Table 1 Missense and high confidence (HC) loss-of-function (LoF) variants identified in KOVA 2 that are pathogenic or likely pathogenic in ClinVar but not found in gnomAD.

From: A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population

Variant class	Locus (hg38)	Base change	AC	AN	AF	Carrier type*	Gene symbol	pLI	ClinVar^**	Dominant or Recessive***	ClinVar condition
LoF (HC)	chr3:128481942	CG > C	1	12,234	0.8 × 10⁻⁴	C	GATA2	0.98	P	D	Lymphedema, primary, with myelodysplasia; GATA2 deficiency with susceptibility to MDS/AML
	chr3:41236467	CAG > C	1	12,148	0.8 × 10⁻⁴	V	CTNNB1	1.00	P	D	Mental retardation, autosomal dominant 19; Inborn genetic diseases
	chr6:79026060	A > C	1	12,150	0.8 × 10⁻⁴	P	PHIP	1.00	P	D	Developmental delay, intellectual disability, obesity, and dysmorphic features
	chr7:128846444	C > T	1	12,136	0.8 × 10⁻⁴	C	FLNC	1.00	P	D	Myofibrillar myopathy, filamin C-related; Myopathy, distal, 4; Cardiomyopathy, familial hypertrophic, 26; Dilated cardiomyopathy, dominant
	chr9:95458142	G > T	1	12,120	0.8 × 10⁻⁴	V	PTCH1	1.00	P	D	Gorlin syndrome
	chr12:868379	C > T	1	12,134	0.8 × 10⁻⁴	C	WNK1	1.00	P	D/R	Hereditary sensory and autonomic neuropathy type IIA
	chrX:40064351	G > A	1	12,224	0.8 × 10⁻⁴	C	BCOR	1.00	P	D	Oculofaciocardiodental syndrome
Missense	chr1:42927147	C > T	1	12,152	0.8 × 10⁻⁴	C	SLC2A1	0.99	LP	D/R	Not provided
	chr2:108753474	A > G	1	9310	1.1 × 10⁻⁴	C	RANBP2	1.00	P	D	Encephalopathy, acute, infection-induced, 3, susceptibility to
	chr3:123296110	G > A	1	12,122	0.8 × 10⁻⁴	P	ADCY5	0.99	LP	D/R	Inborn genetic diseases
	chr3:128483925	C > T	1	12,238	0.8 × 10⁻⁴	P	GATA2	0.98	P	D	Lymphedema, primary, with myelodysplasia; GATA2 deficiency with susceptibility to MDS/AML
	chr5:128395182	C > T	1	12,160	0.8 × 10⁻⁴	P	FBN2	1.00	C	D	Congenital contractural arachnodactyly
	chr5:138570987	T > C	3	10,530	2.8 × 10⁻⁴	P, V	HSPA9	0.97	P	D/R	Even-plus syndrome
	chr6:157206668	C > T	1	12,144	0.8 × 10⁻⁴	V	ARID1B	1.00	LP	D	Coffin-Siris syndrome 1
	chr6:3154909	C > T	1	12,116	0.8 × 10⁻⁴	V	TUBB2A	0.94	P/LP	D	Cortical dysplasia, complex, with other brain malformations 5
	chr7:150952508	G > A	1	12,128	0.8 × 10⁻⁴	C	KCNH2	0.99	LP	D	Arrhythmia; Long QT syndrome 2; Congenital long QT syndrome
	chr7:5528486	G > C	1	12,126	0.8 × 10⁻⁴	V	ACTB	0.99	LP	D	Not provided
	chr9:130872896	C > T	1	12,244	0.8 × 10⁻⁴	C	ABL1	1.00	P/LP	D	Chronic myelogenous leukemia, BCR-ABL1-positive; Lymphoblastic leukemia, acute, with lymphomatous features; Leukemia, Philadelphia chromosome-positive, resistant to imatinib
	chr9:132328351	A > G	1	12,152	0.8 × 10⁻⁴	P	SETX	0.96	P	D/R	Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2
	chr11:119089747	G > A	1	12,144	0.8 × 10⁻⁴	V	HMBS	0.95	P	D	Acute intermittent porphyria
	chr11:119092785	G > A	1	12,138	0.8 × 10⁻⁴	V	HMBS	0.95	LP	D	Not provided
	chr12:47978736	G > A	8	10,014	8.0 × 10⁻⁴	C, P, V	COL2A1	1.00	LP	D	Spondyloepiphyseal dysplasia, Namaqualand type
	chr15:48470646	C > T	1	12,140	0.8 × 10⁻⁴	P	FBN1	1.00	LP	D	Not provided
	chr16:9840706	G > A	1	12,148	0.8 × 10⁻⁴	V	GRIN2A	1.00	P/LP	D	Epilepsy, focal, with speech disorder and with or without mental retardation;
	chr18:44951948	G > A	1	12,250	0.8 × 10⁻⁴	C	SETBP1	1.00	P	D	Chronic myelogenous leukemia, BCR-ABL1 positive; Schinzel-Giedion syndrome

^*C: normal sample of a cancer patient, P: parent of a rare disease patient, V: healthy volunteer.
**P: pathogenic, LP: likely pathogenic.
***D: dominant, R: recessive, D/R: observed in both patterns.

Back to article page

Table 1 Missense and high confidence (HC) loss-of-function (LoF) variants identified in KOVA 2 that are pathogenic or likely pathogenic in ClinVar but not found in gnomAD.

Search

Quick links