pathogenic PKD1 mutations. However, most of these mutations occur only once in a single family, with few duplications. Therefore, it is necessary to investigate more families to confirm known mutations and discover new ones. Gene decoding-based basic and clinical studies of related drugs have shown that cystic disease progression can be delayed to varying degrees. Identifying specific pathogenic genes and alleles can help determine the disease prognosis, influencing disease management and the formulation of treatment plans (9, 36). If gene testing can help predict the benefits that drug therapy, represented by tolvaptan, can bring to ADPKD, it can create greater value for patients (37). However, slowing down cyst progression is not a long-term solution. The fundamental strategy is to reverse the functional re-expression of the pathogenic PKD gene at the physiological level in vivo. Stefan Somlo’s research team at Yale University has established a mouse model of PKD inactivation and reactivation to examine the impact of PKD inactivation on renal structure and function. They found that the re-expression of the PKD gene in the cystic kidney can rapidly reverse ADPKD, reducing cyst cell proliferation, activating autophagy, and restoring the cystic tubules to a normal lumen lined by cubic cells. Since the ADPKD phenotype is reversible, at least partially controlled by the function of the ADPKD gene (38), gene screening plays a crucial role in early diagnosis and intervention. Early diagnosis can benefit patients through lifestyle changes, drug intervention, and understanding of kidney transplantation information.

Kidney transplantation is considered the most effective surgical treatment for end-stage ADPKD (39, 40). Studies have shown that the recurrence rate of ADPKD after transplantation is similar to that of other non-diabetic kidney transplant recipients (41). Moreover, the volume of an autologous polycystic kidney tends to decrease after kidney transplantation (42). Therefore, in cases where there is enough space for kidney transplantation and no risk of bleeding or infection, it may not be necessary to remove the other kidney, which can improve the quality of life of patients. In ADPKD families, gene testing can help select suitable unaffected relatives as potential kidney transplant donors, promoting more transplantation evaluations and preemptive transplantation opportunities for ADPKD patients (43). This approach can improve patient outcomes, as preemptive transplantation before the onset of end-stage renal disease can prevent the need for dialysis, reduce post-operative complications, and improve long-term patient survival rates.

In this study, DNA was extracted from the subject’s blood, but the possibility of interpretation bias caused by chimerism cannot be ruled out. Moreover, the sample size was too small to eliminate all possible biases. In addition, this study did not provide a detailed molecular-level understanding of how new genes affect the functional changes of PC1. Therefore, larger clinical and basic research studies are needed to support more comprehensive genetic testing of ADPKD patients. Follow-up studies of patients and their family members have been extended to observe the relationship between genotype and phenotype more closely over time.

In summary, the findings from this study contribute to the growing body of knowledge on ADPKD genetics and highlight the importance of genetic testing in the diagnosis and management of this disease. By identifying new mutation sites and analyzing their effects on genotype and phenotype, this research provides a better understanding of ADPKD pathogenesis and opens up new avenues for further exploration. Second-generation sequencing technology has proven to be a valuable tool for detecting gene mutations in ADPKD patients, and its use should be encouraged in clinical practice and research. Ultimately, genetic testing can lead to more accurate diagnoses, better disease management, and improved genetic counseling for affected families. Further studies are needed to confirm and expand upon these findings and to elucidate the underlying mechanisms of ADPKD pathogenesis.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: The National Omics Data Encyclopedia (NODE), accession number: OEP004096.

The studies involving humans were approved by the Ethics Committee of the Xinjiang Uygur Autonomous Region People’s Hospital confirms the approval of the project titled “Genotype-Phenotype Characteristics of Nine Novel PKD1 Mutations in Eight Chinese Patients with Autosomal Dominant Polycystic Kidney Disease” with the approval number KY2023032201. The studies were conducted in accordance with the local legislation and institutional requirements. Written informed consent for participation in this study was provided by the participants’ legal guardians/next of kin. Written informed consent was obtained from the individual(s), and minor(s)’ legal guardian/next of kin, for the publication of any potentially identifiable images or data included in this article.

HJ: Conceptualization, Investigation, Methodology, Validation, Supervision, Data curation, Resources, Writing – review and editing, Funding acquisition. XT: Conceptualization, Methodology, Validation, Supervision, Writing – review and editing. JiZ: Investigation, Data curation, Writing – original draft, Methodology, Formal analysis, Software, Resources, Validation. AA: Investigation, Data curation, Writing – original draft, Methodology, Formal analysis, Software, Resources, Validation. DY: Investigation, Methodology, Data curation, Formal analysis, Writing – review and editing. JuZ: Investigation, Methodology, Data curation, Formal analysis, Writing – review and editing. XW: Investigation, Methodology, Data curation, Formal analysis, Writing – review and editing. YR: Investigation, Visualization, Writing – review and editing.