Table 2.

Differential diagnoses and investigation prior to the WES.

Patient	Signs and symptoms	Differential diagnoses	Genetic investigation	Biochemical investigation	Laboratory clue of a possible LD
A	Congenital prelingual hearing loss, intractable seizures, subependymal gray matter heterotopia	FLNA-related disorders	FLNA full gene sequencing and deletion/duplication; CMA	Biotinidase, coenzyme Q10, peroxisomal panel, Smith-Lemli-Opitz screening, quantitative plasma and urine amino acids, CDG screening, oligosaccharide and mucopolysaccharide screening, urinary organic acids	None
B	Progressive encephalopathy, cerebellar ataxia, dysphagia, hyperreflexia, cognitive decline	NCL, GM1 and GM2 gangliosidosis, Farber disease, Creatine deficiency, CDG, Giant axonal dystrophy, Lafora disease, Mitochondrial disease	Comprehensive epilepsy NGS panel; mitochondrial DNA sequencing	Lactate, pyruvate, quantitative plasma and urine amino acids, urinary organic acids, CSF analysis, skin biopsy for storage material. In the affected brother: beta-glucosidase, hexosaminidases, oligosaccharidoses screening, CDG screening, vitamin E, ceruloplasmin, copper, frataxin	One VUS in CLN6 found in a multi-gene NGS panel
C	Developmental delay, neurodegeneration, ataxia, myoclonic epilepsy	Several	CMA; mitochondrial DNA sequencing and deletion testing	Lactate, ammonia, quantitative plasma and urine amino acids, acylcarnitine profile, urinary organic acids, urinary acylglycines, oligosaccharidoses and mucopolysaccharidoses screening, vitamin E, biotinidase, ceruloplasmin, copper, coenzyme Q10, CDG screening, alpha fetoprotein, CSF amino acids analysis, neurotransmitters, purine and pyrimidine panel	None
D	Chronic diarrhea, failure to thrive, systemic autoimmune disorder	MYO5B-related disorder, EPCAM-related disorder, IPEX	CMA; RSF13B, STAT5B, STAT1, NOD2, MYO5B, CD25, and FOXP3 genes sequencing	FOXP3 protein expression, cytokines analyses, CDG screening, T and B cell tests, lactate, alpha-1-antitrypsin, auto-antibodies, CSF analysis	None
E	Corneal clouding, thickened mitral valve, joint pain, contractures	Skeletal dysplasia, Genetic peripheral neuropathies, Lysosomal storage disorder	None	Lysosomal screening panel in blood (alpha-galactosidase, hexosaminidase, alpha-l-iduronidase), Lysosomal screening panel in urine (ceramide trihexoside, sulfatides, olygosaccharides, glycosaminoglycans), mucopolysaccharides screening	Mild elevation of urinary GAG; mild excretion of dermatan sulfate

CDG: congenital disorders of glycosylation; CMA: chromosomal microarray; NCL: neuronal ceroid lipofuscinosis; NGS: next generation sequencing; CSF: cerebral spinal fluid; IPEX: Immunodysregulation, polyendocrinopathy, enteropathy, X-linked; MPS: mucopolysaccharidoses; GAG: glycosaminoglycans.