NM_020822.3(KCNT1):c.3281C>T (p.Thr1094Met) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Aug 14, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000544735.4

Allele description [Variation Report for NM_020822.3(KCNT1):c.3281C>T (p.Thr1094Met)]

NM_020822.3(KCNT1):c.3281C>T (p.Thr1094Met)

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.3281C>T (p.Thr1094Met)
HGVS:
  • NC_000009.12:g.135786300C>T
  • NG_033070.1:g.89116C>T
  • NM_001272003.2:c.3146C>T
  • NM_020822.3:c.3281C>TMANE SELECT
  • NP_001258932.1:p.Thr1049Met
  • NP_065873.2:p.Thr1094Met
  • NC_000009.11:g.138678146C>T
  • NM_020822.2:c.3281C>T
Protein change:
T1049M
Links:
dbSNP: rs373041291
NCBI 1000 Genomes Browser:
rs373041291
Molecular consequence:
  • NM_001272003.2:c.3146C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.3281C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Early infantile epileptic encephalopathy 14 (DEE14)
Synonyms:
DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 14
Identifiers:
MONDO: MONDO:0013989; MedGen: C3554195; Orphanet: 293181; OMIM: 614959
Name:
Epilepsy, nocturnal frontal lobe, 5 (ENFL5)
Synonyms:
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
SCV000652945Invitaecriteria provided, single submitter
Uncertain significance
(Aug 14, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000652945.4

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

Description

This sequence change replaces threonine with methionine at codon 1094 of the KCNT1 protein (p.Thr1094Met). The threonine residue is weakly conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs373041291, ExAC 0.05%). This variant has been observed in one or more individuals who were not affected with KCNT1-related conditions (Invitae). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Benign; Align-GVGD: Class C0). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 6, 2021

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