A case report of CHARGE syndrome caused by a de novo CHD7 gene mutation

Abstract

This article describes the case of a patient with CHARGE syndrome. The clinical data of the patient as well as the whole-genome sequencing results of the child and parents were retrospectively analyzed to determine the pathogenicity of the gene mutation. Genetic testing revealed a heterozygous mutation of the CHD7 gene NM_017780.4: C.4853G >A (P.TP1618ter) in the child, which was identified as a de novo pathogenic mutation. Through this case, we conclude that genetic testing is crucial for accurate diagnosis of deafness. Moreover, paying attention to hearing screening in childhood and strengthening the cognitive level of diagnosis and treatment of syndromic deafness in multiple disciplines can effectively realize early detection, early diagnosis, early intervention, and early rehabilitation of syndromic deafness.

Introduction

CHARGE syndrome (CS) (OMIM 214800), which is also known as Hall-Hittner syndrome, is a rare congenital developmental disorder characterized by autosomal dominant inheritance.^1,2 It was first described by Halls in 1979, ³ with Hittner reporting its clinical features. ⁴ Subsequent reports indicated that it was mostly characterized by coloboma, heart disease, atresia choanae, retarded growth, genital hypoplasia, ear anomalies, and/or deafness. In 1981, it was named CHARGE, which is an acronym for the aforementioned clinical manifestations. ⁵ According to the latest diagnostic criteria, a CHD7 (OMIM 608892) gene mutation is a primary diagnostic criterion for CS.^6,7 This article describes the case of a patient with CS who was initially diagnosed in the audiology department.

Case presentation

Participant

A 6-year-and-4-month-old girl was admitted to the Audiology Department of Guizhou Provincial People’s Hospital on June 7, 2022, due to slurred speech and motor retardation. At 6 months of age, she was unable to sit or crawl, yet she began walking independently by the age of 3 years. Following the father’s awareness that hearing abnormalities could result in poor responses and slurred speech, he sought evaluation in our department. The child has a significant medical history, including emergency surgery for a foreign body obstruction in the trachea at 1 year of age. Regarding her personal and family background, she is the first child of a healthy mother, who delivered at term via cesarean section. The mother reported no instances of hypoxia, asphyxia, or prolonged jaundice postnatally. Furthermore, the parents are not related, and there is no reported history of exposure to radiation or toxic chemicals. There is no known family history of genetic or infectious diseases. Prenatal tests revealed no significant abnormalities.

The child’s father provided written informed consent for CHD7 genetic analysis. Written informed consent for the publication of patient information and images was provided by the parents. This study was approved by the ethics committee of Guizhou Provincial People’s Hospital.

Physical examination

Notable physical findings included facial asymmetry when smiling, with the right nasolabial groove becoming shallow and the forehead lines disappearing. The mouth angle was oblique to the left; further, the right eyelid closure was worse than that of the left eyelid. Furthermore, there was the closure of the left lacrimal point, right side micrognathia, and bilateral “hockey stick” palmar crease with both palms short and wide, displaying a hockey-stick palm-folding pattern (Figure 1(a)). Examination of the ear revealed bilateral auricle deformity (Figure 1(b)). After the cerumen was removed, the tympanic membranes were intact; further, clear light cone marks were visible.

Figure 1.

Clinical manifestations of children with CS. (a) Short and wide palms, hockey-stick-style folded palmprint (arrow). (b) Visible auricle deformity of the right ear. (c) Visible auricle deformity of the left ear; neck hump (arrow).

Auxiliary examination

The results of the air conduction auditory brainstem response testing were as follows: at 95 dBnHL, no waveforms were induced in the left ear; further, the right-ear threshold was 65 dBnHL (Figure 2(a)). Regarding the bone conduction auditory brainstem response: the right-ear threshold was 25 dBnHL (Figure 2(b)). Cochlear Microphonic revealed that no waveforms were induced by 85 dBnHL in the left ears (Figure 2(a), arrow). Regarding the audio steady-state response, the average thresholds in the left and right ears were 100 and 62 dBnHL, respectively (Figure 2(c)). Play audiometry (air conduction plug-in earphone; bone conduction cannot be masked) revealed that the left-ear and right-ear air conduction thresholds were 96 and 66 dBHL, respectively (Figure 2(d)). Moreover, the bilateral bone conduction threshold was 40 dBHL (Figure 2(d)). There was bilateral misproportion and an abnormal amplitude ratio. Videonystagmography revealed left horizontal spontaneous nystagmus (fixation suppression). The visual tracking test revealed a type III curve; moreover, there was weakened visual movement on the left side. The video head impulse test revealed decreased dual horizontal semicircular canal gain with right horizontal saccade as well as decreased dual vertical semicircular canal gain (poor coordination). Computed tomography of the internal auditory canal revealed reduced bilateral cochlear loops, with no visibility of the bilateral external and anterior semicircular canals. There was a possibility of abnormal development of the bilateral stapes combined with bony atresia of the foramen ovale, an enlarged left vestibular aqueduct, and dysplasia in the left mandibular process (Figure 3). Magnetic resonance imaging of the brain revealed no abnormalities. The visual acuity test scores ⁸ for the right and left eyes were 0.6 and 0.8, respectively. An intraocular pressure test ⁹ and slit-lamp examination ¹⁰ revealed no abnormalities. Hiskey-Nebraska Test of Learning Aptitude^11,12 revealed comparable intelligence to that in children of the same age.

Figure 2.

Audiological tests. (a) Air conduct auditory brainstem response; (arrow: Cochlear Microphonic). (b) Bone conduct auditory brainstem response. (c) Auditory steady-state responses. (d) Playaudiometry.

Figure 3.

CT of the internal auditory canal (1: there was a bilateral reduction in the number of cochlear loops).

Genetic testing and data analysis

Written informed consent was obtained from subject’s legally authorized representative (father) for the anonymized information to be published in this article. After informed consent was obtained from the parents, 2 ml of peripheral venous blood was collected from the proband and his parents. Genomic DNA was extracted using a blood genomic DNA kit (Megi Bio; Shanghai Boi Biotechnology Co., Ltd. Shanghai, China). The extracted DNA was sequenced using the DNBSEQ-T7 sequencing platform; further, candidate mutations in the proband and other family members were verified using Sanger sequencing. Off-machine data were compared with the reference genome sequence (HG19) using BWA software; moreover, information regarding the variations was extracted using the Saile Calling algorithm based on the GATK Haplotype Caller. We considered variants with read depth ⩾6, genotype quality ⩾20, and alternate allele frequency >0.1. Variants with minor allele frequencies ⩾0.005 were filtered out using population frequencies from the gnomAD database, dbSNP, and 1000 Genomes. Mutation sites in the coding and clipping regions were retained. Variants were annotated using the ClinVar database, Human Gene Mutation Database, and Diagnostic Variant Database; further, variants with pathogenic or possibly pathogenic annotations were considered. The pathogenicity of the filtered variants was determined based on American College of Medical Genetics and Genomics guidelines. The genetic testing results revealed a heterozygous mutation in the CHD7 gene (NM_017780.4: C.4853G >A(P.TP1618ter)) in the child; however, none of the parents showed this mutation (Figure 4). This indicates that this was a de novo mutation. The ClinGen deafness expert working group confirmed the gene-disease relationship between the CHD7 gene and CS, with the pathogenesis of the disease being attributed to loss of function (dosage sensitivity haploinsufficiency (HI) score ¹³ : 3), which was consistent with PVS1 evidence. Moreover, since this was a novel mutation that was not detected in the parents, it was consistent with the PS2 evidence. In addition, the frequency of this variation was 0 in the Genome Aggregation Database, Westlake BioBank for Chinese database, and China Metabolic Analytics Project database, which is consistent with the PM2 evidence. Taken together, this variation was considered pathogenic.

Figure 4.

Sanger sequencing peak map.

Diagnosis and treatment

CS is diagnosed based on a combination of clinical phenotypes and genotypes. According to the latest 2016 Hale diagnostic criteria, ⁷ our patients presented three major indicators of CS; namely, eye tissue defects, abnormal ear development, and a pathogenic CHD7 gene mutation. In addition, she had three secondary indicators, that is, cranial nerve palsy, hearing impairment, and growth retardation. Accordingly, the patient was diagnosed with CS. Currently, the patient has undergone a binaural examination with hearing aids and speech rehabilitation training for 1 year. Although the patient’s speech remains slightly unclear, the communication expression has become satisfactory. The parents have been advised to regularly review the hearing for adjustment of the hearing aids as well as to continue speech rehabilitation training. Rehabilitation training for coarse and fine movements as well as muscle strength is provided under specialist guidance. Notably, another child by the same parents may have a risk of presenting the same disease. Accordingly, prenatal genetic diagnosis can be performed between 12 and 26 weeks of pregnancy to determine whether the fetus carries the same CHD7 gene mutation as the proband. The patient’s family members were satisfied with our diagnosis and treatment and were willing to follow-up.

Observation and follow-up

One month after diagnosis, the child was referred to pediatrics, where abnormalities of the heart, genitals, spine, and limbs had been ruled out. After 1 year of diagnosis, we followed up on the child’s condition. Currently, the child is attending a normal primary school and has undergone a hearing test and hearing aid device adjustment every 6 months. There has been no further decline in hearing for the time being. The child’s speech condition has slightly improved compared to before, except for a few cases where pronunciation still lacks standards. The daily language communication in learning and life is satisfactory. Sports development has also basically reached the level of peers.

Discussion

The incidence of CS among newborns is rare, occurring in ≈1 in 15,000–10,000 newborns. ¹⁴ Although this disease can be familial, it is sporadic in most cases. Genetic testing for CS is not routinely performed before or during pregnancy; additionally, CS has diverse and heterogeneous clinical manifestations, which may result in erroneous or missed diagnoses. Most patients with CS are diagnosed in the neonatology, ophthalmology, or cardiology departments, with no previous reports of CS being diagnosed in the audiology department. In the present case, the child was initially diagnosed in the audiology department, following thorough physical and laboratory examinations of audiology and vestibular function.

In 2004, the first case of CS associated with a CHD7 gene mutation on chromosome 8q12 was reported. ¹⁵ In recent years, mutations in other genes, such as SEMA3E, SEMA3A, EP300, KMT2D, KDM6A, and PUF60, have been found in patients with CS.^16,17 However, CHD7 remains the only established pathogenic gene associated with CS; further, it is widely expressed in embryonic and adult tissues. ¹⁸ Among CHD7 gene mutations, 44% are nonsense mutations, 34% are stencering mutations, 11% are splicing-site mutations, 8% are missense mutations, and <5% are exon deletions or 8q12.1 microdeletion. ¹⁹ Our patient presented with a nonsense CHD7 gene mutation.

The middle and inner ear malformations led to bilateral mixed deafness; moreover, the absence of a semicircular canal affected the child’s development. Pediatric patients with CS who present dysplasia of the semicircular canal experience slowed development of gross muscle movement and balance function, with the most significant retardation occurring at the age of 2–3 years and even persisting until the age of 6 years.^20–22 Moreover, our patient presented with enlargement of the left vestibular aqueduct, which was characterized by a wide bony vestibular aqueduct with an insufficient intracranial pressure buffer. Under the conditions of increased cerebrospinal fluid pressure, exposure to external forces could easily lead to the rupture of the inner ear membrane, which leads to the mixing of the inner and outer lymphatic fluid, followed by progressive and recurrent hearing decline. Although the congenital ear development and hearing conditions have been clarified, the family should still be aware of the risk of hearing loss and the need to carefully monitor for hearing changes. In addition, our patient presented with left facial nerve palsy, left mandibular process dysplasia, short and wide palms, and “hockey stick” three-finger folding lines, which is consistent with the described CS characteristics of cranial nerve damage, special facial features, and dermatoglyphic anomalies.^23–25

In summary, a review of the patient’s clinical course reveals two primary concerns: (1) The child exhibited developmental abnormalities from an early age, and because the neonatal hearing screening identified normal hearing, the parents did not recognize the child’s hearing issues; (2) the child demonstrated delayed speech development and slow responses, which led the parents and pediatricians to initially focus on potential intellectual deficits, thereby neglecting the significant impact of late-onset hearing impairment on speech development. The treatment process of this case emphasizes the importance of hearing screening in childhood. With the growing global focus on newborn hearing screening, regular hearing assessments for children are likely to become a future trend in continuous hearing healthcare. Additionally, genetic testing is increasingly crucial for the accurate diagnosis of deafness, as early detection directly influences intervention and rehabilitation strategies. Furthermore, the results of genetic testing can prompt clinicians to monitor and identify clinical phenotypes that may have been overlooked or are yet to manifest.

Conclusion

In our case, the late diagnosis impeded the effectiveness of the intervention. Genetic testing is crucial for accurate diagnosis of deafness, and a de novo mutation was discovered during our genetic testing. Moreover, comprehensive childhood hearing screening and facilitating multidisciplinary diagnostic and treatment interventions can facilitate the early detection, diagnosis, treatment, and rehabilitation of syndromic deafness.