rs199473644
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM5PP3_Moderate
The NM_000219.6(KCNE1):c.163G>C(p.Gly55Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G55S) has been classified as Likely benign.
Frequency
Consequence
NM_000219.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 16
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251428Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135910
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.10e-7 AC: 1AN: 1099244Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 557996
GnomAD4 genome Cov.: 16
ClinVar
Submissions by phenotype
not provided Uncertain:1
Has not been previously published in association with arrhythmia to our knowledge; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 17545244) -
Long QT syndrome 5 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at