9-2718166-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_133497.4(KCNV2):​c.427G>T​(p.Glu143*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,460,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

KCNV2
NM_133497.4 stop_gained

Scores

3
3
1

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8

Conservation

PhyloP100: 2.56
Variant links:
Genes affected
KCNV2 (HGNC:19698): (potassium voltage-gated channel modifier subfamily V member 2) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium voltage-gated channel subfamily V. This member is identified as a 'silent subunit', and it does not form homomultimers, but forms heteromultimers with several other subfamily members. Through obligatory heteromerization, it exerts a function-altering effect on other potassium channel subunits. This protein is strongly expressed in pancreas and has a weaker expression in several other tissues. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-2718166-G-T is Pathogenic according to our data. Variant chr9-2718166-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3010.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-2718166-G-T is described in Lovd as [Pathogenic]. Variant chr9-2718166-G-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNV2NM_133497.4 linkc.427G>T p.Glu143* stop_gained Exon 1 of 2 ENST00000382082.4 NP_598004.1 Q8TDN2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNV2ENST00000382082.4 linkc.427G>T p.Glu143* stop_gained Exon 1 of 2 1 NM_133497.4 ENSP00000371514.3 Q8TDN2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000616
AC:
9
AN:
1460632
Hom.:
0
Cov.:
81
AF XY:
0.00000826
AC XY:
6
AN XY:
726508
show subpopulations
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:
0.00000720
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Cone dystrophy with supernormal rod response Pathogenic:5
Jun 07, 2020
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Mar 23, 2024
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 04, 2024
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

PVS1,PM2,PM3(strong) -

Sep 01, 2006
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Aug 23, 2021
Revvity Omics, Revvity
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Pathogenic:2
Jul 17, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Glu143*) in the KCNV2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in KCNV2 are known to be pathogenic (PMID: 16909397, 18235024). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of KCNV2-related conditions (PMID: 16909397, 31960170). ClinVar contains an entry for this variant (Variation ID: 3010). For these reasons, this variant has been classified as Pathogenic. -

May 25, 2023
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Identified in individuals with cone dystrophy with supernormal rod response in published literature (Wu et al., 2006); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31725702, 31960170, 21900228, 23105016, 32552793, 32783370, 16909397) -

KCNV2-related disorder Pathogenic:1
Apr 08, 2024
PreventionGenetics, part of Exact Sciences
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The KCNV2 c.427G>T variant is predicted to result in premature protein termination (p.Glu143*). This variant has been characterized as a founder mutation in Arabian populations and has been reported in the homozygous state in multiple individuals with retinal cone dystrophy 3B (a.k.a., cone dystrophy with supernormal rod response; CDSRR) (Wu et al. 2006. PubMed ID: 16909397; Khan et al. 2012. PubMed ID: 21900228; Abu-Safieh et al. 2013. PubMed ID: 23105016; Khan 2019. PubMed ID: 31725702; Abdelkader et al. 2020. PubMed ID: 31960170; Méjécase et al. 2020. PubMed ID: 32783370). This variant has also been reported in the presumed compound heterozygous state in an individual with a second disease-causing KCNV2 variant and has been observed to co-segregate with disease in a large family (Wu et al. 2006. PubMed ID: 16909397). This variant has not been reported in the gnomAD database, indicating this variant is rare. Nonsense variants in KCNV2 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.64
D
BayesDel_noAF
Pathogenic
0.59
CADD
Pathogenic
42
DANN
Uncertain
1.0
Eigen
Pathogenic
0.81
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.94
D
Vest4
0.59
GERP RS
4.2

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

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

Other links and lift over

dbSNP: rs104894113; hg19: chr9-2718166; API