Antenatal description of large 4q13.2q21.23 deletion and outcomes

Abstract

Background

4q21 microdeletion syndrome is an emergent non‐recurrent genomic disorder characterized by facial dysmorphy, progressive growth retardation, severe intellectual deficit, and absent or severely delayed speech. Deletions occur in clusters along 4q interstitial or terminal regions. 4q chromosomal aberrations are variable in type, size, and breakpoint. Genotype–phenotype correlation is a challenging task. The recurrent antenatal feature associated a posteriori with this syndrome is intrauterine growth retardation. There are very few precise antenatal descriptions of this syndrome.

Methods

We report here the first antenatal history of one of the largest deletion of this region.

Results

Our case harbored a 16.9 Mb deletion encompassing 135 protein coding genes including 20 OMIM morbid genes involved in neurological and cognitive abilities. Those breakpoints overlap two clusters of described microdeletion syndromes of cytogenetic band 4q13 and 4q21.

Conclusion

From the end of the second trimester, set of call signs associated with this syndrome can be completed by: excess of amniotic fluid, mild growth retardation, short long bones, bony anomalies of the extremities, and bulging cheeks. So, emphasis should be placed on the examination of the extremities, and the face during the routine targeted prenatal ultrasound.

1. INTRODUCTION

Rising from the “genome‐first” approach, 4q21 microdeletion syndrome is a newly described non‐recurrent genomic disorder characterized by overlapping deletions of different size over the 4q21 region (MIM: 613509).

Deletions of this region are associated with neurodevelopmental disorders characterized by facial dysmorphy, progressive growth retardation, severe intellectual deficit, and absent or severely delayed speech (Strehle, Gruszfeld, et al., 2012). The critical region of 1.37 Mb lies on sub‐band 4q21.22 and contains five RefSeq genes: PRKG2, RASGEF1B, HNRNPD, HNRPDL, and ENOPH1. More recently, the clinical description of the smallest reported deletion in this region confirmed that PRKG2 and RASGEF1B are critical genes for intellectual disability and speech disorders, while the heterogeneous nuclear ribonucleoprotein HNRNPD and HNRNPDL genes are associated with growth retardation and hypotonia (Hu et al., 2017).

The recurrent antenatal feature associated with this syndrome is intrauterine growth retardation. We report here the first antenatal history of one of the largest deletion of this region. The deletion extending from 4q13.2 to q21.23 is about 16.9 Mb long and occurred in a female fetus.

Our report essentially adds to the literature data with regards to antenatal signs of this syndrome. Since there was a termination of pregnancy, genotype–phenotype discussion is limited to the antenatal dysmorphic features and prognostic of neurodevelopmental aspect.

2. CLINICAL REPORTS

Parents are self‐reported unrelated of Caucasian origin. The 25‐year‐old mother was a second gestational primipara, with no particular personal or familial medical history. The 35‐year‐old father had also no personal or familial history of any disease. He has no children of his own.

The non‐invasive screening testing of the first trimester to detect trisomy 21 was not done. An ultrasound examination was performed at the 20th week of amenorrhea which was normal.

At the 30th week of amenorrhea, a second two‐dimensional ultrasound imaging examination detected hydramnios, growth restriction of the long bones, a small stomach, and hypoplasia of nasal bone. Fetal weight was estimated at 1329 g (3rd percentile).

A thorough ultrasound examination at 32nd week of amenorrhea confirmed hydramnios and revealed cheeks of exaggerated volume compared to the global morphology of the fetus moderate brachycephaly, brachydactyly including bilateral brachymesophalangia of the fifth finger, a sandal sign, short long bones (femur 53 mm, <1st percentile; humerus 46, 1 mm, <1st percentile), growth retardation and a “sandal sign,” in a female fetus (Figure 1a). The fetal weight was estimated at 1378 g (1st percentile).

FIGURE 1.

(a) CGH chromosome 4 deletion of our case and genotype–phenotype correlations regard to already published cases (in bold, shared features); (b) Antenatal ultrasound distinctive features showing surprisingly large cheeks and hands; (c) Postnatal X‐ray showing brachymesophalangia and clinodactyly of the 5th radius; (d) craniofacial dysmorphy.

An amniodrainage was necessary to relieve the mother and collect amniotic fluid for biological analysis.

3. MATERIALS AND METHODS

3.1. Ethical approval and publication consent

Patients consent to publication of their medical and fetal data. In accordance to French law, consent for amniocentesis and for laboratory testing was obtained from each parent.

3.2. Digestive enzyme analysis

After sampling, amniotic fluids were centrifuged and frozen at −20°C. Amniotic fluid assayed enzymes were gamma‐glutamyl‐transpeptidase (GGTP), amino peptidase M (APM), total alkaline phosphatase, and its intestinal fraction (iALP) assayed by the inhibitor method (Muller et al., 1988). Median of raw values for each gestational age have been previously obtained on a large cohort of amniotic fluid samples and are routinely used for biochemical prenatal diagnosis. This screening also included total proteins, AFP (PerkinElmer, Turku, Finland), total proteins (urinary/CSF protein, Olympus, Hamburg, Germany) sodium, potassium, chloride (electrochemical method) calcium, and phosphorus (colorimetric method) assays (Czerkiewicz et al., 2011).

3.3. Comparative genomic hybridization

Comparative genomic hybridization (CGH) was performed with DNA extracted from amniotic cells without culture on the Agilent 60 k chip. The analysis software used was Agilent Cytogenomics 5.0.2.5. The genome reference is hg19/GRCh37.

3.4. Fluorescent in situ hybridization (FISH) and karyotypes

The abnormality detected by CGH was confirmed by the fluorescent in situ hybridization (FISH) on amniotic with the 00_RP11‐91J11/R+Contig 4pter/V probe to explore 4q21.23 region on hundred nuclei.

After cell culture, fetal karyotype was established with a resolution level of 400bpsh and detection of RHG/GTC bands. Twenty‐nine cells and six mitoses were examined.

3.5. Human genomic database

Interpretation of prognosis is based on published cases from literature, the DECIPHER (https://decipher.sanger.ac.uk/) and ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) databases. Both were accessed in February 2023. The genomic coordinates are provided according to Human Genome release hg19. Conversion of hg18 into hg19 genomic coordinates was performed on the UCSC genome browser (genome‐euro.ucsc.edu/cgi‐bin/hgLiftOver). The list of protein coding genes included in the deletion was obtained with BioMart tool of Ensembl browser (ensembl.org/biomart/martview).

4. RESULTS

Related to the opening of the pharyngeal and anal membranes, digestive enzymes are normally present at high level in the amniotic fluid from 12 to 13 weeks of amenorrhea until the 20–22th. Because of the closure of the anal sphincter, levels decrease after 22 weeks of gestation (Boue et al., 1988). Different biochemical patterns can be observed in digestive tract anomalies, primarily bilious vomiting (normal values of ALP with high values for others), or anal leakage (high values for all digestive enzymes). To overcome variations in methods over time, all markers are expressed in multiple of median (MoM) corresponding to the ratio between the observed raw value and the median raw value at the same gestational age. As a consequence, a normal value corresponds to 1 MoM and 5 MoM to the 99th percentile.

On one hand, hydramnios was investigated by digestive enzyme analysis which ruled out esophageal atresia or a swallowing disorder: GGTP 3.6 MoM, LAP 1.5 MoM, PAL normal. On the other hand, biological parameters were in normal range: AFP 0.73 MoM, proteins 3.5 g/L, esophagial atresia index 2.6 (normal if <3); Bartter index 2.5 (normal if >1). The biochemical profile was normal.

CGH revealed a large deletion 4q13.2‐4q21.23 of about 16.9 Mb (hg19, 4: 69,897,310‐86,696,064), confirmed by FISH. This method revealed the absence of hybridization of a complementary probe labeled at the target locus q13.2 of one of the two chromosomes 4. CGH of the parents was unremarkable. As a consequence, this deletion occurred probably de novo in the fetus. After cell culture, the fetal karyotype was 46,XX,del (Czerkiewicz et al., 2011)(q13.2q21.23) whereas parental karyotypes were without any particularities.

In order to evaluate the prognosis of this fetus, we compared her deletion to the postnatal description of a case with similar breakpoints. Hemati et al. described the evolution of a female patient with a 4q12–4q21.21 deletion (hg18; 54,711,575–79,601,919 or hg19; 4: 55,016,818‐79,382,895) presenting syndromic intellectual disability without piebaldism in contrast to previous reported individuals. The phenotype included dolichocephaly, pectus excavatum, hip dysplasia, pes planus, myopia, lens opacities, and an absence of spoken language but not of communication through signs. Craniofacial features were macrocephaly, prominent forehead, high frontal hairline, depressed nasal bridge, and low set ears (Hemati et al., 2015).

In our case, the parents wished to terminate pregnancy. After multidisciplinary concertation, and in accordance with French laws, a termination of pregnancy was carried out at 35 weeks and 6 days post‐amenorrhea. The fetus weighed 2225 g (21e percentile), with short limbs and fingers. Abnormalities of the extremities were detected: foot length was 54 mm (<2.5th p), hands presented brachymesophalangia and bilateral clinodactyly of the 5th radius (Figure 1b).

Dysmorphic features were as described in previous reports except for the patient's remarkably large cheeks.

A whole skeleton X‐ray showed no abnormalities in the morphology or number of structures of the skull, spine, and pelvis. Measured biometric values and bone maturation were consistent with the term: femur 63 mm (10e p), humerus 53 mm (5e p). There were 11 pairs of ribs.

5. DISCUSSION

The spectrum of 4q‐ syndrome is defined by interstitial and terminal regions where deletions appear to occur in clusters along 4q. Key features of this syndrome are mild facial and digital dysmorphism, developmental delay, growth retardation, skeletal and cardiac anomalies, and autism spectrum disorder.

Not every patient carries all characteristics, and other body systems may also be affected. All clinical descriptions of patients with neurodevelopmental phenotypes and proximal 4q chromosomal aberrations are variable in type (losses, gains or complex rearrangements), size (ranging from ∼1.5 Mb to ∼25 Mb) and breakpoints encompassing different chromosome bands and genes. Indeed, genotype–phenotype correlation is a challenging task. Description of small deletion cases are helpful to pinpoint critical genes involved in syndromic intellectual disorders (Strehle, Gruszfeld, et al., 2012).

The 16.9 Mb deletion found in our case occurred in the proximal interstitial region and extended from cytogenetic bands q13.2 to q21.23. There are few descriptions of this specific syndrome usually leading to face dysmorphism, and global neurodevelopmental delay with delayed or absent speech and cerebral anomalies (MIM: 613509).

The deletion found encompassed 135 protein coding genes including 20 OMIM morbid genes, some of which are haplotype‐sensitive and involved in neurological and cognitive abilities (Supplementary Table S1). Those breakpoints overlap two clusters of described microdeletion syndromes of cytogenetic band 4q13 and 4q21. ADAMTS3, ANKRD17 and NU4ATAC9P through the proximal bound are candidates for intellectual disability, growth retardation and congenital heart defect; PRKG2 and RASGEF1B for intellectual disability and speech defect; HNRNPD and HNRNPDL for growth retardation and hypotonia (Bhoj et al., 2013; Hu et al., 2017; Komlósi et al., 2015; Maldžienė et al., 2020).

Craniofacial anomalies are constant but dysmorphic features are very heterogeneous in 4q‐ syndrome. Based on the description of short deletions starting from 4q21.21 to 4q21.23, Strehle et al suggested that the loss of SEC31A on 4q21.22 may affect normal craniofacial development (Strehle, Yu, et al., 2012).

In our case, neither cardiac defects nor cerebral anomalies were detected by ultrasound. No post‐natal neuroimaging was done, but a swallowing disorder of neurological origin may be suspected as hydramnios was not related to a digestive malformation. Dysmorphic features in our case are very mild except those surprisingly large cheeks.

Literature data on antenatal features of this syndrome are poor. The mean antenatal call point is intrauterine growth delay below the third percentile. We propose a set of call signs associated with the ultrasound screening of this syndrome from the end of the second trimester: excess of amniotic fluid, mild growth retardation, short long bones, bony anomalies of the extremities and bulging cheeks.

Full cheeks are not constant in the 4q21 microdeletion syndrome. A clinical series of heterozygous loss of function ANKRD17 gene, link it to a syndrome with intellectual disability, speech delay, and dysmorphism. In this series, a 6‐year‐old female child with triangular face, deep set, thick alae nasi with flared nostrils, and full cheeks is reported. She harbored a 1,15 Mb ranging from 73,303,180 to 74,459,331, containing at least 2 Mendelian genes more, directly or not associated with neurodevelopmental dysmorphic disorders: RASSF6, MTHFD2L (Chopra et al., 2021).

Screening others associations between chromosome 4 and full cheeks, we found description of a girl with chromosomal imbalance with 4q32.2‐qter deletion and chromosome 7 duplication. She harbored increased fetal nuchal translucency, microcephaly, broad nasal bridge, absent of lower incisors, cleft palate, micrognathia (Pierre Robin sequence), and full cheeks (Strehle, Yu, et al., 2012). We found also the case of duplication 4p16.3‐p15.3 segment which seems to be associated to full cheeks through the imbalance of the lysosomal hydrolase alpha‐L‐iduronidase, IDUA gene, responsible for some of the mucopolysaccharidosis‐like facial features such as bulging cheeks (Tschernigg et al., 2002).

Human dysmorphic feature are likely highly polymorphic and genotype–phenotype correlation is complex.

Our take home message is that during the routine targeted prenatal ultrasound, emphasis should be placed on the examination of the extremities, and the face in particular the cheeks, whose volume appeared unexpectedly disproportionate in a context of mild delayed growth.

4q21 microdeletion is a recently described syndrome. Here, we report one of the largest deletions described so far and one of the first detailed antenatal description of this syndrome.

AUTHOR CONTRIBUTIONS

Anna‐Gaëlle Giguet‐Valard collected, analyzed data, and wrote the initial draft of the manuscript. Michèle Gueneret, Valérie Decatrelle, Marie‐Laure Juve, and Soraya Yazza provided and analyzed clinical data, and reviewed the manuscript, Christelle Thevenin and Sophie Dreux provided biological analysis. Patrice Bouvagnet and Michèle Gueneret supervised and approved the submitted version of the manuscript.

FUNDING INFORMATION

The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.

CONFLICT OF INTEREST STATEMENT

The authors have no relevant financial or non‐financial interests to disclose.

Supporting information

Table S1.

Data S1.

Giguet‐Valard, A.‐G. , Thevenin, C. , Dreux, S. , Decatrelle, V. , Juve, M.‐L. , Yazza, S. , Adenet, C. , Lesueur, M. , Bouvagnet, P. , & Gueneret, M. (2024). Antenatal description of large 4q13.2q21.23 deletion and outcomes. Molecular Genetics & Genomic Medicine, 12, e2397. 10.1002/mgg3.2397

DATA AVAILABILITY STATEMENT

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