Prenatal detection of 2q21.1 deletion in a fetus with severe early-onset fetal growth restriction: case report and literature review

1. Introduction

Fetal growth restriction (FGR) is used to diagnose a fetus with an estimated fetal weight (EFW) below the 10^th percentile in an accurately dated pregnancy⁽¹⁾. If EFW is below the 3^rd percentile for gestational age, it is a severe form of FGR⁽¹⁾. The etiology of FGR is complex; it can be from impaired placentation, maternal factors (gestational hypertensive disorders, chronic malnutrition, smoking, drug abuse, exposure to teratogenic substances – anti-seizure medications, antineoplastic agents, ethnicity, constitutional factors) and fetal factors (chromosomal abnormalities – trisomies 13, 18 and 21), genetic syndromes, intrauterine infections, multiple gestations, or inborn errors of metabolism⁽²⁾. If FGR is diagnosed before 32 weeks of gestation, it is called early-onset fetal growth restriction. Early FGR is associated with maternal hypertensive disorders of pregnancy and genetic and structural anomalies of the fetuses⁽¹⁾. Based on the head and abdominal circumference (HC/AC) ratio, FGR has been classified as symmetric or asymmetric⁽¹⁾.

Depending on the size and location of the genomic region involved, 2q21.1 deletion can be associated with various clinical manifestations. Minor deletions (~450 kb) were diagnosed postnatally and were associated with psychomotor delay, behavioral problems, mild dysmorphic features, epilepsy, and tall stature^(3,4), but larger deletions (18.5 Mb) were associated with multiple anomalies detected antenatally by ultrasound scan: congenital cardiac defects, bilateral hydronephrosis, agenesis of the corpus callosum, clenched hands, hypertelorism, micrognathia, sacral dimple, rocker-bottom feet, short neck and excessive skin in the occiput⁽⁵⁾. 

Below the identification of all aneuploidies and triploidies, the single-nucleotide polymorphism (SNP) microarray technique allows the identification of deletions or duplications greater than 100 kb at the entire genome level⁽⁶⁾.

Here, we present one case of 2q21.1 microdeletion detected prenatally by SNP microarray analysis from amniotic fluid, which was associated with severe early-onset FGR without any malformations.

2. Case presentation

A 30-year-old primigravida was referred to our clinic at 22 weeks of pregnancy for severe early-onset FGR (growth percentile [GP] <1%). From anamnesis, we found that the mother had no particular personal or familial medical history, and she was unrelated to her husband. Also, her husband was 33 years old and had no personal or familial history of any disease.

From the history of the current pregnancy, we found that a noninvasive prenatal test was done at the 11^th week of pregnancy without revealing something abnormal, and all laboratory markers of chronic infections (Toxoplasma, rubeola, CMV, herpes viruses) and anemia were in normal parameters. At 22 weeks of pregnancy, it was detected by ultrasound examination a severe symmetrical early-onset FGR (GP<1%). A complete ultrasound examination was done, without revealing anything abnormal. At 23 weeks of pregnancy, an amniocentesis was done, and quantitative fluorescence polymerase chain reaction (QF-PCR) analysis from amniotic fluid showed 46XY chromosomes. The SNP microarray revealed a heterozygous deletion of 350 kb in the chromosomal region 2q21.1, which contains five OMIM genes: SMPD4, MZT2B, CCDC115, IMP4, and PTPN18. These findings were discussed with the parents, and the SNP microarray testing of the parents was also discussed to determine if this deletion was recurrent or de novo. The mother and fetus were closely monitored during the third trimester of pregnancy, and no complications were observed. The umbilical artery, middle cerebral artery, and uterine artery Doppler assessment were in average range throughout the pregnancy (Figures 1 and 2). The fetal growth percentile was below 1% during the pregnancy (Figure 3).

At 37+4 weeks, an 1880 g male infant was delivered by caesarean section, with Apgar scores of 6 and 9 at 1 and 5 minutes. After birth, the newborn experienced hypoglycemia, which was treated with glucose infusions following umbilical vein catheterization. The mother and the newborn were discharged in good condition ten days after birth.

3. Method

We obtained detailed demographic and clinical data (laboratory and ultrasound examinations) from the mother during pregnancy. At 23 weeks of pregnancy, we collected amniotic fluid through amniocentesis for karyotyping. QF-PCR was used for karyotyping, and an SNP microarray for deletions/duplications was performed at the Cytogenomic Medical Laboratory in Bucharest.

Prometaphase chromosomal analysis on amniotic fluid cultures was performed according to standard protocols following the International System for Human Cytogenetic Nomenclature (ISCN), 2020.

DNA for SNP microarray analysis was extracted from amniotic fluid obtained through amniocentesis. The CytoScan 750K array platform (Affymetrix) was used to fragment, amplify and hybridize DNA, which was then scanned with GenScan 3000. The Chromosome Analysis Suite (ChAS) software program was used for microarray analysis. For the genome assembly, NCBI build 37 hg19 was used. Data from NCBI (National Center for Biotechnology Information)⁽⁷⁾, University of California, Santa Cruz, USA (UCSC) Genome Browser⁽⁸⁾, Database of Genomic Variants (DGV)⁽⁹⁾, DECIPHER⁽¹⁰⁾, Online Mendelian Inheritance in Man (OMIM)⁽¹¹⁾ were used to evaluate the significance of the detected copy number variation (CNV).

4. Results

According to the ISCN, 2020, the SNP microarray revealed a 350 kb heterozygous interstitial deletion on the chromosomal region 2q21.1. The chromosomal constitution was reported as 46,XY.arr[GRCh37] 2q21.1(130820741_131170793)x1. This deletion encompasses five genes: SMPD4, MZT2B, CCDC115, IMP4, and PTPN18. The parents were not genetically investigated.

5. Discussion

The most common causes of early FGR are maternal hypertensive disorders of pregnancy and genetic and structural anomalies of the fetuses⁽¹⁾. Among genetic causes of early FGR, there are chromosomal abnormalities, like triploidy, trisomy 18, 21, 13, 16, 7, 69XXX or 69XXY, 47XXX or 47XXY(12,13) submicroscopic chromosomal anomalies like duplication 22q11.2 syndrome, deletion Xp22.3 syndrome, 7q11.23 microdeletion^(12-14), monogenic disorders like Noonan syndrome, achondroplasia, Seckel syndrome, Meier-Gorlin syndrome, Bloom syndrome⁽¹²⁾, and epigenetic changes like Silver-Russell or maternal uniparental disomy (UPD) 16⁽¹²⁾.

Schemmer et al.⁽¹⁵⁾ found in a cohort of 196 chromosomally abnormal fetuses that the crown-rump length (CRL) growth rate of fetuses with trisomy 18, 13 and triploidy in the first trimester was significantly reduced compared with euploid fetuses. CRL growth rate of fetuses with trisomy 21, sex chromosome trisomies, and 45X were not significantly reduced compared with euploid fetuses.

Cai et al.⁽¹⁶⁾ retrospectively investigated the association between early FGR and genetic syndromes in a cohort of 210 pregnant women from a tertiary referral center. They discovered a total rate of pathogenic copy number variations (CNVs) of 12.4%. SNP array detected significantly more pathogenic CNV than karyotype analysis. The detection rates of pathogenic CNVs in fetuses with isolated FGR, FGR combined with ultrasonographic soft markers, and FGR combined with ultrasonographic structural malformations were 6%, 10.4%, and 31.1%, respectively, showing significant differences among the groups⁽¹⁶⁾. Lesser et al.⁽¹⁷⁾ found that early-onset FGR (between 17 and 22+6 weeks) in pregnancies without maternal medical pathologies or genetic and fetal anomalies were associated with high rates of small for gestational age at birth, hypertensive disorders of pregnancy, neonatal morbidity, perinatal death, and iatrogenic preterm delivery. Pasquini et al.⁽¹⁸⁾ found that FGR below the 10^th percentile diagnosed before 26 weeks of gestation in 27% of cases is not isolated. The main etiologies are malformations (single umbilical artery, ventricular septal defect, ventriculomegaly, clubfoot, and omphalocele) and chromosomal abnormalities (trisomy 21, 18, 13, 2, triploidy, 47XXX, 47XXY, 45X). They also emphasized the risk of neonatal death and the possibility of a postnatal diagnosis of a genetic syndrome or neurodevelopmental delay despite normal prenatal tests. Dap et al.⁽¹⁹⁾ found, in a cohort of 67 fetuses diagnosed with severe FGR before 24 weeks (estimated fetal weight below the 3^rd centile), that the incidence of chromosomal abnormalities was 10.5%, and the rate of pathogenic CNV was 4.5%. Rapola et al.⁽²⁰⁾ found that homozygosity for a missense mutation in the BCS1L gene on the chromosomal region 2q33-37 was the etiology of GRACILE syndrome, a rare autosomal recessive disease characterized by FGR, Fanconi-type aminoaciduria, cholestasis, iron overload, profound lactic acidosis, and early neonatal death.

Calis et al.⁽²¹⁾ found that placentas of early-onset FGR showed the highest levels of degeneration compared to placentas of late-onset FGR, small for gestational age and appropriate for gestational age.

Redaelli et al.⁽²²⁾ found one case of severe FGR at 20 weeks of gestation with normal morphology and a single umbilical artery in association with confined placental mosaicism for trisomy 15. 

In our case, we had a severe early symmetrical FGR caused by a 350 kb heterozygous interstitial deletion on the chromosomal region 2q21.1. This deletion encompasses five genes: SMPD4, MZT2B, CCDC115, IMP4, and PTPN18.

SMPD4 gene encodes the enzyme Sphingomyelinase 3 and 4^(23,24). Loss of the SMPD4 gene is associated prenatally with growth restriction, arthrogryposis (clenched hands, foot deformity), cerebral abnormalities (lissencephaly, cerebellar hypoplasia, corpus callosum deformity)⁽²³⁾, and postnatally with neurodevelopmental delay, arthrogryposis, microcephaly, and brain anoma­lies (simplified gyral pattern, hypomyelination, hypoplasia of corpus callosum and brain stem)⁽²⁴⁾. Heterozygosity of SMPD4 is associated with neonatal asphyxia, severe intellectual disability, intractable seizures, cerebellar and brainstem hypoplasia, and dysmorphic features, including a prominent supraorbital ridge, thin upper lip, and prominent antihelix⁽²⁵⁾.

Losses of the Mitotic Spindle Organizing Protein 2B (MZT2B) gene, together with the genes SMPD4, TUBA3E, CCDC115, IMP4, and PTPN18, are associated with varying degrees of intellectual developmental disorder⁽²⁶⁾.

Coiled-Coil Domain Containing 115 (CCDC115) is a protein-coding gene. CCDC115 deficiency causes a disorder of Golgi homeostasis with abnormal protein glycosylation⁽²⁷⁾, which is manifested by early and severe liver fibrosis and cirrhosis associated with neurological symptoms⁽²⁸⁾.

IMP4 is a protein-coding gene. The protein encoded by this gene, along with IMP3 and MPP10, is part of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP) complex, which is necessary for the early cleavage steps of pre-18S ribosomal RNA processing⁽²⁹⁾. Losses of this gene and other genes from the chromosomal region 2q (SMPD4, MZT2B, TUBA3E, CCDC115, PTPN18) are encountered in various forms of intellectual developmental disorder⁽²⁶⁾.

Protein Tyrosine Phosphatase Non-Receptor Type 18 (PTPN18) gene disorder is associated with autistic behavior, delayed speech and language development, and intellectual disability⁽³⁰⁾.

Regarding the size of a deleted chromosomal region from the long arm of chromosome 2, small losses of 216 kb, which comprises genes SMPD4, MZT2B, TUBA3E, CCDC115, IMP4, and PTPN18, are associated with a mild intellectual developmental disorder and attention-deficit-hyperactivity-disorder⁽²⁶⁾, but more significant losses of 10.9 Mb are associated with an intellectual developmental disorder⁽²⁶⁾, or even more critical (18.5 Mb) are associated with multiple anomalies detected antenatally by ultrasound scan: congenital cardiac defects, bilateral hydronephrosis, agenesis of the corpus callosum, clenched hands, hypertelorism, micrognathia, sacral dimple, rocker-bottom feet, short neck and excessive skin in the occiput⁽⁵⁾.

In our case, a 350 kb heterozygous interstitial deletion on the chromosomal region 2q21.1, encompassing five genes (SMPD4, MZT2B, CCDC115, IMP4, and PTPN18), which was diagnosed prenatally, was associated with severe early symmetrical FGR. Given the age of the newborn, we cannot conclude regarding the intellectual development disorder of the newborn. It remains that future follow-up to diagnose eventually intellectual development disorder in this case.

6. Conclusions

We present a rare case of severe early symmetrical FGR caused by a 350 kb heterozygous interstitial deletion on the chromosomal region 2q21.1, encompassing five genes: SMPD4, MZT2B, CCDC115, IMP4, and PTPN18, which was diagnosed prenatally from amniotic fluid. The result of this study may be helpful for antenatal counseling of pregnant women with severe early onset of intrauterine growth restriction.  

CORRESPONDING AUTHOR: Mihai Muntean E-mail: munteanmihai@yahoo.com

CONFLICT OF INTEREST: none declared.

FINANCIAL SUPPORT: none declared.

This work is permanently accessible online free of charge and published under the CC-BY.