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The utility of whole exome sequencing in diagnosing pediatric neurological disorders

   | 23 mar 2021
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Figure 1

Parents of a child with an inherited PNPO gene mutation. They are cousins and both are heterozygous. A) Mother; B) father.
Parents of a child with an inherited PNPO gene mutation. They are cousins and both are heterozygous. A) Mother; B) father.

Figure 2

Brain MRI in a child with acute necrotizing encephalopathy and a positive RANBP2 gene mutation. Brain MRI showing increased T2 hyperintensity of basal ganglia (A, B, and C).
Brain MRI in a child with acute necrotizing encephalopathy and a positive RANBP2 gene mutation. Brain MRI showing increased T2 hyperintensity of basal ganglia (A, B, and C).

Homozyogous, heterozygous and variants of uncertain significance VUS groups.

Homozygous Mutations
#Sex-AgeFamily HistoryConsanguinityClinical CharacteristicsOnsetGenesVariantDiagnoses
1F-6yesyesmotor delay; hypotonia; scoliosis; respiratory difficulties in neonatal period; normal congnitions, areflexia1 yearP1EZO2pathogenic: c.273_279del, p.(Pro92Thrfs*18)piezo-type mechanosensitive ion channel component; OMIM: 613629
2M-1noyessevere hypotonia; reduced tendon reflexes; motor/speech delay; cerebellar atrophy; cerebellar cyst; elevated serum CPKbirthFKRPlikely pathogenic: c.204del, p.(Ser69Profs*60)MDDGA5 (congenital with brain/eye anomalies), type A5 (MDDGA5); OMIM: 613153
3M-2noyesvision loss; nystagmus; severe retinal dysfunction2 monthsRPGRIP1pathogenic: c.1107del, p.(Glu370Asnfs*5)Leber congenital amaurosis type 6, OMIM: 613826
4M-7noyesintractable epilepsy; global developmental delay; poor vision3 yearsTPP1pathogenic: c.616C>T, p.(Arg206Cys)neuronal ceroid lipofuscinosis type 2, OMIM: 204500
5M-8noyespoor hearing; encephalopathy; MRI: white matter changes4 yearsBTDpathogenic: c.1618C>T, p.(Arg540Cys)biotinidase deficiency
6M-6yesyesataxia; delayed motor milestones; mild intellectual delay; MRI: cerebellar atrophy1 yearSPTBN2likely pathogenic: c.6258_6261delGAGA, p.(Lys2088Glyfs*228)infantile-onset spinocerebellar ataxia type 5
7F-8yesyesataxia; delayed motor milestones; mild intellectual delay; MRI: cerebellar atrophy1 yearSPTBN2likely pathogenic: c.6258_6261delGAGA, p.(Lys2088Glyfs*228)infantile-onset spinocerebellar ataxia type 5
8M-9yesyesataxia; oculomotor apraxia; telangiectasia; MRI: cerebellar atrophy3 yearsATMlikely pathogenic: c.9066del, p.(Gly3023Alafs*10)ataxia telangiectasis
Heterozygous Mutations
9F-7nonodelayed language/motor development; intellectual disability; hypotonia; generalized seizures; infantile spasms; visual impairment; normal MRI; normal metabolic profile1 yearNTRK2pathogenic: c.1301A>G, p.(Tyr434Cys)early infantile epilectic encephalopathy type 58, OMIM: 617830
10M-3yesnoacute necrotizing encephalopathy; generalized seizures; spasticity; coma and death; brain MRI: symmetric thalamic hyperintense lesions3 yearsRANBP2pathogenic: c.1754C>T, p.(Thr585Met)acute infection-induced encephalopathy-type 3, OMIM: 608033
11M-4nonodevelopmental delay; neonatal hypotonia; autistic-like behavior; epilepsy1 yearSHANK3likely pathogenic: c.2313+1G>APhelan-McDermid syndrome, OMIM: 606232
12M-9nonoataxia; ADHD; delayed speech/ language development; motor delay; hypotonia; normal EEG and brain MRI2 yearsKAT6Alikely pathogenic: c.1483-1G>Amental retardation type 32, OMIM: 616268
13M-1nonointractable neonatal seizures; normal brain MRI1 monthPACS2pathogenic: c.625G>A, p.(Glu209Lys)early infantile epileptic encephalopathy type 66, OMIM: 618067
14F-4noyesintractable focal seizures; normal brain MRI3 monthsSCN1Alikely pathogenic: c.1377G>C, p.(Gln459His)early infantile epileptic encephalopathy type 6 (Dravet syndrom), OMIM: 607208
Variant(s) of Uncertain Significance
15M-6noyesMCA stroke; dystonia; spasticity; regression of milestones; delayed language/ motor development; focal seizures and abnormal brain myelination on MRI4 yearsITGA7 ARc.1601C>T, p.(Ala534Val)congenital muscular dystrophy/hypotonia, OMIM: 613204
16F-5noyesataxia; frequent falls; macrocephaly, epilepsy and ADHD; MRI: megalencephalic leukoencephalopathy with subcortical cysts2 yearsMLC1 ARc.275C>A, p.(Pro92His)megalencephalic leukoencephalopathy with subcortical cysts type 1, OMIM: 604004
17M-3noyesdelayed speech/language development; dyskinesia; dystonia; infantile onset of the disease; paroxysmal dystonia; MRI: brain atrophy2 yearsSLC6A3 ARc.851G>A, p.(Gly284Glu)infantile Parkinsonism dystonia type 1, DTDS, PMID: 21777827
18M-1yesyesintractable infantile spasms3 monthsPNPO ARc.256T>C, p.(Cys86Arg)PNPO, OMIM: 603287
19F-6yesyesataxia and oculomotor apraxia; brain MRI: molar tooth sign2 yearsCC2D2A ARc.916_927del, p.(Pro306_Leu309del)Joubert syndrome type 9, OMIM: 612285
20M-2noyesfair hair; global developmental delay; hearing impairment; infantile onset of the disease; motor delay; muscular hypotonia; visual impairment; focal epilepsy; MRI: brain atrophy3 monthsSPATA5 AR and TIMMDC1ac.1058A>T, p.(Asp353Val) and c.230T>C, p.Ile77Thr)EHLMRS, OMIM: 616577 mitochondrial complex I deficiency, OMIM: 618251

Cohort demographics: WES positive and negative.

Positive n (%)Negative n (%)
Males145
Females61
Total20 (77.0)a6 (23.0)
Age (mean)4.9 years4.5 years
Consanguinity14 (53.0)4 (15.0)

Whole exome sequencing negative group.

#Sex-AgeFamily HistoryConsanguinityClinical CharacteristicsOnset
1F-1noyesepilepsy and developmental delay; brain MRI: normal4 months
2M-7noyesepilepsy and developmental delay; brain MRI: normal2 years
3M-2nonointractable epilepsy; poor vision and global developmental delay; brain MRI: normal1 year
4M-12noyesglobal developmental delay; brain MRI: basal ganglia enhancement; metabolic work-up: negative6 years
5M-4yesyesintractable focal epilepsy and ADHD1 year
6M-2noyesmicrocephaly; motor delay; brain MRI: white matter changes6 months

American College of Medical Genetics and Genomics (ACMG) classification of variants [17].

Class 1Pathogenic
Class 2Likely pathogenic
Class 3Variant of uncertain significance (VUS)
Class 4Likely benign
Class 5Benign
eISSN:
1311-0160
Lingua:
Inglese
Frequenza di pubblicazione:
2 volte all'anno
Argomenti della rivista:
Medicine, Basic Medical Science, other