19-50323685-C-T

Position:

• chr19-50323685-C-T

Variant summary

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

The ENST00000477616.2(KCNC3):​c.1268G>A​(p.Arg423His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R423C) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KCNC3 ENST00000477616.2 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:20
• Conservation: PhyloP100: 7.76

Genes affected

KCNC3 (HGNC:6235): (potassium voltage-gated channel subfamily C member 3) The Shaker gene family of Drosophila encodes components of voltage-gated potassium channels and is comprised of four subfamilies. Based on sequence similarity, this gene is similar to one of these subfamilies, namely the Shaw subfamily. The protein encoded by this gene belongs to the delayed rectifier class of channel proteins and is an integral membrane protein that mediates the voltage-dependent potassium ion permeability of excitable membranes. Alternate splicing results in several transcript variants. [provided by RefSeq, Mar 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, 6 uncertain in ENST00000477616.2
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr19-50323686-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3251038.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.991
• PP5: Variant 19-50323685-C-T is Pathogenic according to our data. Variant chr19-50323685-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 208671.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-50323685-C-T is described in Lovd as [Pathogenic]. Variant chr19-50323685-C-T is described in Lovd as [Pathogenic]. Variant chr19-50323685-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNC3	NM_004977.3	c.1268G>A	p.Arg423His	missense_variant	2/5	ENST00000477616.2	NP_004968.2
KCNC3	NM_001372305.1	c.1040G>A	p.Arg347His	missense_variant	2/5		NP_001359234.1
KCNC3	NR_110912.2	n.69-2901G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNC3	ENST00000477616.2	c.1268G>A	p.Arg423His	missense_variant	2/5	1	NM_004977.3	ENSP00000434241
KCNC3	ENST00000670667.1	c.1268G>A	p.Arg423His	missense_variant	2/4			ENSP00000499301	P3
KCNC3	ENST00000376959.6	c.1268G>A	p.Arg423His	missense_variant	2/5	5		ENSP00000366158	A2
KCNC3	ENST00000474951.1	c.-74-2901G>A		intron_variant		2		ENSP00000432438

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:20

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Spinocerebellar ataxia type 13 Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn	Aug 05, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	Feb 14, 2023	The missense c.1268G>A(p.Arg423His) variant in KCNC3 gene has been reported in heterozygous state in multiple individuals affected with KCNC3 related disorders (Khare S, et. al., 2017; Coutelier M, et. al., 2017; Duarri A, et. al., 2015). Functional studies show p.Arg423His disrupts the channel activity of the KCNC3 protein and demonstrates a dominant-negative effect (Figueroa KP, et. al., 2010). The p.Arg423His variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). The amino acid change p.Arg423His in KCNC3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 423 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and gain of function are known mechanisms of disease in this gene and are associated with Spinocerebellar ataxia 13 (MIM#605259). (PMIDs: 22289912, 26442672, GeneReviews). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Age of onset (congenital or adult-onset), phenotype and disease progression depend on the location of the variant and its action on the channel, Kv3.3. (PMID: 25756792; 26442672, GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to histidine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools. Very high conservation with a minor amino acid change. (SP) 0600 - Variant is located in the annotated transmembrane S4 domain (UniProt, PMID: 26442672). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as pathogenic in multiple individuals with early onset non-progressive spinocerebellar ataxia. It has been shown to segregate with disease in several families, and there have been at least two reports of de novo cases (ClinVar, LOVD3, PMID: 19953606, 21479265, 25756792, 28467418). (SP) 0902 - This variant has moderate evidence for segregation with disease (PMID: 28467418). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Targeted expression in zebrafish and drosophila models have demonstrated disrupted axonal pathfinding and neurodegeneration consistent with the neurodevelopmental presentations of disease in patients (PMIDs: 21543613, 30862666, 28467418). In addition, patch clamp studies of this variant expressed in Xenopus oocytes have shown significant loss of Kv3.3 channel activity, reduced current amplitude and cell surface expression. (PMIDs: 19953606, 22289912, 25756792). NB. However, patch clamp assays have been shown to be unreliable; therefore results from these studies are used with caution during variant classification. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Nov 15, 2018	- -
Pathogenic, no assertion criteria provided	research	O&I group, Department of Genetics, University Medical Center of Groningen	Jul 22, 2021	- -
Pathogenic, criteria provided, single submitter	research	Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris	Jan 04, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Oct 30, 2020	This sequence change is predicted to replace arginine with histidine at codon 423 of the KCNC3 protein (p.(Arg423His)). The arginine residue is invariant across species (100 vertebrates, UCSC), and is located in the S4 transmembrane segment in the ion transport domain. There is a small physicochemical difference between arginine and histidine. The variant is absent in a large population cohort (rs797044872, gnomAD v2.1 and v3.0). This variant has been identified in multiple individuals with early-onset non-progressive spinocerebellar ataxia, with at least two individuals assumed de novo (PMID: 19953606 , 25756792, 28216058, 28467418). The variant segregates with affected status in multiple families (PMID: 19953606, 28216058, 28467418). A zebrafish model of the variant recapitulates the cerebellar degeneration, and demonstrated differential affects on Purkinje cell excitability, maturation, and viability to an adult-onset associated variant (PMID: 32644043). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (5/5 algorithms). Based on the classification scheme RMH Modified ACMG Guidelines v1.3.0, this variant is classified as PATHOGENIC. Following criteria are met: PS3, PM6_Strong, PP1_Strong, PS4_Moderate, PM2_Supporting, PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID:19953606, 22289912, 25756792, 28467418). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.92; 3Cnet: 0.72). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000208671). The variant has been previously reported as de novo (PMID: 28467418). and observed in multiple (>3) similarly affected unrelated individuals (PMID:19953606, 28467418). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 08, 2014	- -

not provided Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 04, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 04, 2023	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 423 of the KCNC3 protein (p.Arg423His). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects KCNC3 function (PMID: 19953606, 22289912, 25756792, 28467418). 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 KCNC3 protein function. ClinVar contains an entry for this variant (Variation ID: 208671). This missense change has been observed in individual(s) with spinocerebellar ataxia (PMID: 19953606, 25756792, 28467418). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Feb 20, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 17, 2021	DNA sequence analysis of the KCNC3 gene demonstrated a sequence change, c.1268G>A, in exon 2 that results in an amino acid change, p.Arg423His. This sequence change is absent in the gnomAD population database. This sequence change has been previously described in individuals and families with ataxia or spinocerebellar ataxia 13 (PMIDs: 19953606, 25756792, 28467418, 28216058). The p.Arg423His change affects a highly conserved amino acid residue located in the S4 transmembrane segment of the KCNC3 protein. It appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Functional studies show p.Arg423His disrupts the channel activity of the KCNC3 protein and demonstrates a dominant-negative effect (PMIDs: 19953606, 25756792, 28467418). These collective evidences suggest this p.Arg423His change is pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Sep 15, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 10, 2022	Published functional studies demonstrate a damaging effect, resulting in loss of channel activity consistent with a strong dominant negative effect (Figueroa et al., 2010; Duarri et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25356970, 23734863, 22289912, 19953606, 26795593, 21479265, 28216058, 28467418, 25756792, 33624863) -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 16, 2021

The c.1268G>A (p.R423H) alteration is located in exon 2 (coding exon 2) of the KCNC3 gene. This alteration results from a G to A substitution at nucleotide position 1268, causing the arginine (R) at amino acid position 423 to be replaced by a histidine (H). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration has been reported in multiple unrelated patients with early-onset slowly-progressive ataxia (Figueroa, 2010; Duarri, 2015; Khare, 2017). This amino acid position is highly conserved in available vertebrate species. The p.R423H alteration has been shown in multiple independent studies to negatively affect Kv3.3 channel functioning by suppressing current amplitude (Figueroa, 2010), significantly altering gating (Minassian, 2012), or resulting in altered glycosylation and aberrant retention of the mutant channels in the anterograde and/or endosomal vesicles instead of at the plasma membrane (Khare, 2017). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.53
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.91	D;D
Eigen	Pathogenic	0.73
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.94	D;D
M_CAP	Pathogenic	0.81	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.2	.;M
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.92	D
PROVEAN	Pathogenic	-4.7	D;D
REVEL	Pathogenic	0.92
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Polyphen		1.0	D;D
Vest4		0.98
MutPred		0.93		Loss of methylation at R423 (P = 0.0754);Loss of methylation at R423 (P = 0.0754);
MVP		0.99
ClinPred		1.0	D
GERP RS		3.0
Varity_R		0.89
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
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

Other links and lift over

dbSNP: rs797044872; hg19: chr19-50826942;