Perinatal/Neonatal Case Presentation

NPHP3 mutations are associated with neonatal onset multiorgan polycystic disease in two siblings


Two siblings with a severe multiorgan polycystic disease presenting in the neonatal period were identified. Their genetic testing identified compound heterozygous NPHP3 gene mutations, parents being heterozygous carriers. The mutations included a splice-site (c.958-2A>G) and a missense mutation (c.2342G>A; p.G781D), both being extremely rare. NPHP3 encodes for nephrocystin 3 present on the cilia-centrosome complex. We hypothesize that these mutations lead to defective cilia-based signaling, required for normal development of the renal, pancreatic, biliary and portal system. This report outlines a rare neonatal ciliopathy presentation of NPHP3 mutations leading to severe multiorgan failure in two siblings.


Ciliopathies are a genetically heterogeneous group of disorders caused by defects in the cilium-centrosome complex.1 Primary non-motile cilia are microtubule-based structures, located on most vertebrate cells and are highly conserved throughout evolution.2 Primary cilia function as complex sensory organelles involved in cellular signaling and are critical for the normal function of multiple organ systems.1 A constellation of single-gene defects in the cilium-centrosome complex have been identified and shown to lead to ciliopathies with multiorgan involvement.3

In this report, we describe two siblings who presented with severe multiorgan cystic disease in the neonatal period. After extensive genetic testing including sequencing several candidate genes, two novel NPHP3 mutations were identified that segregated in the parents.


A 28-year-old gravida 2, para 1 female presented to obstetric care at 20 weeks gestation with an abnormal fetal ultrasound showing bilaterally enlarged echogenic kidneys. The parents were not consanguineous, and the mother and father had a previous healthy child. An amniocentesis was performed that revealed a normal male karyotype (46, XY) and the FISH for 22q11.2 deletion was normal. A fetal MRI performed at 30 weeks gestation noted situs inversus totalis, bilaterally enlarged multicystic kidneys, no visible amniotic fluid and hypoplastic lung tissue (Figure 1a). An upper abdominal oblong cystic structure, postnatally identified as the pancreas, was also visualized.

Figure 1

MRI studies in the proband showing cysts present in bilateral kidneys and pancreas. (a) Prenatal MRI demonstrating polycystic kidney and bell-shaped pulmonary hypoplasia. (b) Postnatal MRI showing bilateral polycystic kidneys and cystic pancreas. Arrow heads, polycystic kidneys; arrows, bell-shaped hypoplastic lungs; star, cystic pancreas.

Premature birth resulted from spontaneous labor at 32 6/7 weeks of gestation. On initial postnatal imaging studies, prenatal diagnoses were confirmed, including: situs inversus totalis, large polycystic kidneys and large pancreatic cysts (Figure 1b). His degree of pulmonary hypoplasia required intubation with mechanical ventilation throughout his course. He developed renal failure with anuria and a peritoneal dialysis catheter was placed. He developed acholic stools and underwent a workup including an abnormal magnetic resonance cholangiopancreatography showing dilated biliary ducts without obstruction.

His clinical status deteriorated in the setting of presumed sepsis with multiple organ failure, profound hypotension resistant to dopamine and epinephrine, hypoxia and bradycardia. The family opted for no further escalation of medical technology, and he died at 3 months of age.

Postnatal genetic testing included a repeat karyotype that was normal (46, XY), and a normal chromosomal microarray. Based on the age of presentation and the constellation of clinical findings, several candidate genes were sequenced during his neonatal intensive care unit stay with no pathogenic variant identified. These included INVS and NEK8 that are mutated in infantile presentations of polycystic kidney disease.1 Several additional candidate genes associated with nephronophthisis were sequenced after his death. One of those sequenced candidate genes was NPHP3 that encodes for nephrocystin 3. Sequencing of NPHP3 revealed two novel mutations, a paternally inherited acceptor splice-site mutation, c.958-2A>G and a maternally inherited missense variant c.2342G>A postulated to cause the amino-acid substitution p.G781D, a highly conserved residue in vertebrates. These mutations were predicted to be pathogenic by Polyphen-2,4 SIFT (sorting intolerant from tolerant)5, 6 and MutationTaster software.7 NPHP3 mutations are associated with a broad spectrum of early embryonic defects, including situs inversus and multicystic kidneys with a wide age range of presentation.8, 9 While awaiting results from the candidate genes testing sent after his death, the family was also enrolled in an institutional review board-approved research protocol, and the patient’s DNA was sent for whole-genome sequencing (WGS). The WGS data were obtained after the identification of NPHP3 mutations and therefore were not analyzed, but both mutations were present in that data.

A sibling of the proband was spontaneously conceived and prenatal imaging included a 31-week gestation MRI showing polycystic kidneys, multiple pancreatic cysts and severe oligohydramnios with pulmonary hypoplasia. The family declined amniocentesis or maternal-free fetal DNA testing for the known familial mutations. The infant was delivered vaginally following labor induction at 34 4/7 weeks due to severe oligohydramnios and risk of cord compression. Her postnatal imaging confirmed bilateral polycystic kidneys, multiple pancreatic cysts and several hepatic cysts. She also had severe pulmonary hypoplasia requiring mechanical ventilation and elevated direct bilirubin suggestive of a bile duct abnormality, although no definitive high-resolution imaging was performed. Her multiorgan involvement was similar to the proband, except that she had situs solitus. Her family consented to research but not clinical genetic testing, and the splicing mutation (c.958-2A>G) and missense mutation (c.2342G>A) previously seen in her brother were identified.

Her clinical course included initiation of peritoneal dialysis followed by development of severe polymycrobial peritonitis necessitating use of hemodialysis when she required multiple inotropic blood pressure supports and developed worsening hypotension and acidosis and she died at 3 months of age.


Non-motile cilia are microtubule-based structures located on most eukaryotic cells and evolutionarily are extremely well conserved.1, 2 Cilia bend with the flow of fluid, acting as antennae sensing fluid flow, and initiate calcium influx that regulates tissue development. Intact cilium-based signaling is required for normal development of the renal, pancreatic, biliary and portal system. Various aberrations of the cilium-centrosomes can lead to different phenotypes and involve multiple organ systems.3, 10 The kidneys are the most commonly affected organ in ciliopathies with a wide range of defects and severity, whereas pancreatic cysts have been rarely described. The severity of disease associated with ductal plate malformation in ciliopathies is highly variable and is dependent on the degree of remodeling. Our patients exhibited an unusual neonatal presentation of multiorgan defects involving tissues dependent on ciliary function.

Nephronophthisis is a group of rare AR disorders with a broad clinical phenotype that includes cystic kidney disease. The spectrum of disease varies from in utero lethality to subclinical disease until adulthood. Mutations have been identified in all 11 genes (NPHP1 to NPHP11) that encode the nephrocystin proteins expressed in primary cilia, basal bodies and centrosomes.1 Mutations in NPHP1 are most common, leading to juvenile nephronophthisis type 1, whereas NPHP3 mutations are relatively rare.1, 8

NPHP3 defects are phenotypically heterogeneous, ranging from rare, severe neonatal presentation to more common and less severe adolescent presentation, a pattern supported by mouse studies of Nphp3 defects.9, 11, 12 A rare neonatal presentation is seen in our siblings. Two previous case reports have described neonatal presentations of NPHP3 gene mutations leading to different presentations of multiorgan cystic disease, one with homozygous nonsense mutation c.1729C >T (p.Arg577X) in exon 11 of the NPHP3 gene9 and the other with homozygous deletion of the conserved splice acceptor dinucleotide (AG) preceding exon 20 in the NPHP3.13 Recent work has utilized high-throughput mutation analysis to identify additional novel mutations leading to defects in NPHP3, with a higher percentage of infant presentations than previously described.14, 15

In summary, this report outlines a rare presentation of NPHP3-associated ciliopathy in the neonatal period. We suggest that when available, a gene panel should be used to identify the genetic basis for a highly heterogeneous disorder such as a ciliopathy. If such a panel is not available, approaches such as whole-exome or -genome sequencing may be preferable to single-candidate gene sequencing for rapid turnover, lower costs and to alleviate parental anxieties. Further, clinicians should consider genetic testing for ciliopathies in neonates presenting with cysts in multiple organ systems.


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This work was funded by a grant from The Manton Center for Orphan Disease Research.

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Correspondence to K T Leeman or P B Agrawal.

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Leeman, K., Dobson, L., Towne, M. et al. NPHP3 mutations are associated with neonatal onset multiorgan polycystic disease in two siblings. J Perinatol 34, 410–411 (2014).

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  • polycystic kidney disease
  • ciliopathy
  • nephronophthisis
  • NPHP3

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