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
Consequence
NM_133497.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460632Hom.: 0 Cov.: 81 AF XY: 0.00000826 AC XY: 6AN XY: 726508
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Cone dystrophy with supernormal rod response Pathogenic:5
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PVS1,PM2,PM3(strong) -
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not provided Pathogenic:2
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. -
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
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at