Genes in panel
STRs in panel
Prev Next

Genetic epilepsy syndromes

Gene: KCNT1

Green List (high evidence)

KCNT1 (potassium sodium-activated channel subfamily T member 1)
EnsemblGeneIds (GRCh38): ENSG00000107147
EnsemblGeneIds (GRCh37): ENSG00000107147
OMIM: 608167, Gene2Phenotype
KCNT1 is in 5 panels

8 reviews

Rebecca Foulger (Genomics England curator)

I don't know

Review and rating collated by Tracy Lester (Oxford Medical Genetics Laboratories Oxford University Hospitals NHS Foundation Trust, 2019_02_06) on behalf of Wessex and West Midlands GLH for GMS Neurology specialist test group, for Clinical Indication R59 'Early onset or syndromic epilepsy'. Review contributors: John Taylor and Helen Lord. Suggested gene rating: Green.
Created: 6 Aug 2019, 8:38 p.m. | Last Modified: 6 Aug 2019, 8:38 p.m.
Panel Version: 1.189

Tracy Lester (Genetics laboratory, Oxford UK)

Green List (high evidence)

Proposed gain of function mechanism. Misenses are reported in association with epilepsy.AD EIEE14 & AD nocturnal frontal lobe epilepsy type 5 (ENFL5). EIEE14 presents as malignant migrating partial seizures of infancy. Barcia et al, 2012 - 4 diff de novo het mutations in KCNT1 - functional work done. Vanderver et al, 2014 - de novo het mutation. Ishii et al, 2013 - 2 unrelated girls - same de novo het missense mutation. ENFL5 - AD focal epilepsy syndrome - childhood onset of motor clusters in sleep - Derry et al, 2008 & Heron et al, 2012 - 4 unrelated families all had het mutations.
Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Epilepsy, nocturnal frontal lobe, 615005; Epileptic encephalopathy, early infantile, 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

Amy McTague (UCL Institute of Child Health)

Green List (high evidence)

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

Phenotypes
Epileptic encephalopathy, early infantile, 14; Epilepsy, nocturnal frontal lobe, 5

Publications

  • Barcia at al (2012) Nature Genet 44(11): 1255-1261
  • Heron et al (2012) Nature Genet 44(11): 1188-1190

Variants in this GENE are reported as part of current diagnostic practice

Natalie Trump (NHS - Great Ormond Street Hospital)

Green List (high evidence)

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

Phenotypes
Epileptic encephalopathy, early infantile, 14; Epilepsy, nocturnal frontal lobe, 5

Publications

  • Barcia at al (2012) Nature Genet 44(11): 1255-1261
  • Heron et al (2012) Nature Genet 44(11): 1188-1190

Variants in this GENE are reported as part of current diagnostic practice

Manju Kurian (UCL-Institute of Child Health)

Green List (high evidence)

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

Phenotypes
Epileptic encephalopathy, early infantile, 14; Epilepsy, nocturnal frontal lobe, 5

Publications

  • Barcia at al (2012) Nature Genet 44(11): 1255-1261
  • Heron et al (2012) Nature Genet 44(11): 1188-1190

Variants in this GENE are reported as part of current diagnostic practice

Richard Scott (North Thames GMC/UCL)

Green List (high evidence)

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

Phenotypes
Epileptic encephalopathy, early infantile, 14; Epilepsy, nocturnal frontal lobe, 5

Publications

  • Barcia at al (2012) Nature Genet 44(11): 1255-1261
  • Heron et al (2012) Nature Genet 44(11): 1188-1190

Variants in this GENE are reported as part of current diagnostic practice

Richard Scott (Genomics England Curator)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
615005

Publications

Ellen McDonagh (Genomics England Curator)

Comment when marking as ready: A confirmed DD gene for malignant migrating partial seizures of infancy and severe autosomal dominant noctural frontal lobe epilepsy, and all reviewers agree this should be green on this panel. Activating variants cause malignant migrating partial seizures of infancy, and missense/in frame variants severe autosomal dominant noctural frontal lobe epilepsy.
Created: 20 Jan 2016, 12:45 p.m.
Comment on phenotypes: Sourced from reviewers, OMIM and G2P.
Created: 20 Jan 2016, 12:36 p.m.
Comment on mode of inheritance: Monoallelic confirmed for both phenotypes on G2P and OMIM. Not on the imprinted gene list.
Created: 20 Jan 2016, 12:34 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Wessex and West Midlands GLH
  • NHS GMS
  • NIHRBR-RD Consortium SPEED_v3.0_20170404
  • Victorian Clinical Genetics Services
  • Radboud University Medical Center, Nijmegen
  • UKGTN
  • Expert
  • Expert Review Green
Phenotypes
  • Epileptic encephalopathy, early infantile, 14
  • Epilepsy, nocturnal frontal lobe, 5
  • MALIGNANT MIGRATING PARTIAL SEIZURES OF INFANCY
  • SEVERE AUTOSOMAL DOMINANT NOCTURNAL FRONTAL LOBE EPILEPSY
OMIM
608167
Clinvar variants
Variants in KCNT1
Penetrance
None
Publications
  • Barcia at al (2012) Nature Genet 44(11): 1255-1261
  • Heron et al (2012) Nature Genet 44(11): 1188-1190
Panels with this gene

History Filter Activity

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to KCNT1.

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to KCNT1.

11 Dec 2018, Gel status: 4

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Ellen McDonagh: Comment on mode of inheritance

26 Jun 2018, Gel status: 4

Added New Source

Sarah Leigh (Genomics England Curator)

NIHRBR-RD Consortium SPEED_v3.0_20170404 was added to KCNT1. Panel: Genetic Epilepsy Syndromes

25 Jun 2018, Gel status: 4

Added New Source

Sarah Leigh (Genomics England Curator)

Victorian Clinical Genetics Services was added to KCNT1. Panel: Genetic Epilepsy Syndromes

4 Apr 2018, Gel status: 4

Added New Source

Sarah Leigh (Genomics England Curator)

KCNT1 was added to Genetic Epilepsy Syndromes panel. Sources: Expert Review Green,Expert,UKGTN,Radboud University Medical Center, Nijmegen

4 Apr 2018, Gel status: 4

Created

Sarah Leigh (Genomics England Curator)

KCNT1 was created by Sarah Leigh