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 valine with isoleucine at codon 2280 of the RYR1 protein, p.(Val2280Ile). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.000035, a frequency consistent with pathogenicity for MHS. This variant has been reported in three unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, two 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:30864471, PMID:30236257; MHIU Toronto - MH proband CGS 45). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:36208971). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704). A REVEL score of 0.641 supports neither a pathogenic nor a benign status for this variant. This variant has been classified as a Likely Pathogenic. Criteria implemented: PS3_Moderate, PS4_Moderate, PM1.

Variant summary: RYR1 c.6838G>A (p.Val2280Ile) results in a conservative amino acid change located in the RIH domain (IPR000699) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.4e-05 in 250004 control chromosomes. c.6838G>A has been reported in the literature in multiple individuals affected with Malignant Hyperthermia Susceptibility supported by a diagnostic in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (example, Galli_2002, Scalco_2016, Oberg_2016, Knulman_2019, Hudig_2019, Sadhasivam_2019, White_2022). Of these, in one report of families with this variant, eight transmissions of the variant allele and 2 transmissions of the reference allele to affected Malignant Hyperthermia Susceptible individuals was reported (White_2022). This study included this variant among RYR-1 disease causing variants for diagnostic use managed by the European Malignant Hyperthermia Group. These data indicate that the variant is very likely to be associated with disease. One publication reports experimental evidence evaluating an impact on protein function, demonstrating hypersensitivity to an RyR1 agonist in calcium release assays (White_2022). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters to include the ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, reported the variant with conflicting assessments (VUS, n=6; LP, n=2). Based on the evidence outlined above, the variant was classified as likely pathogenic.

Reported in one family affected with malignant hyperthermia; however, familial segregation information was not provided (PMID: 30236257); Reported in two unrelated individuals and multiple affected individuals within one family with malignant hyperthermia susceptibility; however, this variant did not segregate with all affected individuals in this family (PMID: 36208971, 12208234, 30864471); Reported in two unrelated individuals with rhabdomyolysis; one individual was also affected with muscle cramps and elevated CK levels (PMID: 27431030, 30788618); Reported in a patient with muscle weakness and cramps, chronically elevated CK, heat intolerance, and an episode of hyperthermia and leg stiffness who inherited the variant from their mother with a history of multiple uncomplicated general anesthetics (PMID: 31559918); Published functional studies suggest this variant leads to hypersensitivity of the RYR1 channel (PMID: 36208971); In silico analysis supports that this missense variant does not alter protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 16835904, 16115682, 12208234, 27431030, 20301325, 12668474, 33767344, 36208971, 31559918, 30864471, 28007021, 30788618, 30236257)

The c.6838G>A variant, located on the exon 42 of the RYR1 gene, replaces valine with isoleucine at codon 2280 of the RYR1 protein (p.Val2280Ile). This missense change has been observed in three individuals with personal or family histories of malignant hyperthermia syndrome (MHS), with positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) (PMID: 12208234, 30236257, 30864471). This missense variant is located in a mutational hotspot region that is known to contribute to MHS (PMID: 21118704). A functional study in HEK293 cells showed increased sensitivity to RYR1 agonists (PMID: 36208971). Computational prediction (REVEL score 0.641) suggests that this variant may not have deleterious impact on protein structure and function. This variant has been classified as likely pathogenic by the expert panel in ClinVar (ID:133172). This variant is rare (6/250004 chromosomes) in the general population database, gnomAD. For these reasons, the c.6838G>A (p.Val2280Ile) variant in the RYR1 gene is classified as likely pathogenic.

This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 2280 of the RYR1 protein (p.Val2280Ile). This variant is present in population databases (rs193922797, gnomAD 0.004%). This missense change has been observed in individual(s) with clinical features of autosomal dominant RYR1-related conditions and/or malignant hyperthermia susceptibility (PMID: 12208234, 30236257, 30788618, 31559918, 36208971; internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 133172). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt RYR1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects RYR1 function (PMID: 36208971). For these reasons, this variant has been classified as Pathogenic.

PS3_mod, PS4_mod, PM1_mod

Criteria applied: PS3_MOD,PS4_MOD,PM1

The c.6838G>A (p.V2280I) alteration is located in exon 42 (coding exon 42) of the RYR1 gene. This alteration results from a G to A substitution at nucleotide position 6838, causing the valine (V) at amino acid position 2280 to be replaced by an isoleucine (I). Based on data from gnomAD, the A allele has an overall frequency of 0.002% (6/250004) total alleles studied. The highest observed frequency was 0.005% (1/21596) of European (Finnish) alleles. This variant was reported in individuals with features consistent with malignant hyperthermia susceptibility (Galli, 2002; Hudig, 2019). This amino acid position is well conserved in available vertebrate species. Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists (White, 2022). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

This missense variant replaces valine with isoleucine at codon 2280 of the RYR1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function. Although functional studies have not been reported for this variant, it occurs in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to malignant hyperthermia susceptibility (PMID: 21118704). This variant has been reported in at least 4 families or individuals affected with malignant hyperthermia susceptibility (PMID: 16835904, 30236257, 30864471, 36208971, 36208971, ClinVar: SCV001810122.1). It has been shown that this variant segregates with malignant hyperthermia susceptibility in 8 individuals of 1 family (PMID: 36208971). This variant has been identified in 6/250004 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

The RYR1 c.12878C>T (p.Ala4293Val) variant, to our knowledge, has not been reported in the medical literature but has been reported in the ClinVar database as a germline variant of uncertain significance by three submitters. This variant is only observed on 23/994,358 alleles in the general population (gnomAD v.4.1.0), indicating it is not a common variant. Computational predictors suggest that the variant does not impact ryanodine receptor function. Due to limited information, the ClinGen Malignant Hyperthermia Susceptibility Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RYR1 Version 2 (https://cspec.genome.network/cspec/ui/svi/doc/GN012), the clinical significance of this variant is uncertain at this time.The RYR1 c.6838G>A (p.Val2280Ile) variant has been reported in at least five unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, and at least two of these individuals had a positive in vitro contracture test or caffeine halothane contracture test result (Galli L et al., PMID: 16835904; Galli L et al., PMID: 12208234; Hudig K et al., PMID: 30864471; Kushnir A et al., PMID: 32236737; Miller DM et al., PMID: 30236257; Scalco RS et al., PMID: 27431030; White R et al., PMID: 36208971). This variant has been reported in the ClinVar database as a germline likely pathogenic variant by an expert panel. This variant is only observed on 99/1,613,396 alleles in the general population (gnomAD v.4.1.0), indicating it is not a common variant. This variant resides within a region, amino acids 2101-2458, of RYR1 that is defined as a critical functional domain (https://cspec.genome.network/cspec/ui/svi/doc/GN012). Computational predictors suggest that the variant does not impact ryanodine receptor function; however, functional studies in cell culture show an increased sensitivity to ryanodine receptor agonists (White R et al., PMID: 36208971). Based on available information and the ClinGen Malignant Hyperthermia Susceptibility Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RYR1 Version 2 (https://cspec.genome.network/cspec/ui/svi/doc/GN012), this variant is classified as likely pathogenic.

RYR1: PM1, PS3:Moderate, PS4:Moderate, PM2:Supporting

The RYR1 c.6838G>A variant is predicted to result in the amino acid substitution p.Val2280Ile. This variant has been reported in individuals with autosomal dominant RYR1-related disorders, including multiple individuals with malignant hyperthermia (MH) susceptibility confirmed via in vitro contracture testing (IVCT; see, for example, Galli et al. 2002. PubMed ID: 12208234; Scalco et al. 2016. PubMed ID: 27431030; Hudig et al. 2019. PubMed ID: 30864471). It segregated with disease in eight MH-susceptible individuals from one family, although two additional family members who were negative for this variant were also MH-susceptible (White et al. 2022. PubMed ID: 36208971). While this variant has only been reported in the literature in relation to autosomal dominant conditions, at PreventionGenetics, it has been observed with a second RYR1 variant in individuals being tested for autosomal recessive myopathy (Internal Data). In vitro experimental studies indicate this variant impacts protein function (White et al. 2022. PubMed ID: 36208971). It is reported in 0.0046% of alleles in individuals of European (Finnish) descent in gnomAD and has been classified as likely pathogenic by the ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/133172/). This variant occurs in a region of the gene considered to be a hotspot for MH or central core disease (Witherspoon and Meilleur. 2016. PubMed ID: 27855725). This variant is interpreted as likely pathogenic.

This test identified one heterozygous variant (c.6838G>A;p.Val2280Ile) in the RYR1 gene (see Table IIIA). Variants in this gene have been associated with increased risk of malignant hyperthermia (autosomal dominant) and different types of congenital myopathies - central core disease (autosomal dominant or autosomal recessive), multiminicore disease (autosomal recessive), congenital fiber type disproportion (autosomal dominant or autosomal recessive). The RYR1 gene encodes for calcium channels that play a critical role in the movement of skeletal muscles. Risk for malignant hyperthermia is predominantly associated with the use of general anesthesia with specific anesthetics, which can trigger an episode (hypermetabolism, rhabdomyolysis, hyperkalaemia, cardiac arrhythmia). A very small number of individuals with malignant hyperthermia susceptibility appear to be at risk for heat stroke or exercise-induced rhabdomyolysis,). Malignant hyperthermia has been reported to occur in individuals without anesthetic exposure. If an episode is untreated, it can be life threatening. Alternative anesthetic treatments are available for known individuals susceptible to malignant hyperthermia. This variant has been reported in a family susceptible to malignant hyperthermia based on biochemical testing (Galli et al 2002,PMID: 12208234; Galli et al. 2006, PMID: 16835904), and computational evidence is also suggestive of this variant being a pathogenic variant.