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Intellectual disability

Gene: KCNT2

Green List (high evidence)
KCNT2 (potassium sodium-activated channel subfamily T member 2)
EnsemblGeneIds (GRCh38): ENSG00000162687
EnsemblGeneIds (GRCh37): ENSG00000162687
OMIM: 610044, Gene2Phenotype
KCNT2 is in 3 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

Comment on phenotypes: OMIM phenotype updated 27th Feb 2026.
Created: 27 Feb 2026, 1:40 p.m. | Last Modified: 27 Feb 2026, 1:40 p.m.
Panel Version: 9.280
Created: 27 Feb 2026, 1:40 p.m.
Last Modified: 27 Feb 2026, 1:40 p.m.
Panel version: 9.280

Ivone Leong (Genomics England Curator)

Comment on list classification: New gene submitted by expert reviewer. Based on the evidence provided it was decided that there is enough evidence for this gene to be given Green status.
Created: 26 Nov 2019, 2:55 p.m. | Last Modified: 26 Nov 2019, 2:55 p.m.
Panel Version: 2.1116
Comment on mode of pathogenicity: Variants have gain-of-function effect.
Created: 26 Nov 2019, 2:46 p.m. | Last Modified: 26 Nov 2019, 2:46 p.m.
Panel Version: 2.1115
Created: 26 Nov 2019, 2:46 p.m.
Last Modified: 26 Nov 2019, 2:46 p.m.
Panel version: 2.1115

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Heterozygous pathogenic KCNT2 variants cause ?Epileptic encephalopathy, early infantile, 57 (MIM 617771).

At least 3 unrelated affected individuals have been reported :

- PMID: 29069600 - Gururaj et al. 2017 : a male child with EOEE (hypotonia, profound DD and intractable infantile seizures) due to a de novo KCNT2 missense variant (NM_001287819.1:c.720T>A or p.Phe240Leu) identified by exome sequencing.

- PMID: 29740868 - Ambrosino et al. 2018 : A girl with phenotype corresponding to West syndrome later evolving to Lennox-Gastaut syndrome. At the age of 9 years the girl displayed severe ID. Trio exome sequencing revealed a de novo missense KCNT2 variant (NM_001287820.2:c.569G>A or p.Arg190His). A 14 y.o. female recruited through the DDD study with phenotype corresponding to epilepsy of infancy with migrating focal seizures. The girl had poor language development and severe learning disability. Infective and metabolic causes were initially ruled out. Trio exome sequencing revealed a de novo missense SNV (c.569G>C or Arg190Pro).

Overall KCNT2 has been commented to contribute to a phenotypic spectrum similar and overlapping to that of KCNT1 (Ambrosino et al.). [KCNT1 is rated green in both epilepsy and ID panels].

KCNT2 was recently included in the epilepsy panel as green (functional studies summarized in the respective reviews). The gene was also recently added to G2P, associated with 'Developmental and infantile epileptic encephalopathy'. It is not commonly included in gene panels for ID offered by diagnostic laboratories.

As a result, KCNT2 could be considered for inclusion in the ID panel with green (or amber) rating.
Sources: Literature
Created: 11 Nov 2019, 5:49 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
?Epileptic encephalopathy, early infantile 57, MIM 617771

Publications

Created: 11 Nov 2019, 5:49 p.m.

Panel version: 2.1098

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Developmental and epileptic encephalopathy 57, OMIM:617771
  • developmental and epileptic encephalopathy, 57, MONDO:0033366
OMIM
610044
Clinvar variants
Variants in KCNT2
Penetrance
unknown
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Panels with this gene

History Filter Activity

18 Mar 2026, Gel status: 3

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: KCNT2 were set to 29069600; 29740868

18 Mar 2026, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: KCNT2 were changed from Developmental and epileptic encephalopathy 57, OMIM:617771 developmental and epileptic encephalopathy, 57, MONDO:0033366 to Developmental and epileptic encephalopathy 57, OMIM:617771; developmental and epileptic encephalopathy, 57, MONDO:0033366

27 Feb 2026, Gel status: 3

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: KCNT2 were changed from ?Epileptic encephalopathy, early infantile 57, 617771 to Developmental and epileptic encephalopathy 57, OMIM:617771 developmental and epileptic encephalopathy, 57, MONDO:0033366

26 Nov 2019, Gel status: 3

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: kcnt2 has been classified as Green List (High Evidence).

26 Nov 2019, Gel status: 0

Set mode of pathogenicity

Ivone Leong (Genomics England Curator)

Mode of pathogenicity for gene: KCNT2 was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

26 Nov 2019, Gel status: 0

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: KCNT2 were changed from ?Epileptic encephalopathy, early infantile 57, MIM 617771 to ?Epileptic encephalopathy, early infantile 57, 617771

11 Nov 2019, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: KCNT2 was added gene: KCNT2 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: KCNT2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: KCNT2 were set to 29069600; 29740868 Phenotypes for gene: KCNT2 were set to ?Epileptic encephalopathy, early infantile 57, MIM 617771 Penetrance for gene: KCNT2 were set to unknown Review for gene: KCNT2 was set to GREEN