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NM_020822.3(KCNT1):c.1628A>G (p.Gln543Arg) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 12, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002314148.9

Allele description [Variation Report for NM_020822.3(KCNT1):c.1628A>G (p.Gln543Arg)]

NM_020822.3(KCNT1):c.1628A>G (p.Gln543Arg)

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.1628A>G (p.Gln543Arg)
HGVS:
  • NC_000009.12:g.135770306A>G
  • NG_033070.1:g.73122A>G
  • NM_001272003.2:c.1493A>G
  • NM_020822.3:c.1628A>GMANE SELECT
  • NP_001258932.1:p.Gln498Arg
  • NP_065873.2:p.Gln543Arg
  • NC_000009.11:g.138662152A>G
  • NM_020822.2:c.1628A>G
Protein change:
Q498R
Links:
dbSNP: rs200173000
NCBI 1000 Genomes Browser:
rs200173000
Molecular consequence:
  • NM_001272003.2:c.1493A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.1628A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000847407Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Mar 12, 2019) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

A de novo GABRA2 missense mutation in severe early-onset epileptic encephalopathy with a choreiform movement disorder.

Orenstein N, Goldberg-Stern H, Straussberg R, Bazak L, Weisz Hubshman M, Kropach N, Gilad O, Scheuerman O, Dory Y, Kraus D, Tzur S, Magal N, Kilim Y, Shkalim Zemer V, Basel-Salmon L.

Eur J Paediatr Neurol. 2018 May;22(3):516-524. doi: 10.1016/j.ejpn.2017.12.017. Epub 2017 Dec 30.

PubMed [citation]
PMID:
29422393

Details of each submission

From Ambry Genetics, SCV000847407.4

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Oct 26, 2024