ClinVar Genomic variation as it relates to human health

This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions. This sequence variant predicts a substitution of alanine with threonine at codon 4940 of the RYR1 protein, p.(Ala4940Thr). This variant was not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been identified in two unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, both of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4_Moderate (PMID:15731587, personal communication from VCEP laboratory). No functional studies were identified for this variant. This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1_Sup (PMID: 21118704). A REVEL score >0.85 (0.882) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as a Variant of Unknown Significance. Criteria implemented: PS4_Moderate, PM1_Supporting, PP3_Moderate.

This variant has been previously reported as a heterozygous change in patients with Central Core Disease (MIM: #117000; PMID: 32403337, 31321302, 30155738, 14670767), and as a compound heterozygous change in patients with congenital myopathy (PMID: 30155738, 31395954). Functional studies in cells have shown that the c.14818G>A (p.Ala4940Thr) variant significantly reduces the threshold for spontaneous Ca2+ release during store Ca2+ overload (SOICR), which causes uncontrolled muscle contraction (PMID: 28687594). It is absent from the gnomAD population database and thus is presumed to be rare. The c.14818G>A (p.Ala4940Thr) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.14818G>A (p.Ala4940Thr) variant is classified as Pathogenic.

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 4940 of the RYR1 protein (p.Ala4940Thr). This variant is present in population databases (rs118192158, gnomAD 0.0009%). This missense change has been observed in individuals with autosomal dominant central core disease (PMID: 1256913, 12467748, 14670767, 15731587, 23183335, 23558838). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 65927). 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. For these reasons, this variant has been classified as Pathogenic.

The p.Ala4940Thr variant in RYR1 has been previously reported in at least 5 heterozygous individuals with central core disease or RYR1-related myopathy, and segregated in 5 affected relatives (Kraeva 2013 PMID 23183335, Todd 2018 PMID 30155738, Kushnir 2020 PMID 32236737, Davis 2003 PMID 12565913, Quinlivan 2003 PMID 14670767). It has also been reported in at least 1 individual with malignant hyperthermia (MH) susceptibility (Brandom 2013 PMID 23558838, Sambuughin PMID 15731587) and in 1 compound heterozygous individual with myopathy (Todd 2018 PMID 30155738). This variant was absent from large population studies, but has been reported in ClinVar (Variation ID 65927). In vitro evidence in transfected HEK293 cells indicates that this variant affects protien function (Chen 2017 PMID 28687594). In addition, a transgenic C. elegan model with the Ala4940Thr variant showed increased sensitivity to halothane and caffeine and decreased locomotion (Baines 2017 PMID 28325813). Lastly, in a study performed in muscle tissue from patients carrying the Ala4940Thr variant, RYR1 was co-immunoprecipitated with calstabin1, which binds to RYR1 and stabilizes the closed state of the calcium channel. Reduced RYR1-calstabin1 was observed relative to controls, which suggests that the variant results in a leaky RYR1 calcium channel (Kushnir 2020 PMID 32236737). Computational prediction tools and conservation analyses suggest an impact to the protein. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant central core disease but has also been reported in MH susceptibility. ACMG/AMP criteria applied: PM2, PS4_Moderate, PP1_Moderate, PP3, PS3_Moderate.

ACMG categories: PM1,PM2,PP3

PS3, PS4_M, PM1, PM2, PP1, PP3, PP4

Also reported in a patient with malignant hyperthermia susceptibility (Sambuughin et al., 2005); Published functional studies using transgenic C. elegans with the A4940T variant demonstrate a damaging effect of increased sensitivity to halothane and caffeine, with decreased locomotion (Nicoll Baines et al., 2017); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 14670767, 23558838, 12565913, 20301565, 15731587, 12467748, 28325813, 25747005, 23183335, 28687594, 16084090, 1256913, 31321302, 31395954, 31559918, 32403337, 33646171)

Converted during submission to Pathogenic.