Compound heterozygous mutations in CC2D2A cause Meckel–Gruber syndrome: a case report and review of the literature

Abstract

Background

Meckel–Gruber syndrome is a rare autosomal recessive ciliopathy characterized by the triad of occipital encephalocele, polycystic kidney dysplasia, and postaxial polydactyly, with an estimated incidence of 1:13,250 to 1:140,000 live births. Pathogenic variants in CC2D2A, encoding a ciliary transition zone protein, account for 5–15% of MGS cases. This report highlights the diagnostic utility of whole-exome sequencing (WES) in delineating molecular etiologies of MGS and reviews genotype–phenotype correlations associated with CC2D2A mutations.

Case presentation

A 30-year-old Chinese primigravida (G1P0) from Shandong Province was referred at 23 week gestation following prenatal ultrasound detection of fetal anomalies. Key findings included bilateral enlarged hyperechoic kidneys (renal transverse diameter: 35 mm, > 95th percentile), occipital meningoencephalocele (29 × 25 × 12 mm) and bilateral postaxial hexadactyly. Prenatal counseling confirmed the fetal prognosis, and the parents chose to terminate the pregnancy. Postmortem WES revealed compound heterozygous CC2D2A variants.

Conclusions

This case highlights that prenatal ultrasonography remains critical for early detection of MGS hallmarks, especially in resource-limited Settings. Second, WES-based molecular autopsy is crucial for definitive diagnosis and genetic counseling.

Introduction

Meckel–Gruber syndrome is a rare, lethal autosomal recessive condition characterized by typical manifestations of occipital encephalocele, large polycystic kidneys and postaxial polydactyly [1]. It owns extreme phenotypic and genetic heterogeneity, and is associated with mutations in at least one of the 17 genes [1], but these mutations seem to explain only 50–60% of MGS cases [2, 3]. MGS is a lethal disease with a perinatal mortality of 100%. The leading cause of death is pulmonary hypoplasia induced by oligohydramnios, while kidney failure is the main reason of early neonatal death [4, 5]. Fortunately, the typical features of MGS can often be detected by ultrasound in the late first trimester [4]. Here, we report a case in prenatal setting, where significant abnormalities were recognized by ultrasound, and compound heterozygous mutations in CC2D2A inherited from parents were detected by whole-exome sequencing (WES).

Case presentation

A 30-year-old pregnant woman, G1P0, was referred to Peking Union Medical College hospital at 23rd weeks of gestation because of multiple fetal malformations. The couples, both from Shandong Province and of Chinese ethnicity, were healthy and had a non-consanguineous marriage. There is no history of hereditary diseases in the family in the past. Ultrasound revealed meningoencephalocele, polydactyly, bilateral renal enlargement with a polycystic appearance which pushing the liver to the left side of the abdomen, as well as oligohydramnios (Fig. 1). Based on the above appearance, MGS was strongly suspected.

Fig. 1.

Ultrasonography at 23⁺⁶ weeks of gestation. a View of the fetal abdomen indicates enlarged dysplastic cystic kidneys. b Postaxial polydactyly of one foot. c Bone defect in the occipital region with herniation of the brain, approximately 2.5*1.2 cm

After consultation regarding the lethal outcome of MGS, the couple was informed that the prognosis was very poor regardless of the etiology. The couple decided to terminate pregnancy, and with the informed desire of the couple, a postmortem examination and comprehensive genetic evaluation were performed.

Postmortem external examination showed occipital meningoencephalocele, postaxial polydactyly in both hands and feet, and apparent enlargement of the abdomen (Fig. 2). No facial deformity was observed. The gross autopsy also showed occipital encephalocele with partial occipital defect (3 × 2.7 cm). Bilateral enlarged polycystic kidneys occupied the entire abdomen and pushed the liver to the left side (Fig. 3). The histological study confirmed polycystic dysplastic kidneys with partial fibrous hyperplasia (Fig. 4). No other anomalies were found in other organs except spleen deficiency.

Fig. 2.

Appearance of the fetus. a Occipital meningoencephalocele. b Postaxial polydactyly. c Distended abdomen

Fig. 3.

Postmortem examination. a Enlarged polycystic kidneys occupied the entire abdomen and pushed the liver to the left side. b Polycystic kidneys

Fig. 4.

Histology indicated cysts in the kidney and thinning of renal cortex with glomerular atrophy

Quality control: The test was performed using the Illumina next-generation sequencing platform. Library preparation was conducted with the Agilent SureSelectXT Human All Exon V6 kit for target capture, followed by paired-end sequencing (150 bp × 2) to complete whole-exome sequencing of the samples. Data analysis was performed using the GRCh37 (hg19) human reference genome as the standard.

WES trio were performed on the parents and the fetus. A heterozygous frame-shift mutation c.2390dupC (P. s798LFS *7) in exon 20 of fetal CC2D2A inherited from the mother (Fig. 5), and a heterozygous splice mutation c.3594 + 1G > T in intron 29 of CC2D2A inherited from the father (Fig. 6) were detected. According to the ACMG standards and guidelines, these two variants were classified as pathogenic variants (ACMG: PVS1, PM3, PM2_Supporting) [6].CNV analysis was also carried out but did not reveal pathogenic microduplications or microdeletions. Therefore, the compound heterozygous mutations were thought to be the etiology of MGS. Following genetic counseling, the parents were advised of a 25% recurrence risk for MKS. The recommended clinical options included preimplantation genetic testing (PGT) or first-trimester chorionic villus sampling (CVS) for prenatal diagnosis.

Fig. 5.

Heterozygous mutation c.2390dupC (P. s798LFS *7) in exon 20 of fetal CC2D2A gene inherited from the mother

Fig. 6.

Heterozygous mutation c.3594 + 1G > T in intron 29 of fetal CC2D2A gene inherited from the father

Conclusions and discussion

Meckel–Gruber syndrome was first described by Johann Friedrich Meckel in 1822 and thereafter by Georg B. in 1934 [7].The incidence of MGS varies from 1 in 1,300 to 1 in 140,000. It can be much higher in endogamous populations, such as Gujarati Indians, Tatars Hutterites, and in Finland, where 1 in 9000 live births is affected. The occurrence of MGS is more in consanguineous populations, such as Kuwaiti Bedouin tribes and Saudi Arabia (1 in 3530 and 1 in 3500, respectively) [1]. In Gujurat Indians, the consanguineous marriages are so common that the incidence is the highest in current data with 1 in 1300 live births (carrier rate of 1 in 18) [8].

The most common and classic signs of MGS are occipital encephalocele, polycystic kidneys and postaxial polydactyly. Other common features, which occur in 25–40% of MGS, include Dandy–Walker deformity, skeletal deformity, microeye deformity, genital deformity, lip/palate cleft, heart defects and lung dysplasia [1]. Lateral defects have also been reported, including complete or partial translocation of viscera and dextrocardia [9]. A large epidemiological review assessed the incidence of typical phenotypes as follows: encephalocele, 83.8%; polycystic kidneys, 97.7%; polydactyly, 87.3%; fibrotic/cystic changes of the liver, 65.5% in postmortem examination [5]. Therefore, these findings suggested the diagnosis of MGS in prenatal settings. It is interesting to note that polydactyly was not always present in previous cohorts, just as the presence of polycystic kidney was not specific. It may because polydactyly is difficult to detect due to severe oligohydramnios, the absence of polydactyly does not rule out the diagnosis [10, 11]. Our case had a typical triad of MGS, no histological abnormalities were observed in the liver and other organs.

MGS is genetically heterogeneous and allelic to other ciliated diseases, such as Joubert syndrome (JBTS), COACH syndrome, oro-facio-digital syndrome (OFD), nephronophthisis (NPHP), and Bardet–Biedl syndrome (BBS). Ciliopathies with overlapping characteristics with MGS are JBTS, and at least 10 genes have been documented to cause both conditions [1, 12], including the mutations of CC2D2A gene in our case. JBTS usually presents with neurodevelopmental abnormalities with pathologic neuroradiological manifestations, characterized by developmental delay, hypotonia, irregular respiratory abnormalities, abnormal eye movements, and cerebellar vermicular dysplasia/hypoplasia with brain stem abnormalities leading to radiological “molar tooth sign”. Some children with JBTS die in infancy, but most survive, with varying developmental outcomes. In contrast, MGS is a typical perinatal lethal syndrome [12, 13]. In many cases genotype–phenotype correlations have been shown [13]. It has been reported that CC2D2A missense mutations are associated with JBTS, while null alleles lead to MGS. CC2D2A is ubiquitously expressed during early human development, with notable presence in the central nervous system, spinal cord, limbs, and the epithelia of the lungs and digestive tract [13]. Pathogenic mutations in CC2D2A are associated with a high incidence of structural brain anomalies (16/21), which often extend beyond the hallmark occipital encephalocele to include severe manifestations, such as holoprosencephaly and agenesis of the corpus callosum [13]. Analysis confirms occipital encephalocele and polycystic kidneys as cardinal features of MKS, while identifies hepatic ductal plate malformation as a distinct association with TMEM67 mutations (10/19) [2].In addition, the compound heterozygous frame-shift and splicing mutations of CC2D2A led to MGS in our case. Bachmann-Gagescu, R, et al. [14] concluded that the less severe ciliopathy phenotype of Joubert syndrome (JBTS) may be the result of residual function of some mutated CC2D2A allele or partial compensation of modification genes. This could explain why the same gene mutations can lead to a lethal MGS phenotype as well as a milder JBTS phenotype [13, 15]. Although the variable expression of MGS phenotypes can complicate the diagnosis of the disease, recent advances in genetic technology and the widespread use of multiple genomes in molecular detection have significantly improved the diagnosis, genetic counseling and clinical management of MGS.

MGS is a recessive genetic ciliopathy with at least 17 known causal genes involved [1]. Ciliopathies are a group of human diseases caused by dysfunction of primary cilia. The transition zone (TZ) is the structure at the base of the cilia and the junction between the plasma membrane and cilia, which controls the proteins and lipids across the cilia and requires vesicle transport for movement into and out of this zone. The subdistal appendages (SDA) region is located at the bottom of TZ and plays an important role of the maternal centriole [16]. TZ seems to be the hotspot of cilia-related genetic diseases. Two or three major protein complexes have been identified to form TZ. One is MGS complexes, including Tectonic proteins, B9 domain proteins, coiled-coil proteins, such as CC2D2A, CEP290, AHI1 and 5–7 transmembrane or TMEM proteins. The other is NPHP complexes, including NPHP proteins, RPGRIP1 L and others [17].

CC2D2A contains 37 exons encoding 1561 amino acid polypeptides (BP 73–4758). CC2D2A encodes the coiled-coil and C2 domain proteins required for cilia formation, which are identified as potential calmodulin-binding proteins and predicted to be involved in calcium-dependent membrane targeting. Ca2 + signaling plays a key role in the pattern of embryonic development and is closely associated with left–right renal asymmetry and cyst formation [18].Shobi Veleri et al. [19] reported Shh signal transduction is perturbed in CC2D2A(CC2D2A -/-) null allele mouse model, while neural tube defects and polydactyly in CC2D2A-/- embryos are due to disruption of ciliary Shh signaling. The CC2D2A -/- mouse model also showed the presence of mother centrioles (MC) as well as the absence of axoneme, suggesting that CC2D2A plays an important role in ciliary biogenesis, which is consistent with another study [20]. In addition, in CC2D2A-/- mouse embryonic fibroblasts (MEFs), MC lacked or had abnormal SDA, had disorganized microtubules, and even no TZ developed in some CC2D2A-/- MEFs [19]. It has also been suggested that CC2D2A and centrosome protein NINL are physical interaction partners, acting together on vesicle transport in the transformation region [14]. Therefore, CC2D2A is needed for SDA assembly at the mother centriole, stable MT anchoring and docking of transport vesicles, and further refinement of TZ.

In China, prenatal WES test was conducted at certain tertiary hospitals and specialized genetic testing institutions when fetal anomaly was found. Gene panels were seldom used prenatally in China, concerning that phenotypes were not as sufficient as postnatal patients, and time for diagnosis was limited prenatally. As is well-established, mutations in the CC2D2A gene can lead to both MKS and Joubert syndrome [20, 21]. However, the lack of clear genotype–phenotype correlations often contributes to diagnostic errors in clinical practice. For carrier parents, the risk of having a fetus with MKS in each pregnancy is 25%, with equal distribution between both genders. MKS can affect multiple critical organs and systems. Nevertheless, MKS exhibits high clinical heterogeneity, with manifestations varying significantly among cases. Due to the absence of definitive genotype–phenotype correlations, single-gene testing has limited sensitivity in confirming clinically suspected MKS. Both our case report and the study by Zhidan Hong [22] reported normal copy number variation results. In addition, study have indicated that microarray analysis often yields normal findings in MKS case [23]. When multi-gene panels fail to confirm an MGS diagnosis, more comprehensive testing approaches such as WES or whole genome sequencing (WGS) may be warranted. Therefore, whole-exome sequencing (WES) plays a crucial role in resolving diagnostic uncertainty.

In summary, Meckel–Gruber syndrome (MKS) is a lethal genetic condition. This case demonstrates the critical role of prenatal ultrasound in detecting hallmark features of MKS, with trio whole-exome sequencing (trio-WES) as the subsequent first-tier test for a definitive diagnosis. The discovery of novel mutations enriches the known genotypic spectrum of MKS. A conclusive molecular diagnosis is crucial for empowering parents with informed reproductive choices, including the use of preimplantation genetic testing (PGT) to prevent disease recurrence in subsequent pregnancies and improve overall reproductive health outcomes.

Abbreviations

MGS

Meckel–Gruber syndrome

WES

Whole-exome sequencing

ACMG

American College of Medical Genetics and Genomics

CNV

Copy number variation

JBTS

Joubert syndrome

COACH

Oculo-encephalo-hepato-renal syndrome

OFD

Oro-facio-digital syndrome

NPHP

Nephronophthisis

BBS

Bardet–Biedl syndrome

TZ

Transition zone

SDA

Subdistal appendages

MC

Mother centrioles

MEFs

Mouse embryonic fibroblasts

Author contributions

L.L.: conception and design, analysis and interpretation, data collection, manuscript writing, editing and revision. Y.L.: conception and design, analysis and interpretation, editing and revision. X.Z.: conception and design, editing and revision.

Funding

The study was supported by National High Level Hospital Clinical Research Funding (2022-PUMCH-A-088). The funding body was not involved in the design of the study, the collection, analysis or interpretation of the data, and not in writing of the manuscript.

Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Declarations

Ethics approval and consent to participate

The study was approved by the ethics review committee of Peking Union Medical College Hospital (S-K1852). Written informed consent was obtained from the parents.

Consent for publication

Written informed consent was obtained from the patient's parents for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.

Competing interest

The author(s) declare no competing interest.