Table 4.

Genetic characteristics: genes with likely pathogenic variants.

No.	Gene	Accession	Nucleotide	Amino acid	Diseases (OMIM)	Zygosity	Global frequency (ExAC)	Korean frequency (KRGDB)	Inheritancea (OMIM)	ACMG
39	*ABCC2	NM_000392.3	c.2443C > T	p.Arg815Ter	Dubin–Johnson syndrome	Hetero	0.00002826		AR	PVS1, PM2
	*ABCC2	NM_000392.3	c.2302C > T	p.Arg768Trp	Dubin–Johnson syndrome	Hetero	0.00007539	0.000803859	AR	PP3
57	MECP2	NM_004992.3	c.403A > G	p.Lys135Glu	{Autism susceptibility, X-linked 3} Mental retardation Rett syndrome Encephalopathy, neonatal severe	Hetero			XR, XD	PM2, PP3, PP5
60	**Xp22.2p22.33 deletion					Hetero
	**NLGN4X	NM_020742.3	Whole gene deletion		Asperger syndrome susceptibility Autism susceptibility Mental retardation	Hetero
63	Xp22.31p22.33 deletion					Hetero
	NLGN4X	NM_020742.3	Whole gene deletion		Asperger syndrome susceptibility Autism susceptibility Mental retardation	Hetero
66	DLGAP2	NM_004745.4	Whole gene duplication		Autism spectrum disorder	Hetero
69	AUTS2	NM_015570.2	c.2962dleG	p.Glu988LysfsTer37	AUTS2 syndrome Mental retardation	Hetero			AD	PVS1, PM2
75	SCN2A		Exon 15-16 deletion		Epileptic encephalopathy, early infantile	Hetero			AD
76	KAT6A	NM_006766.3	c.3456G > A	p.Trp1152Ter	Mental retardation	Hetero				PVS1, PM2
	*CCDC50	NM_178335.2	c.82_83dupAC	p.Leu29ProsfsTer40	?Deafness,	Hetero			AD	PVS1, PM2
87	HUWE1	NM_031407.5	c.693+1G > A		Mental retardation, syndromic, Turner type	Hetero				PVS1, PM2
94	**TSC2	NM_000548.3	c.4744_4746del	p.Ile1582dle	Tuberous sclerosis-2 Lymphangioleiomyomatosis, somatic	Hetero			AD	PM2, PM4, PM6
95	**TSC2	NM_000548.3	c.2838_122G > A		Tuberous sclerosis-2 Lymphangioleiomyomatosis, somatic	Hetero			AD	PM2, PM6, PP5, PP4
96	CACNG2	NM_006078.3	c.437-2A > G		Mental retardation	Hetero			AD	PVS1, PM2
98	15q24 deletion (2.2Mb)
121	**MECP2	NM_004992.3	c.455C > G	p.Pro152Arg	{Autism susceptibility, X-linked 3} Mental retardation Rett syndrome Encephalopathy, neonatal severe	Hetero			XR, XD	PM2, PM5, PP3, PP5
133	14q31.3-32.12 deletion					Hetero
138	*SLC26A4	NM_000441.1	c.2168A > G	p.His723Arg	Deafness with enlarged vestibular aqueduct; Pendred syndrome	Hetero	0.0001	0.00401929	AR	PP3,PP2,PP5
	*SLC26A4	NM_000441.1	c.919-2A > G		Deafness with enlarged vestibular aqueduct; Pendred syndrome	Hetero	0.0003	0.000803859	AR	PVS1, PP5
142	**SYNGAP1	NM_006772.2	c.980T > C	p.Leu327Pro	Mental retardation	Hetero	–	–	AD	PM2, PP5

Seventeen participants showed likely pathogenic variants. OMIM: Online Mendelian Inheritance in Man; ExAC, population frequency from The Exome Aggregation Consortium; KRGDB, population frequency from the Korean Reference Genome Database; AD, Autosomal dominant; AR. Autosomal recessive; XD, X-linked dominant; XR, X-linked recessive; ACMG, The American College of Medical Genetics and Genomics guideline (Richards et al., 2015); PVS, Very strong evidence of pathogenicity; PM, Moderate evidence of pathogenicity; PP, Supporting evidence of pathogenicity. ^aInheritance of the gene described in OMIM. BOLD: Clinical syndromes and diseases related to neurodevelopmental disorders (ASD, ID, epilepsy).