A novel NKX2-5 mutation causing atrial septal defect and high-degree atrioventricular block in a Chinese family
Year: 2026
Type: article
Study design: Case Report
Abstract: The NKX2-5 gene, located on human chromosome 5q34, plays a pivotal role in cardiac development and function.1 Mutations in NKX2-5 have been linked to a variety of congenital heart defects, including atrial septal defects (ASDs), ventricular septal defects (VSD), and conduction disorders such as atrioventricular block (AVB).2,3 Although various NKX2-5 mutations have been reported, novel variants continue to expand the genotypic and phenotypic spectrum. We describe a Chinese family carrying a previously unreported heterozygous frameshift mutation in NKX2-5, presenting with ASD, high-degree AVB, and atrial fibrillation (AF). This case highlights the importance of genetic testing for accurate diagnosis, risk stratification, and family counselling in congenital heart disease (CHD) with arrhythmias. The proband was a 35-year-old woman from a Chinese family with multiple members affected by ASD (Figure 1). At the age of 26, she underwent surgical ASD closure after being diagnosed with ASD, although detailed operative information was not available. At 34 years of age, she presented to our centre for the first time with recurrent, non-exertional chest tightness and palpitations for more than 1 year. Laboratory tests, including B-type natriuretic peptide, cardiac troponin I, renal function, and thyroid hormone levels, were all within normal ranges. Transthoracic echocardiography demonstrated no significant valvular disease and preserved left ventricular ejection fraction. Holter electrocardiography revealed intermittent high-grade AVB (Figure 2). After multidisciplinary evaluation, a leadless single-chamber pacemaker was implanted in VVI mode, resulting in symptomatic improvement. Family pedigree. Squares indicate males and circles indicate females. Black shading represents individuals diagnosed with atrial septal defect, blue shading represents high-degree atrioventricular block, and red shading represents atrial arrhythmias. Composite colours indicate the coexistence of multiple clinical manifestations. ‘+’ and ‘−’ denote positive and negative genetic test results for the NKX2-5 variant. A question mark inside a symbol indicates unknown clinical status, whereas a question mark below a symbol indicates unknown genetic status. The proband is marked with an arrow Holter electrocardiogram of the proband demonstrating high-grade atrioventricular block At 35 years of age, the proband experienced worsening palpitations. Ambulatory electrocardiography documented paroxysmal AF. After exclusion of contraindications, she underwent radiofrequency catheter ablation at our centre. Bilateral pulmonary vein isolation and cavotricuspid isthmus linear ablation were performed, resulting in restoration of sinus rhythm. No AF was inducible under left atrial stimulation. She was subsequently prescribed rivaroxaban (20 mg once daily) and amiodarone (200 mg three times daily). Family screening was conducted to investigate potential hereditary disease. Transthoracic echocardiography revealed no evidence of ASD in her father. However, her mother, elder sister, and younger brother were all diagnosed with ASD. Notably, the proband’s mother also exhibited the combined clinical phenotype of a defect of the atrial septum, high-grade impairment of atrioventricular conduction, and AF similar to the proband, and no other family member carrying the NKX2-5 variant demonstrated any conduction abnormality or atrial rhythm disturbance. Among the proband’s offspring, the elder daughter and elder son were diagnosed with ASD, whereas the younger son showed no structural abnormality. In the offspring of her younger brother, the elder daughter was diagnosed with ASD, while both sons were unaffected. The offspring of the proband’s elder sister were not evaluated, as he have not yet reached an evaluable age (5 months old). Given the aggregation of ASD in this family, genetic testing was deemed essential for aetiological clarification. With informed consent from the proband and her relatives, peripheral blood samples were collected for genomic DNA extraction. High-throughput sequencing was performed to detect variants in genes associated with the clinical phenotype. The genetic test identified a heterozygous deletion in NKX2-5 (c.604_605del, p.L202Gfs*49), initially detected by high-throughput sequencing and confirmed by Sanger sequencing (Figure 3). Through genetic tests within the family, the identified variant was detected in multiple affected members, all of whom were diagnosed with ASD. Sanger sequencing validation results of the pathogenic mutation of the NKX2-5 gene The NKX2-5 gene plays a critical role in cardiac development, and mutations within this gene can profoundly impair its physiological function, leading to various CHDs and conduction abnormalities. One of the major pathogenic mechanisms underlying NKX2-5 mutations is the alteration of its DNA-binding affinity and protein stability. Such mutations may reduce the DNA-binding affinity of the transcription factor for specific regulatory sequences required for the control of downstream target genes essential for cardiac morphogenesis.4 For example, several mutations have been shown to affect the homeodomain of NKX2-5, which is indispensable for its DNA-binding function. This reduction in binding affinity can cause dysregulated expression of genes required for cardiomyocyte differentiation and proliferation, culminating in structural cardiac malformations such as ASDs and VSDs.4,5 In addition, mutations may also compromise NKX2-5 protein stability, leading to haploinsufficiency, characterized by the presence of only a single functional allele, which further increases susceptibility to CHDs.6,7 The interplay between altered protein stability and DNA-binding capacity highlights the complexity of the genetic architecture of congenital heart defects. In contrast to the two mechanisms described above, frameshift mutations represent another important pathway leading to NKX2-5 dysfunction. These variants arise from small insertions or deletions that shift the reading frame and introduce premature stop codons, resulting in C-terminal truncation and the loss of regulatory domains essential for maintaining proper protein conformation and transcriptional activation. Several pathogenic frameshift mutations have been reported previously, including A88Xfs (c.262delG), A255fsX38, and c.959delC, each truncating different lengths of the C-terminal region and associated with cardiac phenotypes. Functionally, these truncations impair NKX2-5 activity by removing activation domains required for cooperative interactions with cardiac transcriptional partners, thereby weakening downstream gene regulation crucial for atrial septal development and potentially affecting conduction system maturation. Taken together, the loss of the C-terminal portion disrupts both the structural integrity and transcriptional function of NKX2-5, offering a biologically plausible explanation for the structural cardiac abnormalities observed in carriers of frameshift variants.2,8,9 NKX2-5 has been found to be linked to AVB due to its role in the regulation of electrophysiological properties.9 The severity of AVB in patients with NKX2-5 mutations is often influenced by the underlying genetic alteration, with certain mutations leading to more pronounced conduction disturbances. For instance, mutations such as R25C have been associated with significant impairment in cardiac conduction, resulting in higher incidences of complete heart block and necessitating the implantation of pacemakers in affected individuals.10 The relationship between mutation type and clinical phenotype underscores the importance of genetic testing in patients presenting with AVB, as it can guide management strategies and risk assessment for sudden cardiac death, which is notably elevated in this population. In addition to AVB, some NKX2-5 mutations can lead to dysfunction of the sinoatrial node, as seen with the R25C mutation, which has been reported to cause sinus node dysfunction. This dysfunction is characterized by inadequate heart rate response to physiological demands, resulting in symptoms such as syncope or fatigue.11 The interplay between the conduction system and the sinoatrial node is critical for maintaining heart rhythm and synchrony; thus, mutations affecting these structures can have profound implications for cardiac function. The identification of these electrophysiological abnormalities is crucial, as they not only affect the immediate management of patients but also have long-term implications for their prognosis. For instance, patients with NKX2-5 mutations often require close monitoring for the development of arrhythmias and may benefit from the implantation of implantable cardioverter-defibrillators to mitigate the risk of life-threatening ventricular tachyarrhythmias.12 The major finding of this study is the first report of a novel heterozygous frameshift mutation in the NKX2-5 gene (c.604_605del, p.L202Gfs*49). This heterozygous deletion, located in exon 2 of NKX2-5 (which consists of two exons), causes a frameshift and introduces a premature termination codon 49 amino acids downstream of the mutation site, resulting in a truncated NKX2-5 protein predicted to escape nonsense-mediated mRNA decay. The allele frequency of this variant is absent (0) in the gnomAD control population database. Furthermore, analysis of both clinical evidence and genetic data within the proband’s family demonstrated that this variant segregates with the disease phenotype. Taken together, according to the American College of Medical Genetics and Genomics (ACMG) guidelines, this variant (NM_004387.4:c.604_605del) meets the criteria of PVS1_Strong, PM2_Supporting, and PP1_Strong, with a cumulative pathogenicity score of 9, and is classified as a likely pathogenic variant. Previous reports have described various NKX2-5 mutations, including missense and splicing variants, which result in similar phenotypes, with some associated with severe conduction disease and sinus node dysfunction.5,13 The frameshift variant described in our report adds to the expanding mutational spectrum of this gene but shows consistent cosegregation only with the structural phenotype of a defect of the atrial septum within the family. Although both the proband and her mother exhibited high-grade AVB and AF, these electrical manifestations were not present in any other carrier of the variant, and the current evidence is therefore insufficient to establish a direct causal relationship between the variant and atrioventricular conduction disease or atrial rhythm disturbances. Nevertheless, this observation does not entirely exclude a potential association, particularly given that conduction abnormalities may manifest later in life; thus, careful longitudinal follow-up of all genotype-positive but currently asymptomatic relatives is warranted. Alternative explanations, such as postsurgical atrial remodelling, age-related conduction degeneration, or unrelated individual factors, also remain plausible and must be considered when interpreting these findings. This case also underscores the clinical importance of genetic testing in familial CHD. Identification of mutation carriers enables targeted clinical surveillance, timely intervention for conduction disease, and appropriate counselling for at-risk relatives. In conclusion, the novel NKX2-5 variant reported here provides new insight into the genetic basis of ASD with arrhythmias and emphasizes the need for long-term follow-up of both affected individuals and asymptomatic carriers. The authors declare no conflict of interest. No data were generated or analysed for this manuscript. All authors declare no funding for this contribution.
Source: ESC Heart Failure
Authors: Hangyu Liu, Juan Hua, Qinmei Xiong, Liang Xiong, Qi Chen
Institution: Second Affiliated Hospital of Nanchang University
Language: English
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $4,850
OpenAlex ID: W7124682463