Submissions for variant NM_001035.3(RYR2):c.14569A>G (p.Ile4857Val)

dbSNP: rs1085307524

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000489541	SCV000576641	uncertain significance	not provided	2017-04-24	criteria provided, single submitter	clinical testing	A variant of uncertain significance has been identified in the RYR2 gene. The I4857V variant has not been published as pathogenic or been reported as benign to our knowledge. This variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position that is conserved across species and in silico analysis suggests that this variant is probably damaging to the protein structure/function. Additionally, the I4857V variant is located in one of the three hot-spot regions of the RYR2 gene, where the majority of pathogenic missense variants occur (Medeiros-Domingo et al., 2009). However, the I4857V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV002470876	SCV002768254	pathogenic	Catecholaminergic polymorphic ventricular tachycardia 1	2022-02-02	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and gain of function are known mechanisms of disease in this gene and are associated with catecholaminergic polymorphic ventricular tachycardia 1 (CPVT; MIM#604772) (PMIDs: 12459180, 27646203, 29477366). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Penetrance for CPVT is estimated to be 60-70% (PMID: 23549275). (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to valine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (PMID: 19926015). (SP) 0704 - Another variant comparable to the one identified in this case has limited previous evidence for pathogenicity. An alternative change to an asparagine has been reported to be de novo in an individual with dilated cardiomyopathy (PMID: 31931689). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported to be de novo in three unrelated probands (GeneDx, PMID: 28191890). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1204 - Inheritance information for this variant is unknown in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Labcorp Genetics (formerly Invitae), Labcorp	RCV002470876	SCV003459348	uncertain significance	Catecholaminergic polymorphic ventricular tachycardia 1	2022-02-22	criteria provided, single submitter	clinical testing	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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RYR2 protein function. ClinVar contains an entry for this variant (Variation ID: 426248). This variant has not been reported in the literature in individuals affected with RYR2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 4857 of the RYR2 protein (p.Ile4857Val).