9-2729470-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_133497.4(KCNV2):c.1381G>T(p.Gly461*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,746 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_133497.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251346Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135844
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461642Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727128
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74288
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
Nonsense variant predicted to result in protein truncation, as the last 85 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD.; This variant is associated with the following publications: (PMID: 19952985) -
For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the KCNV2 protein in which other variant(s) (p.Leu469Trpfs*35) have been determined to be pathogenic (PMID: 18400204). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 1367585). This premature translational stop signal has been observed in individual(s) with retinal cone dystrophy (PMID: 19952985). This variant is present in population databases (rs149648640, gnomAD 0.009%). This sequence change creates a premature translational stop signal (p.Gly461*) in the KCNV2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 85 amino acid(s) of the KCNV2 protein. -
KCNV2-related disorder Pathogenic:1
The KCNV2 c.1381G>T variant is predicted to result in premature protein termination (p.Gly461*). This variant has been reported along with a second KCNV2 variant in an individual with cone dystrophy (Robson et al. 2009. PubMed ID: 19952985). This variant is reported in 0.0085% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/9-2729470-G-T). Nonsense variants in KCNV2 are expected to be pathogenic. Given the evidence, we interpret c.1381G>T (p.Gly461*) as likely pathogenic. -
Retinal dystrophy Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at