A Novel Homozygous Frameshift Variant in ZNF699 Associated With DEGCAGS Syndrome With Severe Transfusion‐Dependent Anemia in an Indian Child: A Case Report

ABSTRACT

In children with unexplained multisystem involvement—global developmental delay, dysmorphism, skeletal anomalies, and severe transfusion‐dependent anemia—especially from consanguineous families, whole‐exome sequencing should be pursued early to enable timely diagnosis, proactive iron chelation, and genetic counseling.

1. Introduction

DEGCAGS syndrome (OMIM #619488)—an acronym for Developmental delay with Gastrointestinal, Cardiovascular, Genitourinary, and Skeletal abnormalities—is an ultra‐rare autosomal recessive syndromic neurodevelopmental disorder caused by biallelic loss‐of‐function variants in the ZNF699 gene on chromosome 19p13. The syndrome was first formally characterized in 2021 when 13 patients from 12 unrelated consanguineous families were identified through whole‐exome and whole‐genome sequencing of over 33,000 individuals investigated for developmental delay of unknown etiology, establishing five distinct homozygous frameshift variants as causative and defining DEGCAGS as a discrete clinical entity [1].

Since the original description, the global case count has grown incrementally. A consolidated clinical summary across all published patients identified dysmorphic coarse facial features, congenital heart defects, and skeletal anomalies—particularly syndactyly—as the most consistent findings that should prompt early clinical suspicion of DEGCAGS [2]. Next‐generation phenotyping methodology employing Human Phenotype Ontology (HPO) terms was subsequently proposed as a tool for standardized phenotypic documentation of this clinically variable syndrome [3]. The largest cohort to date demonstrated an age‐related clinical presentation and a recognizable facial gestalt, and further identified a distinct DNA methylation episignature in blood that may serve as a diagnostic and classification tool for variants of uncertain significance in ZNF699 [4].

The present case represents a rare and clinically instructive example of DEGCAGS syndrome presenting in the Indian subcontinent, diagnosed in a 3‐year‐old male child of consanguineous parentage through whole‐exome sequencing. The case describes a novel homozygous frameshift variant in ZNF699, currently classified as a variant of uncertain significance (VUS), which demonstrates strong phenotypic concordance with the established DEGCAGS clinical spectrum and came to our attention particularly because of the severity of its hematological course, a dimension that has received limited systematic attention in prior published reports.

2. Case History

A 3‐year‐old male child, the second‐born of third‐degree consanguineous parents, presented to the outpatient department with bilateral purulent ear discharge of 15 days' duration and productive cough with sputum of 6 days' duration, associated with difficulty in breathing. This acute presentation occurred in the context of pre‐existing global developmental delay, failure to thrive, congenital anomalies, and chronic transfusion‐dependent anemia. The current episode began 15 days prior to presentation with bilateral profuse mucopurulent ear discharge—not associated with otalgia—along with productive cough, coryza, and progressive respiratory distress.

The child was born at term via emergency lower‐segment cesarean section due to breech presentation, with a birth weight of 2.5 kg. The neonatal period was complicated: stridor was noted and diagnosed as laryngomalacia, and feeding difficulties were present from early infancy. Postaxial polydactyly of the right hand with shortening of the upper limbs was identified at birth. Echocardiography demonstrated a small ostium secundum atrial septal defect with left‐to‐right shunt. Immunization was up‐to‐date per the national immunization schedule.

Developmental assessment during the first year of life revealed global developmental delay. Gross motor milestones were significantly delayed, with neck holding achieved at 9–10 months and independent sitting delayed beyond the expected age. Speech was absent at the time of presentation. No history of seizures or developmental regression was noted. The child had a history of recurrent hospital admissions since infancy with similar complaints, demonstrating fast breathing with retractions, decreased activity, excessive pallor, difficulty in swallowing, bilateral purulent ear discharge, and progressive developmental delay on each occasion.

On anthropometric assessment at the current presentation, the child weighed 7.8 kg, with a height of 71 cm, head circumference of 45.5 cm, and mid‐upper arm circumference of 12.5 cm—all falling between −1 and −2 standard deviations for age, consistent with failure to thrive. Physical examination revealed multiple dysmorphic features. Craniofacial examination demonstrated epicanthal folds, prominent upper lip vermilion, elongated philtrum, mild retrognathia, bushy eyebrows, frontal hypertrichosis, and coarse facial features. Limb examination revealed postaxial polydactyly of the right upper limb, syndactyly, and bilateral clubfoot, with increased fat pads over the lower limbs. Additional findings included inverted nipples and bilaterally descended testes. Cardiac auscultation revealed a murmur. Chest auscultation demonstrated bilateral wheeze and occasional crepitations. Neurological examination revealed central hypotonia with brisk deep tendon reflexes.

Developmental assessment using a standardized tool yielded a developmental quotient (DQ) of 62.25%, consistent with moderate global developmental delay. MRI of the brain demonstrated restricted diffusion involving the corpus callosum and cerebral white matter on diffusion‐weighted imaging (DWI), without gross structural malformation.

3. Differential Diagnosis, Investigations, and Treatment

Serial complete blood counts demonstrated a progressive, transfusion‐dependent anemia with hemoglobin values ranging from 2.5 to 8.5 g/dL, requiring more than 10 packed red blood cell transfusions over the preceding 2 years. The anemia was associated with relative lymphocytosis and, on at least one occasion, thrombocytopenia, suggesting bicytopenia. Peripheral blood smear demonstrated moderate anisopoikilocytosis with microcytic hypochromic forms, ovalocytes, target cells, and occasional teardrop cells; no hemoparasites were identified. C‐reactive protein was persistently elevated. Ear swab culture was negative for bacterial growth. Serum ferritin had risen to 977.0 ng/mL. Chest radiograph revealed cardiomegaly (Figure 1).

FIGURE 1.

Frontal chest radiograph of the index patient, a 3‐year‐old boy with suspected DEGCAGS syndrome, demonstrating an enlarged cardiac silhouette (cardiomegaly) in the setting of a known ostium secundum atrial septal defect and chronic transfusion‐dependent anemia. Arrow indicates the enlarged cardiac silhouette. R = right side of patient.

High‐performance liquid chromatography (HPLC) demonstrated an elevated fetal hemoglobin (HbF) fraction of 18.7%, initially raising suspicion for beta‐thalassemia (Figure 2). However, whole‐exome sequencing (Neuberg Centre for Genomic Medicine, Ahmedabad) combined with multiplex ligation‐dependent probe amplification (MLPA) for the HBB and HBA1/HBA2 genes did not identify pathogenic variants associated with common hemoglobinopathies by the tests performed; however, these methods do not exclude all possible molecular mechanisms underlying beta‐thalassemia or other hemoglobinopathies. Whole‐exome sequencing identified a homozygous frameshift variant in ZNF699 (Exon 6): c.1623_1626del (p.Tyr542ProfsTer8), with a gnomAD population frequency of 0.0001% (1 heterozygous carrier identified in the gnomAD v2.1.1 database among 141,456 individuals; no homozygotes reported) (Figure 3), with complete gene panel coverage documentation, including 100% coverage of the ZNF699 coding region (Figures 4, 5, 6).

FIGURE 2.

High‐performance liquid chromatography (HPLC) report demonstrating elevated fetal hemoglobin (HbF) fraction of 18.7%, which initially raised suspicion for beta‐thalassemia. The chromatogram shows the hemoglobin variant profile with retention times and peak areas.

FIGURE 3.

Molecular genetic report summarizing the homozygous ZNF699 frameshift variant (c.1623_1626del, p.Tyr542ProfsTer8) identified on whole‐exome sequencing, together with the associated DEGCAGS syndrome disease description.

FIGURE 4.

Gene panel coverage documentation from whole‐exome sequencing analysis, confirming complete (100%) sequencing coverage of the ZNF699 coding region among the genes analyzed.

FIGURE 5.

Gene panel coverage documentation from whole‐exome sequencing analysis (continued), confirming complete (100%) sequencing coverage of the ZNF699 coding region among the genes analyzed.

FIGURE 6.

Gene panel coverage documentation from whole‐exome sequencing analysis (continued), confirming complete (100%) sequencing coverage of the ZNF699 coding region among the genes analyzed.

3.1. Regarding ACMG/AMP Classification Criteria

The variant c.1623_1626del (p.Tyr542ProfsTer8) in ZNF699 (reference transcript NM_152475.3) is a frameshift deletion predicted to result in nonsense‐mediated decay or premature protein truncation. The applicable ACMG/AMP criteria include: PVS1 (null variant in a gene where loss of function is a known mechanism of disease), PM2 (absent from controls or present at extremely low frequency in population databases—gnomAD frequency 0.0001%), and PP4 (patient's phenotype is highly specific for a disease with a single genetic etiology). The variant was classified as a VUS by the reporting laboratory; however, the strong phenotypic concordance with the established DEGCAGS clinical spectrum and the loss‐of‐function mechanism support its interpretation as highly suspicious for clinical relevance in this patient, pending functional confirmation or additional case reports.

The OMIM phenotype was confirmed as DEGCAGS syndrome, autosomal recessive inheritance (OMIM #619488). This variant was classified as a variant of uncertain significance (VUS) by the reporting laboratory; however, it is predicted to result in complete loss of function of the ZNF699 protein through premature protein truncation, a mechanism consistent with previously established pathogenic variants in DEGCAGS. Given the strong concordance between this patient's phenotype and the established DEGCAGS clinical spectrum, together with the loss‐of‐function nature of the variant, its extremely low frequency in population databases (0.0001%), and the homozygous state in a consanguineous family, this variant was interpreted as highly suspicious for clinical relevance and strongly associated with the observed DEGCAGS‐compatible phenotype, despite its formal VUS classification. Parental segregation testing was not performed due to resource limitations; however, given confirmed third‐degree consanguinity and autosomal recessive inheritance, both parents were presumed to be heterozygous carriers, although molecular confirmation was not available, consistent with identity by descent. The elder sibling was reported to be healthy and developmentally normal.

Management during the current admission included topical ciprofloxacin ear drops bilaterally, oral amoxicillin‐clavulanate for respiratory infection, and chlorpheniramine‐phenylephrine for symptomatic relief. Piperacillin‐tazobactam was discontinued on senior review. Packed red blood cell transfusion was continued for transfusion‐dependent anemia; iron profile monitoring was maintained, and nutritional supplementation was continued. Genetic counseling was provided to the family, with emphasis on the 25% recurrence risk for future pregnancies and the availability of prenatal diagnostic options.

4. Conclusion and Results

The child demonstrated clinical improvement during the admission, including resolution of respiratory distress, defervescence, and improved feeding tolerance and was discharged in a hemodynamically stable condition with post‐transfusion hemoglobin of 8.2 g/dL. Given the serum ferritin level approaching the threshold at which iron chelation is typically considered in transfusion‐dependent patients, and cardiomegaly noted on chest radiography, ongoing follow‐up includes echocardiographic re‐evaluation and proactive assessment for iron chelation therapy, alongside continued multidisciplinary developmental and hematological surveillance.

5. Discussion

DEGCAGS syndrome is an ultra‐rare autosomal recessive neurodevelopmental syndrome, and the present case represents, to our knowledge, one of the first clinically and genetically characterized cases reported from the Indian subcontinent, harboring a novel ZNF699 frameshift variant present at an extremely low frequency in population databases (gnomAD v2.1.1: 0.0001%; one heterozygous carrier, no homozygotes) and not previously documented in the literature. The clinical constellation observed—global developmental delay, central hypotonia, coarse facial dysmorphism, postaxial polydactyly, syndactyly, bilateral clubfoot, and congenital heart disease—aligns with the core phenotypic features described across all published DEGCAGS cohorts [1, 2, 3, 4]. The notable absence of gastrointestinal atresia in our patient, a feature considered among the more specific early markers of DEGCAGS, illustrates the remarkable phenotypic variability of this condition, which has been observed even among affected siblings carrying identical variants [4]. Critically, the full phenotypic picture only became apparent in retrospect; each feature had been pursued as an isolated clinical problem across multiple admissions before a unifying diagnosis was established.

The neurological profile of this child warrants specific attention. Global developmental delay with a formal DQ of 62.25%, central hypotonia, absent speech beyond 12 months, and brisk deep tendon reflexes constitute a neurodevelopmental profile consistent with the universal neurodevelopmental impairment described across all previously reported DEGCAGS cases [4]. MRI of the brain demonstrated restricted diffusion involving the corpus callosum and cerebral white matter on DWI—findings that have been documented in other reported DEGCAGS patients and are well recognized in children with complex genetic etiologies [1]. Corpus callosum abnormalities and white matter signal changes in the context of syndromic neurodevelopmental delay serve as an important neuroimaging indicator and should prompt expedited genetic and metabolic evaluation [5]. In this child, the MRI findings were not incidental observations but part of a converging pattern that, in retrospect, pointed consistently toward a single underlying genetic diagnosis.

The ZNF699 gene encodes a large nuclear zinc finger protein belonging to the Krüppel‐associated box (KRAB) domain‐containing zinc finger protein (KRAB‐ZNF) family—the largest family of transcriptional regulators in higher vertebrates, acting primarily through epigenetic gene silencing during development. C2H2‐type zinc finger proteins, the structural class to which KRAB‐ZNF proteins belong, are highly expressed in the developing brain and play critical roles in controlling neural stem cell proliferation, migration, and cell fate determination [6]. Pathogenic variants in several KRAB‐ZNF family members have been linked to a range of neurodevelopmental disorders including intellectual disability, microcephaly, and structural brain abnormalities, providing a plausible mechanistic framework for the severe developmental delay and white matter pathology observed in DEGCAGS [6]. The exact molecular role of ZNF699 remains incompletely understood. All previously reported pathogenic variants, as well as the variant identified in the present case (currently classified as a VUS pending further clinical correlation), are predicted to result in complete loss of function through nonsense‐mediated decay or premature protein truncation, and no functional studies using patient‐derived cells have yet been published.

The most clinically prominent feature in this patient was the progressive, transfusion‐dependent anemia—a dimension that has received limited systematic documentation in prior DEGCAGS literature. Hemoglobin values as low as 2.5 g/dL with a requirement for more than 10 packed red blood cell transfusions over 2 years represent a particularly severe transfusion‐dependent hematological phenotype; however, systematic comparison with previously published cases is limited by the rarity of the condition and heterogeneity in hematological reporting across the literature. The peripheral smear findings, the elevated HbF fraction on HPLC, and the absence of pathogenic variants associated with common hemoglobinopathies by the tests performed are consistent with, but do not definitively establish, that this anemia is related to ZNF699 loss of function; alternative etiologies cannot be entirely excluded based on the available hematological investigations. Hematological abnormalities—primarily anemia and, less frequently, pancytopenia—have been noted in a substantial proportion of DEGCAGS patients across published cohorts, suggesting that hematopoietic dysfunction may represent a core, rather than incidental, feature of this syndrome. Of particular clinical concern in this child is the serum ferritin level of 977.0 ng/mL, approaching the established 1000 ng/mL threshold at which iron chelation is recommended in transfusion‐dependent patients [7]. Early cardiac iron loading has been documented in young children with transfusion‐dependent anemias who received suboptimal or delayed chelation, underscoring the need to act before organ‐level toxicity becomes clinically apparent [8]. Cardiomegaly noted on chest radiography during this admission (Figure 1) further supports the need for echocardiographic re‐evaluation and proactive chelation assessment as part of the ongoing management plan.

Third‐degree consanguinity in this family is not merely a background demographic detail—it is the direct etiological mechanism through which this child inherited two copies of a rare allele that is highly suspicious for clinical relevance. Consanguineous unions substantially elevate the proportion of the genome that is identical by descent, thereby increasing the probability of homozygosity at rare recessive loci—the mechanism by which autosomal recessive conditions manifest in consanguineous families. The impact of consanguinity on the prevalence of rare recessive disorders is well established and is of particular relevance in South Asian and Middle Eastern populations, where consanguineous marriage is culturally practiced [9]. A retrospective analysis of rare genetic disorders at a tertiary Indian genetic center over 22 years identified neuromuscular and neurodevelopmental disorders as among the most prevalent categories, while noting that a substantial proportion of rare disease patients remain undiagnosed even after expert clinical and advanced laboratory evaluation—a reality the present case reflects precisely, having been diagnosed only after years of recurrent admissions and progressive clinical deterioration [10].

The variant identified in this case—a 4‐base pair deletion in exon 6 of ZNF699 predicted to result in a frameshift and premature stop at codon 8 of the new reading frame (p.Tyr542ProfsTer8, gnomAD v2.1.1 frequency 0.0001%, with 1 heterozygous carrier among 141,456 individuals and no homozygotes)—has not been previously reported in the literature or in ClinVar, representing a novel addition to the allelic spectrum of ZNF699‐related disease. While formally classified as a variant of uncertain significance by the reporting laboratory, several converging lines of evidence render this variant highly suspicious for clinical relevance and strongly associated with the observed phenotype in the present patient, including its predicted loss‐of‐function consequence, its extremely low frequency in population databases, and the close phenotypic concordance with the established DEGCAGS clinical spectrum described in this report. Detailed phenotypic correlation of this kind represents a recognized approach to the reclassification of novel variants of uncertain significance and is offered here as the primary evidentiary basis for our diagnostic interpretation. Its homozygous state in a consanguineous family, with both parents presumed to be heterozygous carriers, although molecular confirmation was not available, is consistent with autosomal recessive inheritance through identity by descent. The diagnostic journey in this case—a child investigated across multiple admissions over 3 years, each complaint addressed in isolation, before a single molecular test provided a unifying answer—mirrors the original discovery of DEGCAGS itself, which was possible only through large‐scale exome and genome sequencing combined with data repository analysis [1]. In settings where whole‐exome sequencing remains financially inaccessible, the cost of delayed diagnosis—measured in cumulative transfusions, repeated admissions, and irreversible developmental opportunity—is rarely formally calculated, yet is profoundly real.

This case reports a novel homozygous frameshift variant c.1623_1626del (p.Tyr542ProfsTer8) in ZNF699, currently classified as a variant of uncertain significance, which—supported by strong phenotypic concordance with the established DEGCAGS clinical spectrum—was interpreted as highly suspicious for clinical relevance and strongly associated with DEGCAGS syndrome in a 3‐year‐old child from a consanguineous Indian family. To our knowledge, this represents one of the first such cases reported from the Indian subcontinent. The case may expand the allelic and phenotypic spectrum of DEGCAGS syndrome, particularly with regard to the severity and clinical significance of transfusion‐dependent anemia, which warrants proactive iron chelation assessment before organ toxicity ensues. It reinforces that whole‐exome sequencing should be considered early rather than as a last resort in children with unexplained multi‐system involvement, particularly those born to consanguineous parents. Clinicians should maintain a high index of suspicion for DEGCAGS syndrome in children presenting with global developmental delay, coarse facial dysmorphism, skeletal anomalies, and progressive transfusion‐dependent anemia, even in the absence of gastrointestinal atresia, given the wide phenotypic variability of this condition.

Author Contributions

Arimanda Chaitanya Laasya Reddy: conceptualization, investigation, funding acquisition, writing – original draft, validation, visualization, formal analysis, project administration, supervision, data curation. A. Vamshee Priya: investigation, funding acquisition, validation, methodology, data curation, supervision, resources, project administration. Aditya Pachwa: writing – original draft, writing – review and editing, data curation, project administration, validation, visualization, supervision, methodology. Boilla Abhignya Reddy: writing – original draft, writing – review and editing, formal analysis, data curation, methodology. Lakshya Nehal Samineni: writing – original draft, writing – review and editing. Lanka Gourav Reddy: software, visualization, conceptualization, investigation, funding acquisition.

Funding

The authors have nothing to report.

Consent

Written informed consent was obtained from the parent of the patient for publication of this case report and any accompanying images.

Data Availability Statement

Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.