NM_020822.3(KCNT1):c.1717C>T (p.Arg573Cys) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Aug 9, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001221030.2

Allele description [Variation Report for NM_020822.3(KCNT1):c.1717C>T (p.Arg573Cys)]

NM_020822.3(KCNT1):c.1717C>T (p.Arg573Cys)

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.1717C>T (p.Arg573Cys)
HGVS:
  • NC_000009.12:g.135770395C>T
  • NG_033070.1:g.73211C>T
  • NM_001272003.2:c.1582C>T
  • NM_020822.3:c.1717C>TMANE SELECT
  • NP_001258932.1:p.Arg528Cys
  • NP_065873.2:p.Arg573Cys
  • NC_000009.11:g.138662241C>T
  • NM_020822.2:c.1717C>T
Protein change:
R528C
Links:
dbSNP: rs557219607
NCBI 1000 Genomes Browser:
rs557219607
Molecular consequence:
  • NM_001272003.2:c.1582C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.1717C>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
SCV001393052Invitaecriteria provided, single submitter
Uncertain significance
(Aug 9, 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, SCV001393052.2

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

Description

This sequence change replaces arginine with cysteine at codon 573 of the KCNT1 protein (p.Arg573Cys). The arginine residue is weakly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs557219607, ExAC 0.01%). This variant has not been reported in the literature in individuals with KCNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 500199). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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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