NM_172107.4(KCNQ2):c.1375C>T (p.Gln459Ter) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 7, 2023
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:: RCV001949474.5

Allele description [Variation Report for NM_172107.4(KCNQ2):c.1375C>T (p.Gln459Ter)]

NM_172107.4(KCNQ2):c.1375C>T (p.Gln459Ter)

Gene:

KCNQ2:potassium voltage-gated channel subfamily Q member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.33

Genomic location:

Preferred name:

NM_172107.4(KCNQ2):c.1375C>T (p.Gln459Ter)

HGVS:

NC_000020.11:g.63415053G>A
NG_009004.2:g.62588C>T
NM_001382235.1:c.1321C>T
NM_004518.6:c.1291C>T
NM_172106.3:c.1321C>T
NM_172107.4:c.1375C>TMANE SELECT
NM_172108.5:c.1285C>T
NP_001369164.1:p.Gln441Ter
NP_004509.2:p.Gln431Ter
NP_742104.1:p.Gln441Ter
NP_742105.1:p.Gln459Ter
NP_742106.1:p.Gln429Ter
NC_000020.10:g.62046406G>A

Protein change:

Q429*

Links:

dbSNP: rs2145556764

NCBI 1000 Genomes Browser:

rs2145556764

Molecular consequence:

NM_001382235.1:c.1321C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004518.6:c.1291C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_172106.3:c.1321C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_172107.4:c.1375C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_172108.5:c.1285C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:: Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:: MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002240111	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 7, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 14534157, 23692823, 27779742, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002240111

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 7, 2023)

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

KCNQ2 and KCNQ3 potassium channel genes in benign familial neonatal convulsions: expansion of the functional and mutation spectrum.

Singh NA, Westenskow P, Charlier C, Pappas C, Leslie J, Dillon J, Anderson VE, Sanguinetti MC, Leppert MF; BFNC Physician Consortium..

Brain. 2003 Dec;126(Pt 12):2726-37. Epub 2003 Oct 8.

PubMed [citation]

PMID:: 14534157

Milh M, Boutry-Kryza N, Sutera-Sardo J, Mignot C, Auvin S, Lacoste C, Villeneuve N, Roubertie A, Heron B, Carneiro M, Kaminska A, Altuzarra C, Blanchard G, Ville D, Barthez MA, Heron D, Gras D, Afenjar A, Dorison N, Doummar D, Billette de Villemeur T, An I, et al.

Orphanet J Rare Dis. 2013 May 22;8:80. doi: 10.1186/1750-1172-8-80.

PubMed [citation]

PMID:: 23692823
PMCID:: PMC3670812

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002240111.3

#	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 creates a premature translational stop signal (p.Gln459*) in the KCNQ2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in KCNQ2 are known to be pathogenic (PMID: 14534157, 23692823, 27779742). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KCNQ2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1458320). 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: Sep 29, 2024

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