Table 3.

Summary of all variants and results of Sanger sequencing in one participant (subject #1).

Gene Name and Location	Variant Type	Annotation on ClinVar or SFARI	Encoded Protein	Signaling Pathways/Neuronal Circuitry	Other Conditions Associated with the Variant	Mutation Confirmation by Sanger
SLC12A5 (chr20:46022977:A:G)	Splice region variant	SFARI risk gene	KCC2 (Type 2 K+-Cl− cotransporter)	Enhancement of the NF-κB/MMP-7 signaling pathway; Glycinergic signaling pathway. Regulates neuronal excitability	Epileptic encephalopathy, early infantile	Yes
IER3IP1 (chr18:47156119:A:G)	Splice region variant	Pathogenic on ClinVar	IER3IP1	Although highly expressed in the brain, its role in the CNS circuitry is unknown	Microcephaly, epilepsy, diabetes syndrome	N.A.
AIFM1 (chrX:130136710:T:C)	3 prime UTR	Likely pathogenic on ClinVar	Mitochondrial flavin adenine dinucleotide-dependent oxidoreductase	Ceramide signaling pathway, innate immunity; has known expression and functionsin the CNS	Mitochondrial encephalopathy	No
CEP19 in 3q29 (chr3:196711952:A:G)	SNV	SFARI risk gene	Centrosomal Protein 19	Ciliary entry of intraflagellar transport; Although highly expressed in the brain, its role in the CNS circuitry is unknown	Delayed development (speech delay), mild or moderate intellectual disability, gastrointestinal disorders, morbid obesity	N.A.