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Fetal anomalies

Gene: KCNT1

Amber List (moderate evidence)
KCNT1 (potassium sodium-activated channel subfamily T member 1)
EnsemblGeneIds (GRCh38): ENSG00000107147
EnsemblGeneIds (GRCh37): ENSG00000107147
OMIM: 608167, Gene2Phenotype
KCNT1 is in 4 panels

4 reviews

Natalie Chandler (North Thames GLH)

I don't know

Green on epilepsy, ID, DDG2P. Red on Aus fetal anomalies panelapp. PMID 36307859 Fetus with Increased nuchal translucency, bilateral choroid plexus cysts. PMID: 31872048 MRI13/17 Normal 3 thin CC; 3 myelation delay (1 at 1 month), 11/17 microcephaly (no SD or age measured) All hypotonia 2 noted to only be Axial. PMID: 23086397 3/6 thin CC, 6 hypotonic (4 axial only), 4/6 microcephaly (no SD or age). PMID: 31532509 MRI performed 20-57 days of life 9/16 normal, delayed myelination 6/16; thin CC 5/16, cortico-subcortical atrophy 3/16, subdural hematoma 1/16. Note 1 figure shows normal MRI at 1 month and 29 months delayed myelination and thin CC, earliest abnormal MRI at 1 month. No patients with microcephaly at birth. 1 patient with retroplacental hematoma, 1 in NICU with apnea & hypotonia. 1 known fetal case plus some abnormal MRI findings at 1 month of age.
Created: 20 Feb 2025, 9:35 p.m. | Last Modified: 20 Feb 2025, 9:35 p.m.
Panel Version: 5.15

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Developmental and epileptic encephalopathy 14, MIM#614959

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

Created: 20 Feb 2025, 9:35 p.m.
Last Modified: 20 Feb 2025, 9:35 p.m.
Panel version: 5.15

Achchuthan Shanmugasundram (Genomics England Curator)

This gene and phenotype were reviewed during meetings between November 2024 & January 2025. The meetings included representatives of the Central & South and North Thames R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Stephanie Allen, Natalie Bibb, and Sarah Graham (Central & South GLH), Natalie Chandler and Elizabeth Scotchman (North Thames GLH), and Sunayna Best, Anna De Burca, Natalie Canham, Samantha Doyle, Alice Gardham, Victoria Harrison, Esther Kinning, Sahar Mansour, Soo-Mi Park, and Elizabeth Wall (R21 Clinical Oversight Group).
Created: 20 Feb 2025, 9:40 p.m. | Last Modified: 20 Feb 2025, 9:40 p.m.
Panel Version: 5.16
Comment on list classification: As reviewed by Sarah Graham, PMID:36307859 reported a foetus with increased nuchal translucency and bilateral choroid plexus cysts. Hence, the rating can be updated from red to amber.
Created: 26 Jun 2024, 11:34 a.m. | Last Modified: 26 Jun 2024, 11:34 a.m.
Panel Version: 4.17
Created: 26 Jun 2024, 11:34 a.m.
Last Modified: 26 Jun 2024, 11:34 a.m.
Panel version: 5.16

Sarah Graham (West Midlands Regional Genetics Laboratory, Birmingham Women's and Children’s NHS Foundation Trust)

I don't know

Established pathogenic de novo missense variant p.(Arg474Cys) (https://www.ncbi.nlm.nih.gov/clinvar/variation/265210/) reported in a fetus with increased nuchal translucency and bilateral choroid plexus cysts (Fu 2022 PMID: 36307859, case 170).
Created: 15 Jun 2024, 11:38 a.m. | Last Modified: 15 Jun 2024, 11:38 a.m.
Panel Version: 4.3

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

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

Created: 15 Jun 2024, 11:38 a.m.
Last Modified: 15 Jun 2024, 11:38 a.m.
Panel version: 4.3

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Action taken: Demoted KCNT1 gene rating from Green to Red.
Created: 30 Apr 2019, 8:24 a.m.
DDG2P rating in original PAGE list: Confirmed for MALIGNANT MIGRATING PARTIAL SEIZURES OF INFANCY and Confirmed for SEVERE AUTOSOMAL DOMINANT NOCTURNAL FRONTAL LOBE EPILEPSY.
Created: 11 Dec 2018, 9:05 a.m.
In the original PAGE file, MOP listed as Activating for MALIGNANT MIGRATING PARTIAL SEIZURES OF INFANCY, and listed as All missense/in frame for SEVERE AUTOSOMAL DOMINANT NOCTURNAL FRONTAL LOBE EPILEPSY.
Created: 8 Nov 2018, 4:45 p.m.

Mode of pathogenicity
Other - please provide details in the comments

Created: 8 Nov 2018, 4:45 p.m.

Panel version: 0.228

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • NHS GMS
  • Expert Review Amber
  • PAGE DD-Gene2Phenotype
Phenotypes
  • Developmental and epileptic encephalopathy 14, OMIM:614959
OMIM
608167
Clinvar variants
Variants in KCNT1
Penetrance
None
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

20 Feb 2025, Gel status: 2

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: KCNT1 were changed from SEVERE AUTOSOMAL DOMINANT NOCTURNAL FRONTAL LOBE EPILEPSY; MALIGNANT MIGRATING PARTIAL SEIZURES OF INFANCY; Developmental and epileptic encephalopathy 14, OMIM:614959 to Developmental and epileptic encephalopathy 14, OMIM:614959

20 Feb 2025, Gel status: 2

Added New Source, Set mode of pathogenicity, Set Phenotypes, Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Source NHS GMS was added to KCNT1. Mode of pathogenicity for gene KCNT1 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Added phenotypes Developmental and epileptic encephalopathy 14, OMIM:614959 for gene: KCNT1 Publications for gene: KCNT1 were updated from to 36307859

26 Jun 2024, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: kcnt1 has been classified as Amber List (Moderate Evidence).

26 Jun 2024, Gel status: 1

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene: KCNT1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

30 Apr 2019, Gel status: 1

Added New Source, Status Update

Rebecca Foulger (Genomics England curator)

Source Expert Review Red was added to KCNT1. Rating Changed from Green List (high evidence) to Red List (low evidence)

8 Nov 2018, Gel status: 4

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Added phenotypes SEVERE AUTOSOMAL DOMINANT NOCTURNAL FRONTAL LOBE EPILEPSY for gene: KCNT1

8 Nov 2018, Gel status: 4

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

Rebecca Foulger (Genomics England curator)

gene: KCNT1 was added gene: KCNT1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: KCNT1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: KCNT1 were set to MALIGNANT MIGRATING PARTIAL SEIZURES OF INFANCY