We introduced a 65-day-old female infant with co-occurrence of homozygous variants of two pathogenic genes. In this case, the splicing-site variation c.6940+1G>T of VPS13B gene has been reported in some Chinese patients and its clinical significance on Clinvar was described as likely pathogenic. Because of the clinical heterogeneity and the clinical manifestations vary in different regions, the correlation between genotype and phenotype has not been determined. The clinical manifestations of CS in Finnish patients are highly uniform, and there is phenotypic variability in non-Finnish patients. The common clinical manifestations are psychomotor retardation, microcephaly, characteristic facial features, progressive retinochoroidal dystrophy, hypotonia and neutropenia. With the number of patients gradually increases, more cases with rare clinical manifestations are also increasing, including pulmonary hypertension, congenital defects of the genital organ, insulin resistance, diabetes, febrile convulsion, epilepsy and other clinical manifestations[13, 14]. We reviewed the medical records on the patient, including the growth, development and related examination results. We found that the clinical manifestations of this case were atypical, including hypotonia, dyspnea, poor feeding, poor weight gain, binocular strabismus, neutropenia and other clinical features. The infant was born with premature rupture of membranes 20h in advance and postnatal evaluation was normal, there was no report describing the relationship between premature rupture of membranes and CS. Other manifestations were inconsistent with the typical patients described in previous articles[13, 15, 16]. Only some mothers had oligohydramnios and decreased fetal movement during pregnancy, so we can't determine whether premature rupture of membranes is associated with CS. The birth weight of patient was not significantly abnormal compared with normal newborns. The weight of patient won’t increase because of the poor feeding caused by muscular hypotonia, so infant patients often show poor weight gain rather than typical facial features. Just one case of bilateral strabismus in CS was reported in China, However, due to the absence of fundus examination and obvious clinical heterogeneity among patients with CS, it is impossible to determine whether there is damage to photoreceptor cilia and integrity of retinal structure. So we can’t judge whether strabismus is one of the manifestation of CS.
In 2016, CS was first diagnosed by WES in China. Here, we reviewed all the patients with CS confirmed by gene examinations in China (Table 1) and analyzed the gene variant sites and clinical features. It was found that 5 of 12 patients (including current case) carried c.6940+1G>T variant of VPS13B gene[20-22]. Only this patient was homozygous, and the other 4 cases were heterozygous variation. It can be found that Chinese patients with CS have a high c.6940+1G>T variant carrying rate, which may be a hotspot variation in Chinese population. The variant frequency of this site is 0.01997% in all population ant that is 0.1% in East Asian population. It is obvious that the variant frequency of East Asian population is higher than other populations, and there is little reports about this variation in other populations[23-28]. The c.6940+1G>T variation was first discovered by Chinese doctor in 2016, and has been reported four times in China in recent years[20-22]. This patient is the fifth case but the first homozygous variation patient in China. Due to the early symptoms are atypical and the diagnosis is difficult, only this child is under 1 year of age, which proves the value of WES in early diagnose. Therefore, it is necessary to detect VPS13B gene when newborns exhibit microcephaly, hypotonia, neutropenia and developmental retardation.
SLC26A4 gene variation is one of the main causes of neonatal deafness in China, which can cause both syndromic deafness and non-syndromic deafness[29, 30]. The prevalence of PDS is about 10-7.5/100000, accounting for 10% of congenital deafness cases[9, 31]. The variation of SLC26A4 gene in this patient was c.919-2A>G (intron7), which was described as pathogenic on Clinvar. It can be manifested as PDS, EVA and hereditary deafness. As goiter mostly occurs in children and adolescents, it is easy to be affected by external iodine intake, resulting in atypical goiter in some children. The patient in this study did not appear thyroid abnormalities. The parents refused the examination of CT and MRI, so we don’t know whether there are abnormalities in the vestibular aqueduct and cochlea. Typical PDS patients can find inner ear malformation, EVA and Mondini cochlea. The diagnosis of PDS mainly depends on the typical clinical manifestations, perchlorate excretion test, imaging findings of cochlear dysplasia and enlarged vestibular aqueduct. Therefore, the patient could not be diagnosed with PDS and was temporarily diagnosed with hereditary deafness at discharge. We found the hearing was normal at 1.5-year telephone follow up. There are two cases of double allelic deafness gene variation (both included c.919-2A>G) were reported to have normal hearing, so the possibility of false positive brainstem auditory evoked potentials was not excluded[32, 33]. It was reported that 32.7% of newborns with abnormal hearing screening were fully recovered and 9.7% were partially recovered, but the outcomes of newborns with genetic abnormalities wasn’t mentioned. It has been reported that non syndromic EVA is caused by 0 or 1 SLC26A4 allele variation, while PDS is caused by two allele variants. Therefore, it is a highly reliable indication of PDS.
Because the early symptoms are atypical, it is difficult to make an early diagnosis among infants with CS. With the popularity of WES, the accuracy of clinical diagnosis has been greatly improved. We should consider the possibility of genetic diseases if we find that some clinical manifestations can’t be explained. The patient's deafness gene screening showed SLC26A4 variation, it can provide an explanation for the hearing loss of infants, but some symptoms couldn’t be explained after admission. Hence WES was performed and homozygous SLC26A4 gene variation combined with homozygous VPS13B gene variation were found, which explained other symptoms. Many diseases of the newborn are atypical, especially in some genetic diseases, that further increases the difficulty of diagnosis by neonatal pediatricians. Obviously, WES is worthwhile for early diagnosis of difficult neonatal cases and it is helpful for genetic counseling[36-39]. In recent years, the value of copy number variation analysis based on WES in phenotypic diversity of related genetic diseases has been reported.
Early diagnosis and early intervention are helpful to improve the prognosis of patients, and the treatment mainly relying on multidisciplinary cooperation in symptomatic support treatment. For example, insulin resistance in CS can be avoided by early nutrition education and diet control, early thyroid hormone replacement therapy can avoid goiter in patients with PDS, and hearing aids or cochlear implants can significantly improve the quality of life of people with hearing loss.
In this study, we describe a patient with co-occurrence of homozygous variants SLC26A4 and VPS13B gene. The high frequency of c.6940+1G>T in Chinese population with CS indicates that may be a hotspot variation, and it is helpful to clarify the pathogenicity of this site. It is difficult to make early diagnosis due to the atypical symptoms. WES can effectively help clinical neonatologist make an early diagnosis. The early diagnosis and treatment can significantly improve the quality of life and prognosis of patients. Therefore WES has important diagnostic value in neonatal miscellaneous cases.