Sudden Death in Pediatric Patient With Dilated Cardiomyopathy Due to Founder Variant in NKX2-5: Case Report

Abstract

Background: The NKX2-5 gene encodes a transcription factor that plays a role in atrioventricular nodal and myocardial development. Pathogenic variants of NKX2-5 are associated with congenital heart disease and sudden cardiac death. The missense variant in this case is one of the more common ones in Northern Europe and has high penetrance in familial cases. To our knowledge, this is the youngest person who died due to this variant. Case summary: This was a healthy, asymptomatic 14-year-old male with well-managed mild congenital dilated cardiomyopathy who died unexpectedly in his home. Postmortem examination revealed the NKX2-5 pathogenic missense variant, p.Phe145Leu, as the only explicable cause of death. Discussion: We propose that immediate family members of those who die suddenly due to NKX2-5 disease undergo genetic counseling and longitudinal screening to include this gene, as pathogenic variants in the NKX2-5 gene may manifest in a time-dependent manner.

INTRODUCTION

The NKX2-5 gene encodes a cardiac transcription factor that plays a role in the development and lifetime maintenance of the atrioventricular node and in cardiac development (1). Pathogenic variants in the NKX2-5 gene are associated with familial and nonfamilial atrial septal defect and are often combined with congenital or adult-onset conduction disturbances, cardiomyopathies and sudden cardiac death (2). We present the case of a pediatric patient who was incidentally found to have two secundum atrial defects and mild dilated cardiomyopathy at 4 months of age, remained asymptomatic and in good health throughout childhood and died unexpectedly at 14 years of age due to an NKX2-5 pathogenic missense variant. Among the carriers of this variant, this is the youngest person who died suddenly.

CASE REPORT

The white male patient was born at 35-week’ gestation via vaginal delivery. There was no history of prenatal infection or drug exposure. Pregnancy was by natural conception and was complicated by early contractions in the second trimester, for which his mother received corticosteroids. He was born via uncomplicated spontaneous vaginal delivery, had an unremarkable neonatal course and had no other history of illness. He remained developmentally appropriate and asymptomatic through childhood and up to his time of death.

At 4 months of age, he was referred to a pediatric cardiologist following a routine visit to his pediatrician who had auscultated a murmur. An echocardiogram revealed two secundum atrial septal defects and a mildly dilated left ventricle with mild-to-moderate global systolic dysfunction. Anomalous origin of the left coronary artery from the pulmonary artery (ALCAPA) and aortic coarctation were excluded based on echocardiography. Electrocardiography revealed normal sinus rhythm and was interpreted as normal for age. Metabolic tests performed to explain the mild dilated cardiomyopathy—a comprehensive metabolic panel, a plasma amino acid assay, an acylcarnitine profile and lactate levels—were within normal limits. He was followed by his pediatrician and remained active in sports with no progression of cardiomyopathy. At 14 years of age, he was found by his mother unresponsive in his room in the early morning with his alarm clock ringing. Resuscitative efforts were unsuccessful. He was a nonsmoker and nondrinker with no known history of illicit drug use.

External Examination

The decedent was a well-developed, obese (98.4 kg, BMI: 33.0 kg/m²) young man appearing the given age of 14 years without evidence of trauma.

Internal Examination

The autopsy revealed dilated cardiomyopathy and slight hepatic steatosis. The globoid heart weighed 480 g (expected: 262-560 g [3]), had moderate four-chamber dilatation and unremarkable coronary arteries. The myocardium was homogeneous, red-brown and firm. The left ventricle wall was 1.3 cm (expected: 0.81-1.41 cm [3]), the right ventricle 0.6 cm (expected: 0.19-0.52 cm [3]) and the interventricular septum 1.3 cm (expected: 0.87-1.54 cm [3]) thick. The atria were normal, and the foramen ovale was closed. The posterolateral left ventricle wall had a 3.0 × 1.5 cm area of endocardial fibrosis. There was no evidence of non-compaction. The cardiac valves were unremarkable. The coronary ostia were normally situated and of normal morphology. The stumps of the venae cavae and pulmonary veins were unremarkable. Microscopic examination revealed slight myocyte hypertrophy and unremarkable areas of the sinoatrial and atrioventricular nodes. Postmortem toxicology tests were negative.

Molecular Studies

Genomic DNA (gDNA) was extracted from a postmortem liver sample preserved in RNAlater® and then tested for the panel of Cardiac-Focused Sudden Death Molecular Analysis of 132 genes associated with various forms of cardiac and non-cardiac channelopathy and cardiomyopathy. SureSelectQXT target enrichment workflow (Agilent Technologies) was used, and pair-end sequencing was completed on NextSeq 500 DNA sequencer (Illumina). NGS data analysis was performed using NextGENe v2.4.2.3 and Geneticist Assistant v1.8.2 (SOFTGENETICS®). Genomic reference coordinate is GRCh37/hg19. Sanger sequencing was used to confirm low confidence reportable variants (coverage below 100×, allele frequency less than 25% or allelic read balance of less than 0.25). The test's analytical characteristics were established by the Molecular Genetics Laboratory in the City of New York Office of Chief Medical Examiner through test validation. The Laboratory is accredited by the College of American Pathologists (CAP). The clinical relevance of sequence variants was evaluated in accordance with the standards and guidelines for the interpretation of sequencing variants established by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) (4).

The decedent tested positive for the presence of a pathogenic missense variant in the NKX2-5 gene, i.e., NM_004387.4(NKX2-5):c.433T>C (p.Phe145Leu), by molecular analysis. Variant interpretation was based on the guideline by ACMG/AMP as per the following (5):

• PS1: Equivalent variant chr5:173233109 G > C (Phe145Leu) is classified Likely Pathogenic by LOVD (confirmed using the germline classifier).

• PP3: MetaRNN = 0.961 is greater than 0.939, strong pathogenic.

• PM1: Hot-spot of length 17 amino-acids has 32 missense/in-frame variants (11 pathogenic, 21 uncertain and no benign), which qualifies as moderate pathogenic. UniProt protein NKX25_HUMAN DNA-binding domain ‘Homeobox’ has 109 missense/in-frame variants (40 pathogenic, 69 uncertain and no benign), which qualifies as supporting pathogenic.

• PM5: Alternative variant chr5:173233110A>G (Phe145Ser) is classified Pathogenic by LOVD (confirmed using the germline classifier).

• PP5: ClinVar classifies this variant as Likely Pathogenic, 1 star (criteria provided, reviewed Dec 2023, 1 submission), citing 30354339, associated with Atrial Septal Defect 7.

• PM2: Variant not found in gnomAD genomes, good gnomAD genomes coverage = 31.4. Variant not found in gnomAD exomes, good gnomAD exomes coverage = 42.6.

DISCUSSION

Except for only a few phenotypes being associated with thyroid anomalies (6), heterotaxy, vertebral defects and midline brain malformations (7), pathogenic variants of the NKX2-5 gene are overwhelmingly associated with cardiac abnormalities and conduction disturbances including tetralogy of Fallot, dilated cardiomyopathy, atrial and septal defects, bicuspid aortic valve, left ventricular noncompaction and atrioventricular block.

The NKX2-5 Phe145Leu variant was reported as a likely pathogenic variant once in ClinVar. It is one of the more common variants in Northern Europe and was reported in a six-generation Icelandic family. Twenty-three heterozygous variant carriers had dilated cardiomyopathy, among whom 12 died (range: 25–95 years). This study also reported that the NKX2-5 Phe145Leu variant was associated with high-degree atrioventricular block and atrial septal defect (8). This pathogenic variant explains the decedent's history of dilated cardiomyopathy with left ventricular dysfunction. To our knowledge, his age of 14 years at death makes him the youngest person who died due to this variant; the youngest documented one died suddenly at 25 years of age. The mean age of death is 63 years (8).

In NKX2-5 cardiac disease, atrioventricular block has a delayed onset and is progressive. There are reports of patients with normal electrocardiograms or a benign first-degree atrioventricular block followed by second- and third-degree atrioventricular block and sudden death (9-11). Sudden cardiac deaths have been reported in pediatric and adult cases of NKX2-5 cardiac disease-related atrioventricular block (2). Furthermore, sudden cardiac deaths have been reported in carriers and relatives of patients with NKX2-5 pathogenic variants. The penetrance of serious heart disease among carriers of the same NKX2-5 pathogenic variant discovered in our case (p.Phe145Leu) is high; among those over 40 years of age, 71% have been diagnosed with serious heart disease (8). A study of 39 Danish families with congenital heart disease identified a novel pathogenic truncating variant (c.112delG) of NKX2-5 in one family (2.5%). Pathogenic variants in NKX2-5 were most common in familial cases, and most patients (74%) had atrial septal defect combined with conduction disturbance. Fifteen percent of these patients with familial atrial septal defect and conduction disturbance died suddenly, 47% of whom were confirmed pathogenic variant carriers and 53% of whom were possible carriers. There were no sudden deaths in the nonfamilial cases (2).

Atrial septal defect is observed as an autosomal dominant trait or as sporadic. A phenotype of the NKX2-5 Phe145Leu variant is congenital secundum atrial septal defect and progressive atrioventricular block that eventually requires pacemaker implantation. Advances in medical management of patients with congenital heart defects have increased the survival of affected individuals into adulthood. Long-term follow-up has identified patients with previously undiagnosed syndromes that presented later in life, and mouse models of NKX2-5 pathogenic variants develop dysrhythmias and abnormal contractility as adults (1).

Autopsy studies of sudden cardiac death in the setting of atrioventricular block have revealed fibrotic replacement of the AV bundle (8), but this is neither specific to NKX2-5 disease nor does its absence exclude atrioventricular block as the mechanism of death. To our knowledge, no histopathologic autopsy studies have been performed on hearts in cases of death due to NKX2-5 disease. However, one study using a knock-in mouse model (Arg52Gly, NKX2-5^+/R52G) has shown that affected mice develop atrioventricular nodal atrophy and fibrosis (12).

CONCLUSION

Since cases with the NKX2-5 Phe145Leu variant have been shown to be associated with sudden cardiac death (8), we recommend that immediate family members of those with or who die suddenly from this pathogenic variant or phenotype undergo clinical screening and genetic counseling. As pathogenic variants in the NKX2-5 gene may manifest in a time-dependent manner, longitudinal screening of individuals harboring them may be required (13). The immediate family is considering targeted variant testing.

Authors

Nicholas Scibetta, DO, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai

Roles: B, C, D

Barbara A. Sampson, MD, PhD, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai

Roles: A, B, C, D, 6

Yingying Tang, MD, PhD, Molecular Genetics Laboratory, Office of Chief Medical Examiner

Roles: B, C, D, 6

Bruce D. Gelb, MD, The Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

Roles: B, C, D, 6