rs118192244

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong

The NM_172107.4(KCNQ2):​c.2127del​(p.Val710SerfsTer220) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: not found (cov: 33)

Consequence

KCNQ2
NM_172107.4 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:5O:1

Conservation

PhyloP100: -1.06
Variant links:
Genes affected
KCNQ2 (HGNC:6296): (potassium voltage-gated channel subfamily Q member 2) The M channel is a slowly activating and deactivating potassium channel that plays a critical role in the regulation of neuronal excitability. The M channel is formed by the association of the protein encoded by this gene and a related protein encoded by the KCNQ3 gene, both integral membrane proteins. M channel currents are inhibited by M1 muscarinic acetylcholine receptors and activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 1 (BFNC), also known as epilepsy, benign neonatal type 1 (EBN1). At least five transcript variants encoding five different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.188 CDS is truncated, and there are 3 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 20-63407135-CA-C is Pathogenic according to our data. Variant chr20-63407135-CA-C is described in ClinVar as [Pathogenic]. Clinvar id is 7390.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNQ2NM_172107.4 linkuse as main transcriptc.2127del p.Val710SerfsTer220 frameshift_variant 17/17 ENST00000359125.7 NP_742105.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNQ2ENST00000359125.7 linkuse as main transcriptc.2127del p.Val710SerfsTer220 frameshift_variant 17/171 NM_172107.4 ENSP00000352035 A1O43526-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
36
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:5Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Seizures, benign familial neonatal, 1 Pathogenic:2Other:1
Pathogenic, no assertion criteria providedclinical testingNeuroMeGen, Hospital Clinico Santiago de Compostela-- -
not provided, no classification providedliterature onlyGeneReviews-BFNE (benign familial neonatal epilepsy) -
Pathogenic, no assertion criteria providedliterature onlyOMIMSep 12, 2006- -
Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 11, 2023Experimental studies have shown that this frameshift affects KCNQ2 function (PMID: 2847176, 16260777). This sequence change results in a frameshift in the KCNQ2 gene (p.Val710Serfs*220). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 163 amino acid(s) of the KCNQ2 protein and extend the protein by 56 additional amino acid residues. This variant is not present in population databases (gnomAD no frequency). This frameshift has been observed in individuals with benign familial neonatal convulsions (PMID: 12847176, 16966552, 27535030). This variant is also known as c.2043del. ClinVar contains an entry for this variant (Variation ID: 7390). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. This variant disrupts a region of the KCNQ2 protein in which other variant(s) (p.Cys774Leufs*91) have been determined to be pathogenic (PMID: 23692823). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingGeneDxJul 22, 2014c.2127delT: p.Val710SerfsX220 (V710SfsX220) in exon 17 of the KCNQ2 gene (NM_172107.2). The normal sequence with the base that is deleted in braces is: GCCCCC{T}GTCC.The c.2127delT mutation in the KCNQ2 gene has been reported previously in association with benign familial neonatal seizures (Coppola et al., 2003). The deletion causes a frameshift starting with codon Valine 710, changes this amino acid to a Serine residue and creates a premature Stop codon at position 220 of the new reading frame, denoted p.Val710SerfsX220. This results in the replacement of the last 163 amino acids of the KCNQ2 protein with 219 incorrect amino acids. The variant is found in INFANT-EPI panel(s). -
Developmental and epileptic encephalopathy, 7 Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics Munich, Klinikum Rechts Der Isar, TU MünchenNov 15, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
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SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs118192244; hg19: chr20-62038488; API