Prenatal diagnosis and genetic counseling of a de novo 16q24.3 microdeletion in a Chinese family

Abstract

Background

Copy number variations represent a key source of genomic variability, encompassing both benign and pathogenic alterations. Accurate interpretation of copy number variations identified through prenatal screening is critical for effective genetic consultation and clinical management. Microdeletions within the 16q24.3 locus remain understudied, thereby complicating genetic counseling for affected cases.

Case presentation: This study describes the prenatal diagnostic workup and genetic counseling process for a Chinese family with a fetus carrying a de novo 16q24.3 microdeletion.

Conclusion

Conventional cytogenetic techniques exhibit limited sensitivity for the detection of chromosomal microdeletions and microduplications. A multimodal approach integrating prenatal ultrasound, karyotyping, chromosomal microarray analysis, and genetic counseling enhances the diagnostic accuracy of such chromosomal anomalies during pregnancy.

Introduction

Copy number variations (CNVs) constitute a major class of genomic structural variants that contribute to both physiological diversity and disease pathogenesis. ¹ The widespread adoption of chromosomal microarray analysis (CMA) in clinical diagnostics across China has facilitated the identification of numerous novel CNVs. CMA, also known as “molecular karyotyping,” is a high-resolution molecular cytogenetic technique that enables the comprehensive detection of chromosomal abnormalities associated with genetic disorders and developmental anomalies through a bioinformatic analysis. ² Despite its diagnostic utility, the clinical significance of several newly discovered CNVs remains incompletely elucidated. ³ In particular, microdeletions involving the 16q24.3 chromosomal region remain underreported, posing diagnostic challenges in genetic counseling practice. This study describes the prenatal detection and clinical management of a de novo 16q24.3 microdeletion identified in a Chinese pedigree.

Case report

In 2024, a 30-year-old primigravida (Gravida 1, Para 0 (G1P0)) underwent amniocentesis at 18 weeks of gestation following a finding of high-risk fetal trisomy 21 on first-trimester combined screening. Her 30-year-old spouse reported no family history of congenital anomalies or genetic conditions. The pregnancy was conceived spontaneously, and prenatal ultrasound examinations revealed no structural abnormalities in the fetus. Cytogenetic analysis of cultured amniotic fluid cells confirmed a normal female karyotype (46, XX).

CMA was performed on uncultured amniocytes using the Affymetrix CytoScan 750 K chip, which includes 550k non-polymorphic markers and 200k single nucleotide polymorphism (SNP) markers distributed throughout the human genome, with an average marker density of approximately 1 per 4 kb. This platform enables genome-wide detection of chromosomal aneuploidies, microdeletions/microduplications (CNVs), and regions of homozygosity (ROH), with a typical resolution of 100 kb for duplications and 50 kb for deletions. CNVs smaller than these thresholds are generally not reported. ⁴ CMA identified a 52 kb chromosomal microdeletion in the region of 16q24.3, reported according to the International System of Cytogenomic Nomenclature 2020 (ISCN 2020) as arr(GRCh37) 16q24.3(89,508,862_89,561,087)x1 (Pathogenicity: Variant of uncertain significance (VUS))(Figure 1).

Figure 1.

CMA detected a 52 kb chromosomal microdeletion in the region of 16q24.3 arr(GRCh37) 16q24.3(89,508,862_89,561,087)x1. : The breakpoints of the 52 kb segment. CMA: chromosomal microarray analysis.

Because this 52 kb chromosomal microdeletion was identified in the fetus, we performed both CMA and traditional karyotyping on the peripheral blood samples obtained from the parents. The karyotyping and CMA results were normal; consequently, the 16q24.3 microdeletion identified in the fetus was determined to be a de novo mutation. Following genetic counseling, the parents chose to proceed with the pregnancy. An ultrasound performed at 29 weeks of gestation revealed no abnormalities. After receiving additional genetic counseling, the parents reaffirmed their decision to continue the pregnancy. At 39 weeks of pregnancy, the mother delivered a baby girl via vaginal delivery. The newborn underwent a thorough physical examination, which revealed generally normal results. Apgar scores were 9/10/10. At the 12-month checkup, the baby demonstrated appropriate development. We will continue to monitor the infant’s growth and development, including both physical and intellectual progress, with a particular attention on the nervous and skeletal systems.

The reporting of this study conforms to Case Report (CARE) guidelines. ⁵

Discussion

The deleted region of 16q24.3 contains several protein coding genes: ANKRD11, GAS11, GAS8-AS1, and TCF25.

GAS11, GAS8-AS1, and TCF25 are not considered to be haploinsufficient genes. GAS11 encodes a microtubule-associated protein and serves as a core component of the intraflagellar transport complex B (IFT-B). It plays a crucial role in the assembly and maintenance of cilia, which are essential for the structure and function of these hair-like cellular projections. Cilia act as cellular “antennae,” critical for signal transduction (e.g. Hedgehog signaling), motility, and sensing the extracellular environment. Dysfunction of GAS11 has been associated with ciliopathies. ⁶

GAS8-AS1 encodes a protein identified as mitochondrial ribosomal protein L51 (MRPL51). It localizes to mitochondria and is a component of the mitochondrial ribosome large subunit (mt-LSU). Its primary function is to participate in mitochondrial protein translation, assisting in the synthesis of proteins essential for mitochondrial function, including respiratory chain complexes. Consequently, it plays an indirect but vital role in cellular energy metabolism (adenosine triphosphate (ATP) production). ⁷

TCF25 encodes a KRAB domain-containing transcription factor. Proteins of this class typically function as transcriptional repressors by binding to DNA and recruiting corepressor complexes to inhibit the expression of downstream genes. Studies suggest that TCF25 is involved in cell cycle regulation, potentially modulating cell proliferation by influencing the expression of cell cycle proteins such as cyclin E1. Additionally, it is also in the development and progression of certain cancers (e.g. renal cell carcinoma and hepatocellular carcinoma) and may act as an oncogene. ⁸

ANKRD11 has been listed as haplosensitive genes in databases such as Online Mendelian Inheritance in Man (OMIM), Clinical Genome Resource (ClinGen), or Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). ANKRD11 encodes an ankyrin-repeat–containing nuclear protein that acts as a transcriptional coregulator. It modulates the expression of genes involved in neurogenesis, skeletal development, and cell cycle control by recruiting chromatin-remodeling complexes and histone deacetylases. Loss of one functional copy (haploinsufficiency) impairs the transcriptional coregulatory and chromatin-modifying functions of ANKRD11, resulting in KBG syndrome (OMIM #148050), whose cardinal features include the following: (a) Neurodevelopmental deficits. Mild to moderate intellectual disability, speech delay, autism-spectrum behaviors, and in some cases, epilepsy or electroencephalogram (EEG) abnormalities; (b) Skeletal anomalies. Postnatal short stature due to impaired growth-plate chondrocyte differentiation, delayed bone age, and occasional scoliosis or other skeletal dysplasias; (c) Craniofacial, dental, and upper gastrointestinal tract abnormalities. Macrodontia of the upper central incisors, broad forehead, hypertelorism, and a short nose.

Therefore, ANKRD11 haploinsufficiency leads to a multisystem developmental disorder dominated by cognitive, growth, and craniofacial abnormalities.^9,10

In our study, genetic testing identified a 52 kb heterozygous deletion at 16q24.3 (89,508,862_89,561,087) that removes exon 1 of the haploinsufficient gene ANKRD11 (NM_013275.6). This exon is located within the 5′ untranslated region (5’UTR). Loss-of-function variants in ANKRD11 are associated with KBG syndrome. Because the deletion involves only the 5’UTR, it is uncertain whether it disrupts gene function.

The 5'UTR region contains essential transcriptional regulatory elements, translation initiation sites, and mRNA stability signals. Therefore, its deletion may lead to reduced transcriptional efficiency, abnormal translation, or mRNA degradation, thereby affecting the functional expression levels of the ANKRD11 protein. Unlike the typical loss-of-function variants causing KBG syndrome, ¹¹ this variant retains the complete coding sequence, and this copy number variant is classified as a variant of uncertain clinical significance.

Cases involving only ANKRD11 gene deletions exhibit relatively milder phenotypes, whereas 16q24.3 microdeletion syndromes affecting the neighboring genes (ZFPM1, CDH15, and ZNF778) are associated with more severe neurological malformations and higher rates of congenital heart disease. ¹²

Researchers have reported a case involving a 138-kb intragenic ANKRD11 deletion encompassing exon 1, in which the patient exhibited borderline intellectual disability (intelligence quotient (IQ) 77) and mild growth retardation. In contrast, a female patient with a 220-kb deletion resulting in a complete loss of ANKRD11 (including the 5′UTR) presented with more pronounced clinical features, including short stature (−2 standard deviation score (SDS)), distinctive facial appearance, conductive hearing loss, and behavioral problems. ¹³ These observations suggest that retention of the 5'UTR may confer a protective effect, resulting in an incomplete or milder phenotypic expression.

The literature indicates that KBG syndrome is typically milder in female patients. A cohort study of 186 patients with KBG syndrome reported that female patients accounted for 46% of cases, with a tendency of exhibiting milder intellectual disability (37% mild vs. 26% in males) and lower rates of moderate-to-severe impairment. ¹¹ In the present case, the combination of female sex and the presence of 5'UTR-only deletion suggests a relatively favorable prognosis. According to the relevant literature,^9–13 after comprehensive genetic analysis and counseling, and after being fully informed of the associated risks, the parents elected to continue the pregnancy. At the 12-month follow-up, the infant demonstrated normal development.

However, it must be explicitly noted that a 12-month follow-up is insufficient to definitively exclude the KBG phenotype. In KBG syndrome, hallmark features, including macrodontia (particularly of the permanent secondary incisors), mild intellectual disability, and characteristic behavioral nuances (e.g. attention deficits and social difficulties), typically do not become apparent until the eruption of permanent secondary incisors (approximately 7–9 years of age) or the start of formal schooling.^11,12 Therefore, normal developmental milestones at 12 months do not rule out later manifestation of the KBG phenotype. Long-term structured neurodevelopmental and dental monitoring is essential. We recommend regular assessments of physical development, cognitive development, behavior, and school performance beginning at preschool age along with dental examination. Such longitudinal surveillance will enable early identification of potential features and timely intervention.

Conclusion

We present a case of a fetus with a de novo 52 kb microdeletion involving the 5'UTR regulatory region of ANKRD11 (16q24.3), which was initially classified as a VUS. This case illustrates the key clinical challenge of counseling parents when a de novo VUS is identified in a noncoding but regulatory region of a known haploinsufficient gene. Our integrated approach, combining prenatal ultrasound, karyotyping, CMA, and a thorough literature review, enabled us to provide evidence-based counseling. We highlighted that female sex and the presence of 5'UTR-only deletion may confer a relatively favorable prognosis. However, we emphasize the need for long-term neurodevelopmental and dental follow-up given the late-onset nature of key KBG syndrome features. This case underscores that for VUS in regulatory regions of haploinsufficient genes, genetic counseling should move beyond binary classification of pathogenicity toward a nuanced discussion of predicted functional impact, sex-specific variability, and the necessity of postnatal surveillance.