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 Arginine with Histidine at codon 530 of the RYR1 protein, p.(Arg530His). The maximum allele frequency for this variant among the six major gnomAD populations is AMR: 0.000145, a frequency consistent with pathogenicity for MHS. This variant has been reported in five unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, all 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:19191329, PMID:19191333, PMID:30236257, PMID:35718563). A functional study was published for this variant looking at acidification rates in B-lymphocytes, this assay is not considered a standard assay by the ClinGen RYR1 VCEP for MHS (PMID:27646467). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID:21118704). This variant segregates with MHS in 2 individuals (PMID:19191333). A REVEL score >0.85 supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Likely Pathogenic. Criteria implemented: PS4_Moderate, PM1, PP3_Moderate.

The p.Arg530His variant in RYR1 has been reported in at least 7 individuals, including 1 Turkish and 1 Swiss individual, with King-Denborough syndrome, segregated with disease in 3 affected relatives from 1 family (PMID: 19191329, 30236257, 30155738, 26578207, 19191333, 16917943), and has been identified in 0.01446% (5/34590) of Latino chromosomes, 0.006152% (1/16256) of African chromosomes, and 0.005274% (6/113770) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs111888148). Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population and individuals with this disease are clinically indistinguishable from the general population unless given anesthesia (PMID: 9199552). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a dominant frequency for a disease with clinical variability or reduced penetrance. This variant has also been reported in ClinVar as a VUS, pathogenic, and likely pathogenic variant (Variation ID: 133101). In vitro functional studies provide some evidence that the p.Arg530His variant may impact protein function and may be partially rescued by a RYR1 antagonist (PMID: 19191333). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. One additional variant, resulting in a different amino acid change at the same position, p.Arg530Leu, has been reported as a VUS in association with disease in ClinVar (Variation ID: 212096). The p.Arg530His is located in a region of RYR1 that is essential to regulating the sensitivity of a calcium channel, suggesting that this variant is in a functional domain and supports pathogenicity (PMID: 16084090). In summary, this variant meets criteria to be classified as pathogenic for King-Denborough syndrome in an autosomal dominant manner based on in vitro functional studies, population data, and multiple occurrences of affected individuals with this variant reported in the literature. ACMG/AMP Criteria applied: PS3, PM2, PS4_Moderate, PM1, PP3, PP1 (Richards 2015).

Criteria applied: PS4,PS3_SUP,PM2_SUP,PP3

Identified in the heterozygous state in association with malignant hyperthermia in published literature (PMID: 27646467, 19191333); Identified in an infant with malignant hyperthermia who harbored a second pathogenic RYR1 variant on the opposite allele (in trans) (PMID: 33625594); Published functional studies demonstrate that this variant results in altered channel function as compared to controls (PMID: 19191333, 32236737); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27147545, 33767344, 16917943, 19191329, 25637381, 30236257, 30155738, 19191333, 32236737, 34426522, 31589614, 31301762, 34849273, 33146414, 30291343, 27646467, 33625594, 26578207, 37787745)

The RYR1 c.1589G>A (p.Arg530His) variant is a missense variant that has been reported in two studies, in which it is found in a heterozygous state in a total of four individuals with malignant hyperthermia susceptibility, including three affected individuals from one family (Zullo et al. 2009; Levano et al. 2009). The p.Arg530His variant was shown to segregate with disease in the family (Zullo et al. 2009). The p.Arg530His variant was absent from 200 controls and is reported at a frequency of 0.000259 in the Latino population of the Exome Aggregation Consortium. Epstein-Barr virus immortalized B lymphocytes from an affected individual showed significantly higher extracellular acidification for the p.Arg530His variant compared to wild type (Zullo et al. 2009). Based on the evidence, the p.Arg530His variant is classified as a variant of unknown significance but suspicious for pathogenicity for malignant hyperthermia susceptibility. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The p.Arg530His variant in RYR1 has been reported in 3 individuals with malignant hyperthermia (MH) and segregated with disease in 2 affected members from 1 family (Zullo 2009 PMID: 19191333, Levano 2009 PMID: 19191329, Miller 2018 PMID: 30236257). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 133101) and has been identified in 0.005% (6/113770) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). In vitro functional studies support an impact on the protein (Zullo 2009 PMID: 19191333, Hoppe 2016 PMID: 27646467), and computational prediction tools and conservation analysis are consistent with pathogenicity. In addition, this variant is located within the intracellular calcium-release channel domain, which is enriched with pathogenic variation and is considered a critical functional domain (Tilgen 2001 PMID: 11741831). Moreover, this variant has been classified as a diagnostic mutation by the European Malignant Hyperthermia Group (EMHG; https://www.emhg.org/diagnostic-mutations). 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 MH. ACMG/AMP criteria applied: PP3, PS3_Moderate, PS4_Supporting, PM1.

Variant summary: RYR1 c.1589G>A (p.Arg530His) results in a non-conservative amino acid change located in the RIH domain (IPR000699) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 251494 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in RYR1 causing Malignant Hyperthermia Susceptibility (5.6e-05 vs 8.8e-05), allowing no conclusion about variant significance. c.1589G>A has been reported in the literature as a heterozygous/compound heterozygous genotype in individuals affected with Malignant Hyperthermia Susceptibility or Neuromuscular Disease (example, Levano_2009, Zullo_2009, Todd_2015, Miller_2018, Kushnir_2020, Herman_2021, Tsutsumi_2021). These data indicate that the variant is very likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function reporting increased acidification rate of lymphoblastoid cells and immortalized B-lymphocytes in response to 4-chloro-mcresol (4-CmC) (example, Zullo_2009, Hoppe_2016). Multiple clinical diagnostic laboratories and an expert panel (ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel) have submitted clinical-significance assessments for this variant to ClinVar after 2014 with a majority consensus as pathogenic/likely pathogenic (n=9) (VUS, n=2 to include the expert panel). Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 530 of the RYR1 protein (p.Arg530His). This variant is present in population databases (rs111888148, gnomAD 0.01%). This missense change has been observed in individuals with autosomal dominant malignant hyperthermia susceptibility (PMID: 19191329, 19191333, 30236257). It has also been observed to segregate with disease in related individuals. This variant has been reported in individual(s) with clinical features of autosomal recessive congenital myopathy (PMID: 26578207); however, the role of the variant in this condition is currently unclear. ClinVar contains an entry for this variant (Variation ID: 133101). 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 RYR1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects RYR1 function (PMID: 19191333, 27646467). For these reasons, this variant has been classified as Pathogenic.

The RYR1 c.1589G>A; p.Arg530His variant (rs111888148) is reported in the literature in multiple individuals and families affected with malignant hyperthermia (Levano 2009, Miller 2018, Mungunsukh 2019, Robinson 2006, Tsutsumi 2021, Zullo 2009). This variant is found in the general population with an overall allele frequency of 0.006% (14/251,494 alleles) in the Genome Aggregation Database. This variant occurs in the functionally important N-terminal domain, and computational analyses predict that this variant is deleterious (REVEL: 0.93). Functional assays indicate lymphoblastoid cell lines exhibit increased acidification in response to 4-chloro-m-cresol compared to cells expressing wildtype RYR1 (Zullo 2009), although this is not considered a standard assay. Based on available information, this variant is considered to be likely pathogenic. References: Levano S et al. Increasing the number of diagnostic mutations in malignant hyperthermia. Hum Mutat. 2009 Apr;30(4):590-8. PMID: 19191329. Miller DM et al. Genetic epidemiology of malignant hyperthermia in the UK. Br J Anaesth. 2018 Oct;121(4):944-952. PMID: 30236257. Mungunsukh O et al. Estimating prevalence of malignant hyperthermia susceptibility through population genomics data. Br J Anaesth. 2019 Sep;123(3):e461-e463. PMID: 31301762. Robinson R et al. Mutations in RYR1 in malignant hyperthermia and central core disease. Hum Mutat. 2006 Oct;27(10):977-89. PMID: 16917943. Tsutsumi YM et al. Malignant hyperthermia in a 16-day-old infant with congenital diaphragmatic hernia: a case report. J Anesth. 2021 Apr;35(2):311-314. PMID: 33625594. Zullo A et al. Functional characterization of ryanodine receptor (RYR1) sequence variants using a metabolic assay in immortalized B-lymphocytes. Hum Mutat. 2009 Apr;30(4):E575-90. PMID: 19191333.

The c.1589G>A (p.R530H) alteration is located in exon 15 (coding exon 15) of the RYR1 gene. This alteration results from a G to A substitution at nucleotide position 1589, causing the arginine (R) at amino acid position 530 to be replaced by a histidine (H). Based on data from gnomAD, the A allele has an overall frequency of 0.006% (14/251494) total alleles studied. The highest observed frequency was 0.016% (1/6140) of Other alleles. This variant was reported in multiple individuals, and was shown to segregate with disease in one family, with a reported malignant hyperthermia (MH) event, a positive IVCT, and/or a family history of MH (Levano, 2009; Zullo, 2009; Miller, 2018). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

RYR1: PM1, PS4:Moderate, PM5:Supporting, PS3:Supporting

The RYR1 c.1589G>A variant is predicted to result in the amino acid substitution p.Arg530His. This variant has been reported to be causative for malignant hyperthermia (MH) in two unrelated families, with functional evidence supporting pathogenicity (Zullo et al. 2009. PubMed ID: 19191333; Robinson et al. 2006. PubMed ID: 16917943). At PreventionGenetics we have observed this variant in the compound heterozygous state in two patients with congenital myopathy. This variant is reported in 0.014% of alleles in individuals of Latino descent in gnomAD. We classify this variant as likely pathogenic for both dominant and recessive RYR1-related disorders.