Submissions for variant NM_000540.3(RYR1):c.14537C>T (p.Ala4846Val)

dbSNP: rs118192143

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV001390401	SCV001592125	pathogenic	RYR1-related disorder	2023-08-27	criteria provided, single submitter	clinical testing	ClinVar contains an entry for this variant (Variation ID: 65925). For these reasons, this variant has been classified as Pathogenic. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on RYR1 protein function. This missense change has been observed in individual(s) with autosomal recessive congenital myopathy (PMID: 17226826, 24950660, 30611313; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant has been reported in individual(s) with autosomal dominant centronuclear myopathy (PMID: 17204054); however, the role of the variant in this condition is currently unclear. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 4846 of the RYR1 protein (p.Ala4846Val).
GeneDx	RCV000119525	SCV003842466	likely pathogenic	not provided	2023-03-01	criteria provided, single submitter	clinical testing	Observed with additional RYR1 variants on the opposite allele (in trans) in an adult with mild dusty core and central core disease, and reduced RYR1 protein level via western blot (Garibaldi et al., 2019); Identified in a child with congenital myopathy who was also found to harbor the Y3933C and R3366H RYR1 variants commonly reported on the same allele (in cis); however parental testing was not performed therefore it is unknown whether all variants occurred in cis or on the opposite allele (in trans) (Rocha et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 17204054, 17226826, 25958340, 30611313, 33458582, 24950660, 28269792, 35627144, 20681998)
GeneReviews	RCV000056172	SCV000087260	pathologic	Central core myopathy	2010-05-11	no assertion criteria provided	curation	Converted during submission to Pathogenic.
Leiden Muscular Dystrophy (RYR1)	RCV000119525	SCV000154432	not provided	not provided		no assertion provided	not provided
All of Us Research Program, National Institutes of Health	RCV003996484	SCV004831608	uncertain significance	Malignant hyperthermia, susceptibility to, 1	2023-12-18	flagged submission	clinical testing	This missense variant replaces alanine with valine at codon 4846 of the RYR1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with autosomal dominant malignant hyperthermia in the literature, although it is associated with autosomal recessive myopathy (ClinVar variation ID: 65925). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Due to insufficient evidence, this variant is classified as a Variant of Uncertain Significance for autosomal dominant malignant hyperthermia.