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NM_020822.3(KCNT1):c.2782C>T (p.Arg928Cys) AND Autosomal dominant nocturnal frontal lobe epilepsy 5

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Jun 15, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000032797.17

Allele description [Variation Report for NM_020822.3(KCNT1):c.2782C>T (p.Arg928Cys)]

NM_020822.3(KCNT1):c.2782C>T (p.Arg928Cys)

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.2782C>T (p.Arg928Cys)
HGVS:
  • NC_000009.12:g.135779411C>T
  • NG_033070.1:g.82227C>T
  • NM_001272003.2:c.2647C>T
  • NM_020822.3:c.2782C>TMANE SELECT
  • NP_001258932.1:p.Arg883Cys
  • NP_065873.2:p.Arg928Cys
  • NP_065873.2:p.Arg928Cys
  • NC_000009.11:g.138671257C>T
  • NM_020822.2:c.2782C>T
Protein change:
R883C; ARG928CYS
Links:
OMIM: 608167.0005; dbSNP: rs397515405
NCBI 1000 Genomes Browser:
rs397515405
Molecular consequence:
  • NM_001272003.2:c.2647C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.2782C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal dominant nocturnal frontal lobe epilepsy 5
Synonyms:
Epilepsy, nocturnal frontal lobe, 5; CILIARY DYSKINESIA, PRIMARY, 28, WITHOUT SITUS INVERSUS; CILIARY DYSKINESIA, PRIMARY, 28, WITH SITUS INVERSUS
Identifiers:
MONDO: MONDO:0014002; MedGen: C3554306; Orphanet: 98784; OMIM: 615005

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000056565OMIM
no assertion criteria provided
Pathogenic
(Nov 1, 2012)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000211892GeneReviews
no classification provided
not providedgermlineliterature only

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

SCV001523119Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 7, 2020)
de novoclinical testing

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

SCV001752425Génétique des Maladies du Développement, Hospices Civils de Lyon
no assertion criteria provided
Pathogenicunknownclinical testing

SCV002549823Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 15, 2022)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedde novoyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Severe autosomal dominant nocturnal frontal lobe epilepsy associated with psychiatric disorders and intellectual disability.

Derry CP, Heron SE, Phillips F, Howell S, MacMahon J, Phillips HA, Duncan JS, Mulley JC, Berkovic SF, Scheffer IE.

Epilepsia. 2008 Dec;49(12):2125-9. doi: 10.1111/j.1528-1167.2008.01652.x. Epub 2008 May 9.

PubMed [citation]
PMID:
18479385

Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy.

Heron SE, Smith KR, Bahlo M, Nobili L, Kahana E, Licchetta L, Oliver KL, Mazarib A, Afawi Z, Korczyn A, Plazzi G, Petrou S, Berkovic SF, Scheffer IE, Dibbens LM.

Nat Genet. 2012 Nov;44(11):1188-90. doi: 10.1038/ng.2440. Epub 2012 Oct 21.

PubMed [citation]
PMID:
23086396
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000056565.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 6 affected members of an Australian family of British descent with autosomal dominant nocturnal frontal lobe epilepsy-5 (ENFL5; 615005) (family B of Derry et al., 2008), Heron et al. (2012) identified a heterozygous 2782C-T transition in the KCNT1 gene, resulting in an arg928-to-cys (R928C) substitution at a highly conserved residue in the intracellular C-terminal region adjacent to an NAD(+)-binding site. The mutation, which was identified by whole-exome capture and sequencing and confirmed by Sanger sequencing, segregated with the phenotype in this family and was not identified in 111 control samples or in several large control databases. No functional studies were performed. The mean age at seizure onset was 4.6 years, and 5 of the 6 had refractory seizures and behavioral or psychiatric problems. Three had intellectual disability.

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

From GeneReviews, SCV000211892.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001523119.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Génétique des Maladies du Développement, Hospices Civils de Lyon, SCV001752425.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002549823.1

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

Description

_x000D_ Criteria applied: PS3, PS4, PP3, PP4

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

Last Updated: Oct 26, 2024