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NM_020822.3(KCNT1):c.1193G>A (p.Arg398Gln) AND KCNT1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 13, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003398586.5

Allele description [Variation Report for NM_020822.3(KCNT1):c.1193G>A (p.Arg398Gln)]

NM_020822.3(KCNT1):c.1193G>A (p.Arg398Gln)

Gene:
KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_020822.3(KCNT1):c.1193G>A (p.Arg398Gln)
HGVS:
  • NC_000009.12:g.135765188G>A
  • NG_033070.1:g.68004G>A
  • NM_001272003.2:c.1058G>A
  • NM_020822.3:c.1193G>AMANE SELECT
  • NP_001258932.1:p.Arg353Gln
  • NP_065873.2:p.Arg398Gln
  • NP_065873.2:p.Arg398Gln
  • NC_000009.11:g.138657034G>A
  • NM_020822.2:c.1193G>A
Protein change:
R353Q; ARG398GLN
Links:
OMIM: 608167.0007; dbSNP: rs397515407
NCBI 1000 Genomes Browser:
rs397515407
Molecular consequence:
  • NM_001272003.2:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.1193G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
KCNT1-related disorder
Synonyms:
KCNT1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004104638PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Apr 13, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004104638.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The KCNT1 c.1193G>A variant is predicted to result in the amino acid substitution p.Arg398Gln. This variant has been reported in at least 14 individuals with KCNT1-related epilepsy (see for example, Heron et al. 2012. PubMed ID: 23086396; Kim et al. 2014. PubMed ID: 25482562; Møller et al. 2015. PubMed ID: 26122718; Allen et al. 2016. PubMed ID: 26648591; Barcia et al. 2019. PubMed ID: 31872048) and is documented to have occurred de novo in at least 3 cases (Abdelnour et al. 2018. PubMed ID: 29291456; Monies et al. 2019. PubMed ID: 31130284; Borlot et al. 2020. PubMed ID: 32167590). In vitro experimental studies suggest that this variant impacts protein function (Milligan et al. 2014. PubMed ID: 24591078). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating it is rare or absent in the general population. Taken together, this variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 4, 2025