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NM_020822.3(KCNT1):c.862G>A (p.Gly288Ser)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 30, 2021)
Last evaluated:
Sep 9, 2020
Accession:
VCV000126421.11
Variation ID:
126421
Description:
single nucleotide variant
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NM_020822.3(KCNT1):c.862G>A (p.Gly288Ser)

Allele ID
131953
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 135759686 (GRCh38) GRCh38 UCSC
9: 138651532 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.138651532G>A
NC_000009.12:g.135759686G>A
NG_033070.1:g.62502G>A
... more HGVS
Protein change
G288S, G243S
Other names
-
Canonical SPDI
NC_000009.12:135759685:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA151134
OMIM: 608167.0010
dbSNP: rs587777264
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Sep 1, 2017 RCV000114361.8
Pathogenic 3 criteria provided, single submitter Nov 15, 2018 RCV000255411.5
Pathogenic 1 criteria provided, single submitter Sep 9, 2020 RCV000627792.4
Pathogenic 1 criteria provided, single submitter Dec 4, 2019 RCV001265540.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNT1 - - GRCh38
GRCh37
1216 1274

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Nov 15, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000321803.7
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The G288S variant in the KCNT1 gene was identified in two unrelated individuals with malignant migrating partial seizures in infancy and was reported to have … (more)
Pathogenic
(Sep 09, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, 5
Early infantile epileptic encephalopathy 14
Allele origin: germline
Invitae
Accession: SCV000553815.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces glycine with serine at codon 288 of the KCNT1 protein (p.Gly288Ser). The glycine residue is highly conserved and there is a … (more)
Pathogenic
(Sep 01, 2017)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 14
(Autosomal dominant inheritance)
Allele origin: de novo
Baylor Genetics
Accession: SCV000807324.1
Submitted: (Oct 16, 2017)
Evidence details
Publications
PubMed (2)
Comment:
This mutation has been previously reported as disease-causing and was found twice in our laboratory de novo in individuals with infantile onset epileptic encephalopathy
Pathogenic
(Dec 04, 2019)
criteria provided, single submitter
Method: clinical testing
KCNT1-Related Epilepsy
Allele origin: germline
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV001443687.1
Submitted: (Jul 31, 2020)
Evidence details
Comment:
This variant is a recurrent gain of function alteration at a CG dinucleotide sequence in the pore region of the KCNT1 channel. The c.862G>A variant … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 14
(Autosomal dominant inheritance)
Allele origin: de novo
Génétique des Maladies du Développement, Hospices Civils de Lyon
Accession: SCV001433979.1
Submitted: (Sep 29, 2020)
Evidence details
Comment:
20A3406
Pathogenic
(Dec 01, 2013)
no assertion criteria provided
Method: literature only
DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 14
Allele origin: germline
OMIM
Accession: SCV000147973.4
Submitted: (Apr 01, 2014)
Evidence details
Publications
PubMed (1)
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001930053.1
Submitted: (Sep 23, 2021)
Evidence details
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001954177.1
Submitted: (Sep 30, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Genetic heterogeneity in 26 infants with a hypomyelinating leukodystrophy. Arai-Ichinoi N Human genetics 2016 PMID: 26597493
De novo KCNT1 mutations in early-onset epileptic encephalopathy. Ohba C Epilepsia 2015 PMID: 26140313
Mutations in KCNT1 cause a spectrum of focal epilepsies. Møller RS Epilepsia 2015 PMID: 26122718
Molecular findings among patients referred for clinical whole-exome sequencing. Yang Y JAMA 2014 PMID: 25326635
A recurrent KCNT1 mutation in two sporadic cases with malignant migrating partial seizures in infancy. Ishii A Gene 2013 PMID: 24029078

Text-mined citations for rs587777264...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 02, 2021