rs796052676

chr8-132180246-G-Achr8-132180246-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_004519.4(KCNQ3):c.688C>T(p.Arg230Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R230H) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNQ3 NM_004519.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:19 O:2
• Conservation: PhyloP100: 6.79

Genes affected

KCNQ3 (HGNC:6297): (potassium voltage-gated channel subfamily Q member 3) This gene encodes a protein that functions in the regulation of neuronal excitability. The encoded protein forms an M-channel by associating with the products of the related KCNQ2 or KCNQ5 genes, which both encode integral membrane proteins. M-channel currents are inhibited by M1 muscarinic acetylcholine receptors and are activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 2 (BFNC2), also known as epilepsy, benign neonatal type 2 (EBN2). Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in NM_004519.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr8-132180245-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 424397.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.982
• PP5: Variant 8-132180246-G-A is Pathogenic according to our data. Variant chr8-132180246-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 205963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-132180246-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNQ3	NM_004519.4	c.688C>T	p.Arg230Cys	missense_variant	4/15	ENST00000388996.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNQ3	ENST00000388996.10	c.688C>T	p.Arg230Cys	missense_variant	4/15	1	NM_004519.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1461802 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727192

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:19 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Seizures, benign familial neonatal, 2 Pathogenic:9 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 03, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Jun 08, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	Aug 03, 2022	ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderated, PM5 moderated, PM6 moderated, PP3 supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	May 18, 2017	- -
Likely pathogenic, criteria provided, single submitter	research	Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine	Sep 09, 2015	This study shows that diverse genetic causes underlie CVI. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 16, 2021	The KCNQ3 c.688C>T (p.Arg230Cys) variant is a missense variant that has a well-documented association with KCNQ3-related disorders. Across a selection of the available literature, it has been reported in at least eight individuals with features that included intellectual disability, autism, EEG abnormalities, seizures, staring spells, strabismus, hypotonia, and structural abnormalities on brain MRI (Rauch et al. 2012; Epi4K Consortium et al. 2013; Deciphering Developmental Disorders Study 2017; Geisheker et al. 2017; Lindy et al. 2018; Trinh et al. 2019; Sands et al. 2019; Valentino et al. 2021). In at least four of these individuals, the variant occurred de novo. The p.Arg230Cys variant is not reported in version 2.1.1 or version 3.1.1 of the Genome Aggregation Database despite its location in a region of good sequencing coverage, which suggest the variant is rare. In vitro analyses have demonstrated that this variant, which affects a crucial gating residue in the S4 transmembrane segment, stabilizes the activated state of the channel, allowing current to flow throughout the physiological voltage range and resulting in gain of function (Miceli et al. 2015; Barro-Soria 2019; Sands et al. 2019). Additional amino acid changes affecting this residue have also been reported in association with KCNQ3-related disorders (Landrum et al. 2016). Based on the available evidence, the p.Arg230Cys variant is classified as pathogenic for KCNQ3-related disorders. -
not provided, no classification provided	literature only	GeneReviews	-	Variant found in 4 unrelated persons, all de novo, in studies focused on different phenotypes -
Likely pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 01, 2016	This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2,PP3. -
Pathogenic, criteria provided, single submitter	research	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 25, 2024	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 21, 2022	Published functional studies demonstrate a gain-of-function stabilization of the ion channel's activated state (Miceli et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23020937, 26350515, 25740509, 31036916, 31238879, 23934111, 28628100, 28135719, 29655203, 28191890, 31177578, 31618753, 31981491, 31175295, 31785789, 33004838, 27535533) -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -

Intellectual disability Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Diagnostic Laboratory, Strasbourg University Hospital	Apr 20, 2020	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Pediatric Genetics Clinic, Sheba Medical Center	May 13, 2021	- -

KCNQ3-related developmental disability Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille

-

- -

Benign neonatal seizures Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 27, 2023

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 230 of the KCNQ3 protein (p.Arg230Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with neurodevelopmental disorders and early-onset epileptic encephalopathy (PMID: 23020937, 23934111, 26350515, 28135719, 28628100, 29655203). In at least one individual the variant was observed to be de novo. This variant is also known as p.Arg110Cys, g.133192493G>A. ClinVar contains an entry for this variant (Variation ID: 205963). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt KCNQ3 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects KCNQ3 function (PMID: 25740509, 30578330). For these reasons, this variant has been classified as Pathogenic. -

Intellectual disability, severe Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Duke University Health System Sequencing Clinic, Duke University Health System

Apr 20, 2023

- -

Seizures, benign familial infantile, 5 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Equipe Genetique des Anomalies du Developpement, Université de Bourgogne

Aug 28, 2018

- -

Autistic behavior Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

New York Genome Center

Feb 03, 2020

The de novo missense variant c.688C>T, p.Arg230Cys identified in this individual has been reported as de novo variant in several patients with Neurodevelopmental disability (nonverbal, with autism spectrum disorder or autistic features and multifocal status epilepticus during sleep) [PMID: 31177578].The p.Arg230Cys is situated in the mutational hotspot of KCNQ3 gene, and functional studies indicate that it causes a gain-of-function stabilization of the ion channel's activated state [PMID: 31177578; PMID: 25740509]. Patients with p.Arg230Cys variant are usually ambulatory by 2 years of age, but were either nonverbal or had single words only and were cognitively impaired with ASD or autistic features [PMID: 31177578; PMID: 31238879].This variant is also not reported in gnomAD database, indicating this is a rare allele. Based on the available evidence, the de novo missense variant c.688C>T, p.Arg230Cys in the KCNQ3 gene is classified as pathogenic. -

Severe neurodevelopmental delay Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genetics Laboratory - UDIAT Centre Diagnòstic, Hospital Universitari Parc Tauli

Jul 10, 2019

- -

Benign neonatal seizures;C0238111:Lennox-Gastaut syndrome;C3714756:Intellectual disability Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

Variant interpretted as Pathogenic and reported on 10-08-2018 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
Cadd	Pathogenic	34
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	D;.;.;.;.
Eigen	Pathogenic	0.93
Eigen_PC	Pathogenic	0.85
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Pathogenic	1.0	D;D;D;D;D
M_CAP	Pathogenic	0.68	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.1	H;.;.;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.93	D
PROVEAN	Pathogenic	-7.6	D;.;D;D;.
REVEL	Pathogenic	0.96
Sift	Pathogenic	0.0	D;.;D;D;.
Sift4G	Pathogenic	0.0	D;D;D;D;.
Polyphen		1.0	D;.;.;D;.
Vest4		0.95
MutPred		0.89		Loss of MoRF binding (P = 0.0045);.;.;Loss of MoRF binding (P = 0.0045);.;
MVP		0.99
MPC		2.4
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.92
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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

Other links and lift over

dbSNP: rs796052676; hg19: chr8-133192493; COSMIC: COSV66466182;