NM_020822.3(KCNT1):c.862G>A (p.Gly288Ser) AND not provided

Clinical significance:Pathogenic (Last evaluated: Nov 15, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000255411.5

Allele description [Variation Report for NM_020822.3(KCNT1):c.862G>A (p.Gly288Ser)]

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

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.862G>A (p.Gly288Ser)
HGVS:
  • NC_000009.12:g.135759686G>A
  • NG_033070.1:g.62502G>A
  • NM_001272003.2:c.727G>A
  • NM_020822.3:c.862G>AMANE SELECT
  • NP_001258932.1:p.Gly243Ser
  • NP_065873.2:p.Gly288Ser
  • NC_000009.11:g.138651532G>A
  • NM_020822.2:c.862G>A
Protein change:
G243S; GLY288SER
Links:
OMIM: 608167.0010; dbSNP: rs587777264
NCBI 1000 Genomes Browser:
rs587777264
Molecular consequence:
  • NM_001272003.2:c.727G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.862G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000321803GeneDxcriteria provided, single submitter
Pathogenic
(Nov 15, 2018)
germlineclinical testing

Citation Link,

SCV001930053Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedPathogenicgermlineclinical testing

SCV001954177Human Genetics - Radboudumc,Radboudumc - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedPathogenicgermlineclinical testing

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000321803.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 occured de novo, although maternity and paternity were not confirmed (Ishii et al., 2013). This variant has also been identified at GeneDx as a confirmed de novo variant in a patient with infantile-onset epileptic encephalopathy. The G288S variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This variant is a non-conservative amino acid substitution that occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret G288S as a pathogenic variant.

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001930053.1

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

From Human Genetics - Radboudumc,Radboudumc - VKGL Data-share Consensus, SCV001954177.1

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

Last Updated: Oct 2, 2021

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