A male neonate in his first day of life was admitted to the Neonatal Intensive Care Unit (NICU) because of the respiratory failure, significant diffuse muscle weakness, and hypotonia (Fig. 1). He was born in the 39th week of pregnancy by caesarean section. The neonate presented with apnea and bradycardia and was intubated in the first minute of life. He scored 2/4/4/4 Apgar points after 1/3/5/10 min of life, respectively. A few dysmorphic features were clearly visible: dolichocephaly, prominent forehead, bitemporal narrowing, hypertelorism, up-turned nose, tent-shaped upper lip, high arched palate, micrognatia, low-set ears, and pectus excavatum were present (Figs. 2, 3, and 4). Moreover, a significant, diffuse muscle weakness, and hypotonia were observed since the delivery. The primitive reflexes were poorly expressed: the sucking, rooting, palmar grasp, and plantar reflexes were partially present, while Moro reflex was absent in the patient. The weight at the time of birth was 3080 g (27th centile, − 0.62SD), the length - 56 cm (97th centile, + 1,86SD), and the head circumference - 36 cm (84th centile, + 0.98SD). After 4 months of life, the patient’s weight increased to 6420 g (57th centile, + 0.17SD), the length to 66.5 cm (96th centile, + 1,7SD), and the head circumference to 42.2 cm (77th centile, + 0.74SD), according to “PED(Z) pediatric calculator” online [13].
At the beginning of the hospitalization, the child required mechanical ventilation. Then, the non-invasive CPAP (continuous positive airway pressure) support was sufficient, initially in the day and night, and later only during the sleep. After 54 days of respiratory support, at the end of the hospital stay, the infant has been breathing without any help. He was discharged home, with a pulse oximetry monitoring, oxygen support on demand (an oxygen concentrator), and a suction device. After 2 weeks, the mother observed a deterioration of the respiratory function, which resulted in rehospitalization. The child required mechanical ventilation again. After performing tracheostomy, he was discharged home again; however, mechanical ventilation had to be continued.
The patient could not swallow nutrition and saliva, but the sucking reflex was partially retained. He was fed via a nasogastric tube, and then via PEG (percutaneous endoscopic gastrostomy) tube. Before PEG placement, the gastroesophageal reflux was excluded with esophageal pH-monitoring.
In the course of the hospitalization, there was no improvement in the primitive reflexes and the muscular strength. The tendon reflexes were absent, as well. Tachycardia, tachypnea, and dyspnea were observed, when the child was crying. The volume of the voice was low. The ophthalmic consultation showed no significant abnormality in vision. The infant was able to keep the eye contact with the surroundings and to react appropriately to the sounds. What is more, he reacted well to his mother’s presence. In the USG (ultrasonography) imaging, there were no testicles present in the scrotum.
The newborn underwent a thorough diagnostic process on account of muscle weakness. The brain ultrasound at the beginning of the hospitalization was normal, but after few weeks, a slight ventriculomegaly, without increased intracranial pressure, was observed. MRI (magnetic resonance imaging) in T2-weighted image showed an increased signal in a cortical white matter (Fig. 5). The serum creatine phosphokinase level was normal, the same as the levels of ammonia, VLCFA (very-long chain fatty acids), and lactic acid. The level of 2-ketoglutaric acid in urine was elevated in organic acids profile according to GC/MS (gas chromatography/mass spectrometry) method, but the results did not indicate any congenital, metabolic defects that could have been related to them. There was also no metabolic acidosis. Therefore, the metabolic diseases, which might have been the cause of the muscle weakness, have been ruled out. As a next step, genetic analyses have been performed, as given below.
The child was first diagnosed for spinal muscular atrophy and Prader-Willi syndrome. The first MLPA (multiplex ligation-dependent probe amplification) analysis (SALSA MLPA P060 SMA kit) showed the presence of two copies of exon 7 and 8 of SMN1 gene and one copy of exon 7 and 8 of SMN2 gene (rsa SMN1ex7(P060)x2, rsa SMN1ex8(P060)x2, rsa SMN2ex7(P060)x1, rsa SMN2ex8(P060)x1). The second MLPA analysis (SALSA MLPA ME028 Prader Willi/Angelman kit) showed no deletion in the region 15q11 (rsa (ME028)x2) and proved the correct methylation pattern in this locus. These two analysis excluded the abovementioned diseases.
As a next step, the arrayCGH (array comparative genomic hybridization) analysis was performed (Agilent ISCA 8x60K V2), with normal results, what excluded the presence of pathological CNVs (copy number variations) in this patient.
Subsequently, the NGS-based panel analysis was performed. The peripheral blood sample of the patient was sent to Blueprint Genetics Company’s Laboratory in Helsinki, where the DNA sequence and copy number variation analyses were performed (The Blueprints Genetics Comprehensive Muscular Dystrophy/Myopathy Panel (version 4, May 01 2018) Plus Analysis). The test covered 73 genes, proven to be connected with congenital myopathy. The results have shown that the patient is hemizygous for MTM1 mutation c.197C>G, p.(Thr66Arg), which is a variant of uncertain significance (VUS). The variant was classified according to Blueprint Genetics Variant Classification Schemes modified from ACMG guideline 2015 [14]. The laboratory performed also further bioinformatical tests. In silico analysis was executed with Polyphen, MutationTaster, and SIFT software. All tools showed a high probability of the variant being damaging and thus a possible connection between the mutation and the proband’s phenotype. The presence of this variant has been confirmed in the patient’s second blood sample with targeted Sanger sequencing. Then, the family history has been analyzed and further tests were performed: patient’s mother, father, healthy brother, and mother’s twin brother have been tested with the targeted Sanger sequencing for this variant. Mother turned out to be a heterozygous carrier of this variant, whereas the mutation was absent in the father, healthy brother, and mother’s twin brother (Fig. 6). Segregation analysis, with the absence of the variant in healthy males, strengthens the probability that the variant is causative in presented patient.