NM_172107.4(KCNQ2):c.1888-1G>A AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 12, 2021
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:: RCV001323136.7

Allele description [Variation Report for NM_172107.4(KCNQ2):c.1888-1G>A]

NM_172107.4(KCNQ2):c.1888-1G>A

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.1888-1G>A

HGVS:

NC_000020.11:g.63407376C>T
NG_009004.2:g.70265G>A
NM_001382235.1:c.1942-1G>A
NM_004518.6:c.1804-1G>A
NM_172106.3:c.1834-1G>A
NM_172107.4:c.1888-1G>AMANE SELECT
NM_172108.5:c.1795-1G>A
NC_000020.10:g.62038729C>T

Links:

dbSNP: rs2079980924

NCBI 1000 Genomes Browser:

rs2079980924

Molecular consequence:

NM_001382235.1:c.1942-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_004518.6:c.1804-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_172106.3:c.1834-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_172107.4:c.1888-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_172108.5:c.1795-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001514038	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 12, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30977854, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001514038

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 12, 2021)

germline

clinical testing

PubMed (2)
[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

Use of a Dynamic Genetic Testing Approach for Childhood-Onset Epilepsy.

Balciuniene J, DeChene ET, Akgumus G, Romasko EJ, Cao K, Dubbs HA, Mulchandani S, Spinner NB, Conlin LK, Marsh ED, Goldberg E, Helbig I, Sarmady M, Abou Tayoun A.

JAMA Netw Open. 2019 Apr 5;2(4):e192129. doi: 10.1001/jamanetworkopen.2019.2129.

PubMed [citation]

PMID:: 30977854
PMCID:: PMC6481455

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001514038.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has been observed in individual(s) with clinical features of KCNQ2-related conditions (PMID: 30977854, Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in the last intron (intron 16) of the KCNQ2 gene. While this is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product.

#	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 5, 2024

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