A novel 3q interstitial deletion including GATA2 and ZNF148: A case report

GATA2 and ZNF148 have both been mapped to chromosome 3q. Pathogenic variants in GATA2 have been associated with immunodeficiency and high risk for myelodysplasia, acute myeloid leukemia, and chronic myelomonocytic leukemia. Gain‐of‐function variants in ZNF148 have previously been suggested as a mechanism for agenesis of the corpus callosum (ACC). Here, we report a novel 10.4 Mb interstitial deletion on 3q12.33q22.1 including GATA2 and ZNF148 in a child with developmental delay, agenesis of the corpus callosum, and vertebral segmentation defects. With this diagnosis, we were able to suggest preemptive referrals to hematology/oncology and allergy/immunology for close monitoring of early myelodysplasia. We also propose a possible link between ZNF148 loss of function variants and ACC.


| INTRODUCTION
Individuals with 3q interstitial deletions have previously been reported in the medical literature with several overlapping features, including developmental delay, corpus callosum differences, hypotonia, and some distinctive facial features.A number of the previously reported deletions have included GATA2.Haploinsufficiency of GATA2 has been associated with Emberger syndrome (OMIM #614038) and immunodeficiency (OMIM #614172).Emberger syndrome can manifest with clinical findings such as deafness, recurrent cellulitis, immunodeficiency, acute myeloid leukemia, pancytopenia, and myelodysplasia.GATA2 is located on 3q21.3.Previously reported individuals with deletions of 3q including GATA2 have a wide spectrum of phenotypes including myelodysplasia, cytopenias, various infections, and pulmonary alveolar proteinosis and lymphedema (Greenmyer et al., 2022).Some of these individuals were displaying symptoms of myelodysplasia and recurrent infection at the time of reporting, though these features were not reported for most.It has been previously suggested that the young age of subjects presented in case reports may be contributing to the underreporting of manifestations of myelodysplastic syndromes in interstitial deletions of 3q involving GATA2.However, the importance of monitoring for hematologic disease is vital in children with GATA2 deletions.
Another gene located on 3q21 is ZNF148.Pathogenic variants in ZNF148 have previously been associated with a neurodevelopmental disorder characterized by global developmental delay, absent/ hypoplastic corpus callosum, and distinctive facial features (OMIM #617260).Initially, a dominant negative or gain-of-function effect was hypothesized as the mechanism by which variants affecting the last exon of ZNF148 lead to the associated features (Stevens et al., 2016).
More recently, another report of 22 individuals with variants in ZNF148, including a whole-gene deletion, found that corpus callosum anomalies are not a consistent feature in this disorder (Szakszon et al., 2024).
Here, we report an individual with a 10.4 Mb deletion of 3q12.33q22.1 including the entirety of both GATA2 and ZNF148 and review the existing literature regarding interstitial deletions of 3q.These genes were chosen for focus because GATA2 and ZNF148 have definitively emerged as being linked to human disease since the first published papers describing interstitial deletions on 3q variants.We emphasize the importance of establishing care with a hematology/oncology team for individuals with interstitial deletions of 3q involving GATA2.We also provide an additional report of haploinsufficiency of ZNF148 in an individual with corpus callosum differences, suggesting that the role of this gene in development of the corpus callosum remains complex and requires further study.

| CASE REPORT
The subject is a four-year-old female at the time of reporting, born at term via an uncomplicated spontaneous vaginal delivery.Growth parameters at birth were appropriate for gestational age.Around 2 months of age, the subject was noted to be hypotonic.Imaging of the head and spine were obtained, showing agenesis of the corpus callosum as well as thoracolumbar segmentation differences of the spinal column.
At 2 years of age, the subject was referred to our clinic for further evaluation.She was globally developmentally delayed.She was also noted to be of shorter stature (at the 7th percentile for age) than would be expected for her predicted mid-parental height.The family history was negative for other individuals with developmental delays or short stature.
Given the involvement of GATA2, the subject was referred to hematology/oncology and allergy/immunology for evaluation.A renal ultrasound, echocardiogram, serum calcium and parathyroid hormone level, and referral to pediatric ophthalmology were also recommended based on the other deleted genes.The subject's parents were offered genetic testing and declined, but due to the large size of the deletion, it is assumed to be de novo.
At the subject's most recent follow-up in our clinic at 3.5 years old, she was walking independently and able to feed herself with some utensil use.She still did not have consistent speech and she continued to receive physical, occupational, and speech therapies.
Growth parameters were at the 6th percentile for height, 70th percentile for weight, and 5th percentile for head circumference.Physical exam at that time was notable for bitemporal narrowing, tall forehead, and flat midface.Her workup with hematology/oncology and allergy/ immunology, including bone marrow biopsy, had been reassuring with no significant findings, though she continued to be followed closely by both teams.Echocardiogram, serum calcium, and parathyroid hormone were normal.Ophthalmology exam showed retinal hypopigmentation of unclear etiology for which she was referred to a retinal specialist.A renal ultrasound had not yet been performed.

| DISCUSSION
A review of the existing literature involving interstitial 3q deletions reveals several overlapping clinical features.Most notably, >50% of patients were reported to have distinctive craniofacial features, developmental delay, and hypotonia.Other shared features include agenesis of the corpus callosum, genitourinary anomalies, microcephaly, eye abnormalities, and poor growth, noted in >25% of patients.While less common, several patients also had cardiac and renal defects, as well as musculoskeletal abnormalities (Table 1, Figure 1) (Arai et al., 1982;Callier et al., 2009;de Ru et al., 2005;Fujita et al., 1992;Genuardi et al., 1994;Greenmyer et al., 2022;Jenkins et al., 1985;Jewett et al., 1993;Lawson et al., 1995;Lawson-Yuen et al., 2006;Malan et al., 2010;Materna-Kiryluk et al., 2014;McMorrow et al., 1986;Molin et al., 2012;Noda et al., 1998;Ogata et al., 1998;Ogilvie et al., 1998;Okada et al., 1987;Wolstenholme et al., 1994;Xie et al., 2017).This case report serves as a reminder that individual genes included within a larger microdeletion may require particular attention; thus, all genes involved in non-recurrent deletions should be appropriately reviewed and management/surveillance recommendations specifically tailored.All of the known disease-causing genes in this region were reviewed and GATA2 and ZNF148 were chosen for their immediate clinical relevance to the patient.
The novel interstitial deletion of chromosome 3q in the subject reported here likely explains her global developmental delay, but the inclusion of GATA2 within the deleted region has a significant impact on her health maintenance moving forward.Because haploinsufficiency of GATA2 has been associated with immunodeficiency syndromes in the past, patients with interstitial deletions of chromosome 3 including GATA2 are at increased risk for this phenotype.Though many of the reported individuals with 3q deletions including GATA2 have not been known to have signs of myelodysplasia, many of the case reports were published prior to the complete characterization of GATA2 haploinsufficiency.Also, the age of the subjects at the time of reporting must be taken into consideration.The average age of reporting of patients with a GATA2 deletion is around 7 years old.
When considering that two out of the three reported patients over the age of nine with this deletion have been found to have myelodysplastic syndromes, it brings to light the importance of continued hematologic monitoring of this population.We suggest patients with larger interstitial 3q deletions involving GATA2 be screened for potential immunodeficiency and/or myelodysplastic syndromes.Though no rigid guidelines exist for asymptomatic patients with GATA2 haploinsufficiency, previous studies have suggested peripheral blood counts every 3-6 months and bone marrow biopsy cytogenetics every 1-2 years to monitor for any changes (Hsu et al., 2015).

Agenesis of the corpus callosum (ACC) has been previously
reported in association with several chromosome aberrations involving gene deletions on chromosomes 1, 4, 6, 8, and 17, with several candidate genes reported within each (Palmer & Mowat, 2014).ACC has also more recently been associated with variants in ZNF148 (Stevens et al., 2016).Stevens et al. reported four patients with de novo truncating variants in ZNF148, all of which affected the last exon of the gene, and all of whom had underdevelopment of the corpus callosum.It was hypothesized that due to the location of the variants, the encoded protein escaped nonsense-mediated decay and thus had a dominant negative (or gain-of-function) effect.Szakszon et al. then reported 22 additional patients with variants in ZNF148, of which just over one third had anomalies of the corpus callosum.One of the reported individuals had a whole-gene deletion of ZNF148 and did not have ACC.There are a number of overlapping deletions in the DECIPHER database including ZNF148, one of which was a de novo deletion and included hypoplasia of the corpus callosum as part of the phenotype (Firth, 2009).On our literature review, of the 12 subjects with 3q deletions previously reported to have ACC, seven have ZNF148 within the deleted region, including our subject.Thus, we propose that while the impact of different variants in ZNF148 on development of the corpus callosum will require further studies and functional characterization, haploinsufficiency as a potential mechanism cannot be entirely disregarded.
showing the deletion on 3q found in our subject as well as additional previously reported interstitial deletions of 3q, both overlapping and non-overlapping.Location of GATA2 and ZNF148 are indicated in green and red respectively.Deletions reported in individuals with known myelodysplasia are indicated with a green asterisk while deletions reported individuals with known agenesis of the corpus callosum are indicated with a red asterisk.
T A B L E 1 Summary of the reported features of individuals with 3q interstitial deletions in the literature.Some deletion breakpoints are estimated based on available information, as indicated.

| CONCLUSION
With the limited number of recently reported individuals with 3q interstitial deletions, there is still more to be learned about the phenotypes patients will present with.Our subject's deletion is novel and helps to expand the phenotype of 3q interstitial deletions, based on which genes are involved.As the development of potential additional features in the future remains to be seen, continued monitoring by appropriate subspecialists will be vital in the coming years.We suggest in patients with similar deletions, close follow-up with hematology/oncology teams as well as allergy/immunology teams should be carefully considered.

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Our participant underwent a chromosomal microarray as part of clinical workup.The sample was collected via a buccal swab.The microarray was performed at GeneDx using the Affymetrix CytoScan HD microarray system.Informed consent was obtained from the family regarding additional chart review and publication of this paper.Our review of the literature was performed using terms "3q interstitial deletion," "GATA2," "ZNF148."This study makes use of data generated by the DECIPHER community.A full list of centers who contributed to the generation of the data is available from https:// deciphergenomics.org/about/statsand via email from contact@ deciphergenomics.org.DECIPHER is hosted by EMBL-EBI and funding for the DECIPHER project was provided by the Wellcome Trust (grant number WT223718/Z/21/Z).Those who carried out the original analysis and collection of the data bear no responsibility for the further analysis or interpretation of the data.