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NM_020822.3(KCNT1):c.2849G>A (p.Arg950Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: May 20, 2021)
Last evaluated:
May 17, 2021
Accession:
VCV000286710.8
Variation ID:
286710
Description:
single nucleotide variant
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NM_020822.3(KCNT1):c.2849G>A (p.Arg950Gln)

Allele ID
270947
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 135784031 (GRCh38) GRCh38 UCSC
9: 138675877 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.138675877G>A
NC_000009.12:g.135784031G>A
NG_033070.1:g.86847G>A
... more HGVS
Protein change
R950Q, R905Q
Other names
-
Canonical SPDI
NC_000009.12:135784030:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10605542
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Jun 13, 2020 RCV000650627.4
Pathogenic 1 criteria provided, single submitter Feb 15, 2017 RCV001004680.1
Pathogenic 1 criteria provided, single submitter May 17, 2021 RCV001420735.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Oct 23, 2020 RCV000498228.4
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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
Uncertain significance
(Mar 28, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000340255.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Jun 21, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000589673.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R950Q variant in the KCNT1 gene has been previously reported as a de novo change in multiple individuals previously tested at GeneDx and in … (more)
Pathogenic
(Feb 15, 2017)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 14
(Autosomal dominant inheritance)
Allele origin: unknown
Génétique des Maladies du Développement, Hospices Civils de Lyon
Accession: SCV001164136.1
Submitted: (May 24, 2019)
Evidence details
Publications
PubMed (1)
Pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
(Autosomal dominant inheritance)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001447907.1
Submitted: (Oct 23, 2020)
Evidence details
Pathogenic
(Jun 13, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, 5
Early infantile epileptic encephalopathy 14
Allele origin: germline
Invitae
Accession: SCV000772474.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces arginine with glutamine at codon 950 of the KCNT1 protein (p.Arg950Gln). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(May 17, 2021)
criteria provided, single submitter
Method: clinical testing
Seizures
(Sporadic)
Allele origin: de novo
Génétique des Maladies du Développement, Hospices Civils de Lyon
Accession: SCV001623055.1
Submitted: (May 20, 2021)
Evidence details
Comment:
missense variant absnet from gnomad. Previously described in the litterature. de novo

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
High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. Hamdan FF American journal of human genetics 2017 PMID: 29100083
A targeted resequencing gene panel for focal epilepsy. Hildebrand MS Neurology 2016 PMID: 27029629
Mutations in KCNT1 cause a spectrum of focal epilepsies. Møller RS Epilepsia 2015 PMID: 26122718
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KCNT1 - - - -

Record last updated Nov 20, 2021