NM_020822.3(KCNT1):c.1226C>T (p.Pro409Leu) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Apr 1, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_020822.3(KCNT1):c.1226C>T (p.Pro409Leu)]

NM_020822.3(KCNT1):c.1226C>T (p.Pro409Leu)

KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_020822.3(KCNT1):c.1226C>T (p.Pro409Leu)
  • NC_000009.12:g.135765649C>T
  • NG_033070.1:g.68465C>T
  • NM_001272003.2:c.1091C>T
  • NM_020822.3:c.1226C>TMANE SELECT
  • NP_001258932.1:p.Pro364Leu
  • NP_065873.2:p.Pro409Leu
  • NC_000009.11:g.138657495C>T
  • NM_020822.2:c.1226C>T
Protein change:
dbSNP: rs1064794752
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001272003.2:c.1091C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.1226C>T - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000569874GeneDxcriteria provided, single submitter
Likely pathogenic
(Apr 1, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000569874.4

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


The P409L variant in the KCNT1 gene has not been reported previously as a pathogenic variant noras a benign variant, to our knowledge. The P409L variant was not observed in approximately 6500individuals of European and African American ancestry in the NHLBI Exome Sequencing Project,indicating it is not a common benign variant in these populations. The P409L variant is asemi-conservative amino acid substitution, which may impact secondary protein structure as theseresidues differ in some properties. This substitution occurs at a position that is conserved acrossspecies. In silico analysis predicts this variant is probably damaging to the protein structure/function.Therefore, we interpret P409L as a likely pathogenic variant

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

Last Updated: Feb 27, 2021

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