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NM_172107.4(KCNQ2):c.2329C>T (p.Pro777Ser) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 15, 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:
RCV000815524.14

Allele description

NM_172107.4(KCNQ2):c.2329C>T (p.Pro777Ser)

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.2329C>T (p.Pro777Ser)
Other names:
p.P777S:CCC>TCC
HGVS:
  • NC_000020.11:g.63406934G>A
  • NG_009004.2:g.70707C>T
  • NM_001382235.1:c.2383C>T
  • NM_004518.6:c.2245C>T
  • NM_172106.3:c.2275C>T
  • NM_172107.4:c.2329C>TMANE SELECT
  • NM_172108.5:c.2236C>T
  • NP_001369164.1:p.Pro795Ser
  • NP_004509.2:p.Pro749Ser
  • NP_742104.1:p.Pro759Ser
  • NP_742105.1:p.Pro777Ser
  • NP_742106.1:p.Pro746Ser
  • NC_000020.10:g.62038287G>A
  • NM_172107.2:c.2329C>T
  • NM_172109.1:c.*26811C>T
Protein change:
P746S
Links:
dbSNP: rs748400155
NCBI 1000 Genomes Browser:
rs748400155
Molecular consequence:
  • NM_001382235.1:c.2383C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004518.6:c.2245C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172106.3:c.2275C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172107.4:c.2329C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172108.5:c.2236C>T - missense variant - [Sequence Ontology: SO:0001583]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000955983Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 15, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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, SCV000955983.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 777 of the KCNQ2 protein (p.Pro777Ser). This variant is present in population databases (rs748400155, gnomAD 0.003%). This missense change has been observed in individuals with KCNQ2 related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 205850). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 16, 2024