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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 11, 2026
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:: RCV000650627.12

Allele description [Variation Report for NM_020822.3(KCNT1):c.2849G>A (p.Arg950Gln)]

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

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.2849G>A (p.Arg950Gln)

HGVS:

NC_000009.12:g.135784031G>A
NG_033070.1:g.86847G>A
NM_001272003.2:c.2714G>A
NM_020822.3:c.2849G>AMANE SELECT
NP_001258932.1:p.Arg905Gln
NP_065873.2:p.Arg950Gln
NC_000009.11:g.138675877G>A
NM_020822.2:c.2849G>A

Protein change:

R905Q

Links:

dbSNP: rs886043455

Molecular consequence:

NM_001272003.2:c.2714G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020822.3:c.2849G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 14 (DEE14)
Synonyms:: Early infantile epileptic encephalopathy 14
Identifiers:: MONDO: MONDO:0013989; MedGen: C3554195; Orphanet: 293181; OMIM: 614959

Name:: Autosomal dominant nocturnal frontal lobe epilepsy 5
Synonyms:: Epilepsy, nocturnal frontal lobe, 5; 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000772474	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 11, 2026)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 26122718, 27029629, 29100083, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000772474

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 11, 2026)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in KCNT1 cause a spectrum of focal epilepsies.

Møller RS, Heron SE, Larsen LH, Lim CX, Ricos MG, Bayly MA, van Kempen MJ, Klinkenberg S, Andrews I, Kelley K, Ronen GM, Callen D, McMahon JM, Yendle SC, Carvill GL, Mefford HC, Nabbout R, Poduri A, Striano P, Baglietto MG, Zara F, Smith NJ, et al.

Epilepsia. 2015 Sep;56(9):e114-20. doi: 10.1111/epi.13071. Epub 2015 Jun 30.

PubMed [citation]

PMID:: 26122718
PMCID:: PMC5915334

A targeted resequencing gene panel for focal epilepsy.

Hildebrand MS, Myers CT, Carvill GL, Regan BM, Damiano JA, Mullen SA, Newton MR, Nair U, Gazina EV, Milligan CJ, Reid CA, Petrou S, Scheffer IE, Berkovic SF, Mefford HC.

Neurology. 2016 Apr 26;86(17):1605-12. doi: 10.1212/WNL.0000000000002608. Epub 2016 Mar 30.

PubMed [citation]

PMID:: 27029629
PMCID:: PMC4844234

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000772474.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 950 of the KCNT1 protein (p.Arg950Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with infantile seizures, epilepsy and developmental delay (PMID: 26122718, 27029629, 29100083). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 286710). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt KCNT1 protein function with a negative predictive value of 80%. This variant disrupts the p.Arg950 amino acid residue in KCNT1. Other variant(s) that disrupt this residue have been determined to be pathogenic (internal data database). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 1, 2026

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