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NM_020822.3(KCNT1):c.1928G>A (p.Arg643Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Nov 4, 2021)
Last evaluated:
Nov 3, 2021
Accession:
VCV000386260.15
Variation ID:
386260
Description:
single nucleotide variant
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NM_020822.3(KCNT1):c.1928G>A (p.Arg643Gln)

Allele ID
370648
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 135771015 (GRCh38) GRCh38 UCSC
9: 138662861 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.138662861G>A
NC_000009.12:g.135771015G>A
NG_033070.1:g.73831G>A
... more HGVS
Protein change
R643Q, R598Q
Other names
-
Canonical SPDI
NC_000009.12:135771014:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00032
The Genome Aggregation Database (gnomAD) 0.00010
The Genome Aggregation Database (gnomAD), exomes 0.00023
Trans-Omics for Precision Medicine (TOPMed) 0.00022
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
Links
ClinGen: CA5327107
dbSNP: rs141281093
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 20, 2016 RCV000717701.1
Likely benign 1 criteria provided, single submitter Nov 26, 2020 RCV001088079.2
Uncertain significance 1 criteria provided, single submitter Nov 3, 2021 RCV001770293.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 1, 2021 RCV000659136.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNT1 - - GRCh38
GRCh37
1240 1298

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 20, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000848559.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Likely benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, 5
Early infantile epileptic encephalopathy 14
Allele origin: germline
Invitae
Accession: SCV000772488.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Likely benign
(May 01, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000527832.5
Submitted: (Sep 23, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28166811)
Uncertain significance
(Mar 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000780951.9
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Nov 03, 2021)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 14
Allele origin: germline
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002011508.1
Submitted: (Nov 04, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs141281093...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 20, 2021