rs368769268
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001036.6(RYR3):āc.4507A>Gā(p.Met1503Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000379 in 1,581,338 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M1503I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001036.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR3 | NM_001036.6 | c.4507A>G | p.Met1503Val | missense_variant | 34/104 | ENST00000634891.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.4507A>G | p.Met1503Val | missense_variant | 34/104 | 1 | NM_001036.6 | P4 | |
RYR3 | ENST00000389232.9 | c.4507A>G | p.Met1503Val | missense_variant | 34/104 | 5 | A1 | ||
RYR3 | ENST00000415757.7 | c.4507A>G | p.Met1503Val | missense_variant | 34/103 | 2 | A2 | ||
RYR3 | ENST00000634418.1 | c.4507A>G | p.Met1503Val | missense_variant | 34/102 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000100 AC: 2AN: 199142Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 106874
GnomAD4 exome AF: 0.00000280 AC: 4AN: 1429130Hom.: 0 Cov.: 32 AF XY: 0.00000283 AC XY: 2AN XY: 707576
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
Epileptic encephalopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 12, 2020 | This sequence change replaces methionine with valine at codon 1503 of the RYR3 protein (p.Met1503Val). The methionine residue is highly conserved and there is a small physicochemical difference between methionine and valine. This variant is present in population databases (rs368769268, ExAC 0.007%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15"). This variant has not been reported in the literature in individuals with RYR3-related disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at