22q11.2 duplication syndrome and LZTR1-related Noonan syndrome type 10 overlapping phenotypes in a dual diagnosis - fetal hydrops: a case report

Abstract

Background

Nonimmune factors are the most common cause of fetal hydrops, which are characterized by the accumulation of pathological fluid due to various causes. The etiology of this disease is complex, with a relatively high mortality rate, and the prognosis largely depends on the underlying cause. Notably, fetal hydrops attributable to genetic causes, such as chromosomal abnormalities or gene mutations, are typically associated with a poor prognosis.

Case presentation

A fetus diagnosed with severe nonimmune fetal hydrops at 27 weeks of gestation presented with multiple abnormalities on prenatal ultrasound, including progressively thickened nuchal translucency (NT) and nuchal fold (NF), cystic hygroma, pleural effusion, and renal pelvis duplication. Amniotic fluid cytogenetic analysis revealed a normal karyotype. Integrated chromosomal microarray analysis (CMA) and trio-based whole-exome sequencing (Trio-WES) revealed a pathogenic 2.82 Mb duplication at chromosome 22q11.21, designated as arr[GRCh37] 22q11.21(18984188–21804597)x3, associated with 22q11.2 duplication syndrome, which was inherited from the father. Additionally, a heterozygous missense variant in the LZTR1 gene NM_006767.3: c.848G > A (p.Arg283Gln) was detected and classified as pathogenic, associated with Noonan syndrome type 10, maternally inherited. After comprehensive counseling and careful consideration, the parents elected to terminate the pregnancy.

Conclusion

This study revealed that fetuses carrying both a pathogenic copy number variant of duplication in the 22q11.2 region and a heterozygous pathogenic missense variant of the LZTR1 gene (c.848G > A) simultaneously constitute the main genetic basis for its multisystem abnormalities and severe hydrops. This study highlights the role of multiple genetic superimposition effects in the formation of complex fetal phenotypes and emphasizes that in genetic counseling and prenatal diagnosis, a combined strategy of CMA and Trio-WES should be adopted to improve the detection rate of complex genetic diseases and the accuracy of recurrence risk assessment.

Background

Fetal hydrops is a severe pregnancy complication defined by pathological fluid accumulation in fetal soft tissues and body cavities. The ultrasound diagnostic criteria require at least two abnormal fluid collections in body cavities, including pleural effusion, ascites, pericardial effusion (thickness > 3 mm), or skin edema (thickness > 5 mm), and are frequently associated with polyhydramnios or placental thickening (≥ 4 cm during the second trimester) [1]. The estimated incidence ranges from approximately 1 in 3,000 to 1 in 1,700 pregnancies. It is broadly classified into immune and nonimmune forms, with nonimmune fetal hydrops (NIHF) accounting for 85–95% of all cases [2].

NIHF has a complex etiology, being associated with a generally poor prognosis and a high mortality rate. The clinical outcome often depends on the underlying cause. Common etiologies include cardiovascular malformations, hematologic abnormalities secondary to fetal anemia, thoracic structural defects, intrauterine infections, placental or umbilical cord abnormalities, and genetic factors [3]. Among the genetic causes, chromosomal abnormalities account for approximately 28.8% of NIHF cases, and monogenic diseases account for about 17.8% [4]. Notably, genetically mediated fetal hydrops is typically associated with poor prognosis. Thus, comprehensive etiological evaluation is crucial for guiding clinical management and providing accurate genetic counseling.

Current genetic testing strategies for NIHF primarily include karyotype analysis, CMA, and next-generation sequencing (NGS) approaches. Karyotype analysis can identify chromosomal aneuploidy abnormalities, whereas CMA is used to detect genomic abnormalities such as microdeletions and microduplications. With the development of sequencing technology, NGS techniques (such as exome sequencing) have been gradually applied to cases of NIHF with unknown causes, providing an effective means to identify pathogenic gene variations [5].

This study reports a fetus that presented with multiple prenatal ultrasound abnormalities, including thickened NT and NF, pleural effusion, and renal pelvis duplication, which subsequently progressed to severe hydrops fetalis. Through combined CMA and Trio-WES testing, the fetus was diagnosed with a dual diagnosis of 22q11.2 duplication syndrome and Noonan syndrome type 10 associated with an LZTR1 pathogenic variant. This is the first reported case of disease manifestation due to the co-occurrence of these two conditions, providing novel clinical and genetic evidence for understanding the polygenic superimposition mechanism underlying NIHF.

Case presentation

The pregnant woman was 32 years old, gravida 1, para 0, and had conceived naturally. At 13^+ 3 weeks of gestation, ultrasound screening revealed a singleton viable intrauterine pregnancy with increased NT measuring 4.0 mm. At 23^+ 1 weeks of the second trimester, an ultrasound examination revealed a thickened NF (6.9 mm) in the fetus, right pleural effusion (maximum depth of approximately 2.3 mm), and suspected right renal pelvis duplication. Both parents reported no significant medical history, denied consanguinity, and had no family history of genetic disorders. To further clarify the diagnosis, ultrasound-guided amniocentesis was performed, and 30 mL of amniotic fluid was collected for cytogenetic and molecular genetic prenatal diagnosis. Additionally, 3 mL peripheral blood samples were collected from each parent for family genetic variation analysis. The results were as follows:

1. Chromosome karyotype analysis: G-banding results revealed that the fetal karyotype was 46,XX, with no numerical or structural abnormalities.

2. CMA: Using SNP array technology (Cytoscan 750K chip), a 2.82 Mb duplication in the 22q11.2 region was detected, with the genomic coordinates arr[GRCh37] 22q11.21(18984188-21804597)×3. This variant was rated as pathogenic and was associated with 22q11.2 duplication syndrome (Fig. 1A).

3. Trio-WES: Sequencing was performed using the high-throughput sequencing platform MGISEQ-2000. A heterozygous missense variant NM_006767.3: c.848G>A (p.Arg283Gln) was detected in the LZTR1 gene of the fetus. This variant is recorded in ClinVar (ClinVar ID: 561716). According to the updated ACMG/AMP guidelines for variant interpretation issued by the ClinGen RASopathy Variant Curation Expert Panel (VCEP) [6], the variant is classified as pathogenic(PM2_supporting + PP3 + PS4 + PM6_strong), associated with autosomal dominant Noonan syndrome type 10. Pedigree analysis revealed that the missense variant was inherited from the mother, whereas the 22q11.2 duplication was inherited from the father.

4. Sanger sequencing verification: Primers were designed for the above LZTR1 variant site for amplification and sequencing. The results confirmed that both the fetus and the mother carried the heterozygous c.848G>A (p.Arg283Gln) missense variant (Fig. 1B).

Fig. 1.

A CMA revealed that the fetus carries arr[GRCh37] 22q11.21(18984188–21804597)×3. B Sanger sequencing identified a heterozygous pathogenic missense variant, NM_006767.3:c.848G > A (p.Arg283Gln), in the LZTR1 gene in both the fetus and the mother, while the father was found to carry the wild-type genotype

At 27 weeks of gestation, a follow-up ultrasound revealed that the NF had further thickened to 9.56 mm with associated lymphatic cyst formation, bilateral pleural effusion (maximum depths of approximately 12 mm on the left and 27 mm on the right), bilateral renal pelvis duplication, and polyhydramnios, consistent with progression to nonimmune fetal hydrops. (Fig. 2).

Fig. 2.

Ultrasonic image of the fetus at 27 weeks of gestation. A Increased nuchal fold thickness (9.56 mm). B Formation of a lymphatic cyst in the posterior cervical region. C Right pleural effusion. D Left pleural effusion. E Right renal pelvis duplication. F Left renal pelvis duplication

After genetic counseling and informed consent from the family, the pregnant woman decided to terminate the pregnancy and underwent induction at 27^+ 2 weeks. The induced fetus was female, and the manifestations of “short neck and thickened neck skin”, and “full chest contour” were consistent with the prenatal ultrasound findings. Additionally, low-set ears, micrognathia and abdominal protrusions were observed; no abnormalities were found in the spine, limbs, or external genitalia (Fig. 3). Owing to the family’s refusal of autopsy, no further pathological examination was conducted.

Fig. 3.

Images of the fetus after termination of pregnancy

Discussion

This study reports a fetus with severe fetal hydrops. Comprehensive genetic testing confirmed the co-occurrence of a 22q11.2 duplication and a heterozygous LZTR1 gene variant c.848G > A, corresponding to 22q11.2 duplication syndrome and Noonan syndrome type 10, respectively. By integrating clinical phenotypic findings with molecular genetic data, this study systematically analyzes the phenotypic features of the two syndromes, explores potential mechanisms underlying their copathogenic effects, and summarizes the implications for genetic counseling.

The 22q11.2 region is highly susceptible to nonallelic homologous recombination due to its enrichment in low-copy repeats (LCRs), which frequently leads to recurrent deletions or duplications, constituting the primary genetic mechanism underlying 22q11.2 deletion/duplication syndrome [7]. In this case, the fetal 2.82 Mb duplication is located between LCR-A and LCR-D and shows high overlap (96.71%) with the typical 22q11.2 duplication syndrome region—22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (including TBX1) [ISCA-37446], encompassing multiple critical genes including TBX1, LZTR1, PI4KA, and CRKL. The region has a triplosensitivity score of 3, indicating established pathogenicity. The penetrance of 22q11.2 duplication is approximately 21.9% [8], with clinical manifestations exhibiting substantial heterogeneity, ranging from asymptomatic or mildly affected individuals to those with severe malformations, developmental delay, and intellectual disability. Additional clinical features include cleft palate, hypotonia, thymic aplasia, congenital heart disease, and urogenital malformations. Approximately, 70% of 22q11.2 duplications (LCR A-D) are inherited from parents who exhibit normal or only mild phenotypic abnormalities [9]. Nevertheless, even individuals inheriting duplication from clinically unaffected or minimally affected parents may develop significant clinical manifestations, posing a major challenge for prenatal genetic counseling in cases of fetal 22q11.2 duplication.

Mary et al.‘s [10] cohort study demonstrated that NT thickening and cardiovascular malformations are key prenatal ultrasound features associated with 22q11.2 duplication. Among 43 fetuses carrying the 22q11.2 duplication (LCR A-D), 15 (34.9%) exhibited NT thickening and 16 (37.2%) had cardiovascular malformations, including atrioventricular septal defects, tetralogy of Fallot, and valvular abnormalities. Notably, two fetuses in this cohort presented with renal pelvis duplication and fetal hydrops, both of whom died during the neonatal period, suggesting that this phenotypic combination may be indicative of a poor prognosis. Although no cardiac structural abnormalities were detected in the present case, the presence of NT thickening, renal pelvis duplication, and subsequent development of hydrops is consistent with the more severe end of the phenotypic spectrum observed in 22q11.2 duplication syndrome.

The application of Trio-WES enabled the identification of a heterozygous pathogenic variant c.848G > A (p.Arg283Gln) in the LZTR1 gene in this fetus. The LZTR1 protein plays a critical role in regulating the RAS/MAPK signaling pathway, and its dysfunction is associated with impaired lymphatic drainage and cardiovascular abnormalities [11]. Prenatal features of Noonan syndrome due to LZTR1 variants include NF thickening, increased NT, lymphatic cysts, pleural effusion, pericardial effusion, polyhydramnios, fetal hydrops, cardiac malformations, and renal anomalies [12–13]. The LZTR1 c.848G > A (p.Arg283Gln) variant identified in this case has been repeatedly reported in association with Noonan syndrome type 10, a condition predominantly characterized by lymphatic dysplasia, including NT/NF thickening, ascites, chylothorax, peripheral edema, and hypertrophic cardiomyopathy, with variable phenotypic heterogeneity among individuals [14–16]. The observed findings in this fetus, NF thickening with lymphatic cyst formation, progressive pleural effusion, and severe hydrops—are highly consistent with the core phenotypic manifestations of Noonan syndrome.

Notably, the LZTR1 gene is located within the 22q11.2 region and has been implicated as a candidate gene for the bladder exstrophy-epispadias complex (BEEC) phenotype in individuals with a 22q11.2 duplication [17]. This dual association suggests that LZTR1 may contribute to disease pathogenesis through distinct genetic mechanisms: it can cause Noonan syndrome via a monogenic inheritance pattern, while also playing a role in urinary tract malformations in the context of 22q11.2 duplication. The bilateral renal pelvis duplication observed in this fetus may reflect the shared impact of LZTR1 dysregulation on urinary system development across both genetic contexts.

In this case, the parents were asymptomatic carriers of a 22q11.2 duplication and an LZTR1 pathogenic variant, respectively. The fetus exhibited severe hydrops fetalis, supporting the “second-hit” pathogenic model [18]. The 22q11.2 duplication provides a genetic susceptibility background, with increased gene dosage in the region potentially disrupting the development of multiple organ systems. The LZTR1 variant is primarily associated with impaired lymphatic drainage. The existence of a direct functional interaction between the two remains undetermined. However, it is plausible that the combined effects of 22q11.2 duplication mediated genetic dosage alteration and the LZTR1 variant driven dysregulation of the RAS/MAPK pathway may impair lymphatic and cardiovascular development, and might be related to to the severity of fetal hydrops. This mechanistic hypothesis requires validation through targeted functional studies.

In terms of genetic counseling, this case indicates that even if both parents are asymptomatic carriers, the fetus may still present with severe clinical manifestations due to the genetic additive effect. In subsequent pregnancies, offspring inheriting both variants (with a 25% recurrence risk) are at high risk of severe fetal hydrops, whereas those inheriting only one variant (with a 50% recurrence risk) may exhibit milder or atypical phenotypes. To reduce the risk of recurrence, preimplantation genetic testing (PGT) is recommended to select embryos that are either unaffected or heterozygous for a single variant. Additionally, for fetuses with prenatal findings such as increased NT thickness and pleural effusion suggesting lymphatic dysplasia, even if CMA has identified pathogenic copy number variants (CNVs), if there is a low penetrance situation, the necessity of performing Trio-WES should still be considered to comprehensively assess coexisting monogenic variations, providing a more complete basis for genetic counseling and perinatal management.

This study has the following limitations: First, the family refused an autopsy, thus no pathological evidence of the fetal internal organs and lymphatic system could be obtained, and all phenotypes relied on prenatal ultrasound. Second, although the parents reported being asymptomatic, they did not undergo systematic clinical physical examinations (such as special facial feature assessment, echocardiography, developmental tests, etc.), so it cannot be completely ruled out that the parents have mild phenotypes. Third, as the family decided to terminate the pregnancy after genetic counseling, no intrauterine intervention (such as thoracentesis or pleuroamniotic shunt) was performed, precluding assessment of treatment responsiveness in this specific form of fetal hydrops. Fourth, as previously mentioned, the functional interplay between the two variants remains undetermined, and the proposed combined effect requires experimental validation through targeted functional assays.

Conclusion

This case indicates that the co-occurrence of a 22q11.2 microduplication and a heterozygous LZTR1 c.848G > A (p.Arg283His) missense variant in the fetus is strongly associated with severe non-immune hydrops fetalis and multisystem congenital anomalies. In prenatal cases of complex non-immune fetal hydrops, even when both parents are asymptomatic carriers, clinicians should consider both incomplete penetrance and the potential superposition effect of multiple concurrent genetic variants. Accordingly, a comprehensive genetic evaluation integrating CMA and Trio-WES is recommended to enable accurate genotype–phenotype correlation, thereby supporting evidence-based genetic counseling and reliable recurrence risk estimation.

Abbreviations

NT

Nuchal Translucency

NF

Nuchal Fold

CMA

Chromosomal microarray analysis

Trio-WES

Trio-based whole-exome sequencing

NIHF

Nonimmune fetal hydrops

Authors’ contributions

Q.F. designed study.X.L.H. collected the samples and conducted genetic counseling.H.F.N and Y.C.Y conducted genetic testing and analyzed the results.Z.X.Z and Z.C.Z collected data and searched literature.H.F.N wrote the manuscript.Q.F. and Z.C. revised the manuscript.All authors reviewed the manuscript.

Funding

This work was funded by the Shenzhen Science and technology Program (No.

RCBS20231211090700001)

Data availability

Data and materials are available on reasonable request. The data and materials that support the findings of this study are available from the corresponding author on reasonable request.

Declarations

Ethics approval and consent to participate

The study was approved by the Ethics Committee of the Seventh Affiliated Hospital of Sun Yat-sen University (KY-2025-470-01).

Consent for publication

Written informed consent was obtained from the family regarding the publication of the case.

Competing interests

The authors declare no competing interests.