• delete

NM_020822.3(KCNT1):c.3563C>T (p.Thr1188Met) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Feb 23, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description

NM_020822.3(KCNT1):c.3563C>T (p.Thr1188Met)

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.3563C>T (p.Thr1188Met)
  • NC_000009.12:g.135791857C>T
  • NG_033070.1:g.94673C>T
  • NM_001272003.2:c.3491C>T
  • NM_020822.3:c.3563C>TMANE SELECT
  • NP_001258932.1:p.Thr1164Met
  • NP_065873.2:p.Thr1188Met
  • NC_000009.11:g.138683703C>T
  • NM_020822.2:c.3563C>T
Protein change:
dbSNP: rs370090905
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001272003.2:c.3491C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.3563C>T - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000573550GeneDxcriteria provided, single submitter
Uncertain significance
(Feb 23, 2017)
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, SCV000573550.3

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


A variant of uncertain significance has been identified in the KCNT1 gene. The T1188M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The T1188M variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The T1188M variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Feb 27, 2021

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