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 threonine with methionine at codon 2206 of the RYR1 protein, p.(Thr2206Met). The maximum allele frequency for this variant among the six major gnomAD populations is EAS: 0.00005, a frequency consistent with pathogenicity for MHS. This variant has been reported in 67 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, 63 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 (PMID: 30236257, 12059893, 24433488, 23558838, 10484775, 25735680, 25960145, 16163667, 11575529, 12220451, 12434264, 15731587, 17081152, 18505122, 22696611, 9497245, 25268394, 31559918). This variant has been identified in at least three individuals with negative IVCT/CHCT results, BS2 (PMID: 30236257). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists PS3_Moderate (PMID: 27586648). An ex vivo assay in patient derived myotubes from two related individuals showed an increased sensitivity to RYR1 agonists (PMID: 12220451). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PM5 (PMID: 21118704). Another variant that has been assessed as pathogenic occurs at this codon, p.(Thr2206Arg), PM5. This variant segregates with MHS in nine individuals, PP1_Strong (PMID: 12059893, 25960145). A REVEL score >0.85 (0.95) supports a pathogenic status for this variant, PP3_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386). Criteria implemented: PS4, PS3_Moderate, PM1_Supporting, PM5, PP1_Strong, PP3_Moderate, BS2.

The RYR1 c.6617C>T; p.Thr2206Met variant (rs118192177) is reported in the literature in several individuals affected with malignant hyperthermia and segregates with disease in families (selected references: Brandom 2013, Manning 1998, Wehner 2002). Results of caffeine challenge in patients and in vitro assessment of calcium homeostasis are consistent with malignant hyperthermia (Murayama 2016, Wehner 2002). The variant is reported as pathogenic by several sources in the ClinVar database (Variation ID: 12977) and is listed in the general population with an overall allele frequency of 0.002% (6/282,614 alleles) in the Genome Aggregation Database. The threonine at codon 2206 is highly conserved and computational analyses predict that this variant is deleterious (REVEL: 0.95). Based on available information, this variant is considered to be pathogenic. References: Brandom BW et al. Ryanodine receptor type 1 gene variants in the malignant hyperthermia-susceptible population of the United States. Anesth Analg. 2013 May;116(5):1078-86. PMID: 23558838. Manning BM et al. Identification of novel mutations in the ryanodine-receptor gene (RYR1) in malignant hyperthermia: genotype-phenotype correlation. Am J Hum Genet. 1998 Mar;62(3):599-609. PMID: 9497245. Murayama T et al. Genotype-Phenotype Correlations of Malignant Hyperthermia and Central Core Disease Mutations in the Central Region of the RYR1 Channel. Hum Mutat. 2016 Nov;37(11):1231-1241. PMID: 27586648. Wehner M et al. Increased sensitivity to 4-chloro-m-cresol and caffeine in primary myotubes from malignant hyperthermia susceptible individuals carrying the ryanodine receptor 1 Thr2206Met (C6617T) mutation. Clin Genet. 2002 Aug;62(2):135-46. PMID: 12220451.

Identified in the heterozygous state in association with malignant hyperthermia in published literature (Manning et al., 1998; Monnier et al., 2005; Ibarra et al., 2019); Identified in the heterozygous state in two siblings with myalgia and suspected rhabdomyolysis in published literature (Witting et al., 2018); Published functional studies demonstrate enhanced sensitivity to caffeine and 4-chloro-m-cresol (Wehner et al., 2002; Murayama et al., 2016); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 15448513, 27586648, 30236257, 19648156, 18505122, 11575529, 12059893, 12208234, 23558838, 16917943, 18564801, 25558065, 32552793, 32665702, 33087929, 9497245, 16163667, 31206373, 23919265, 29635721, 12220451, 30611313, 31127727, 32528171, 32419263, 31321302, 19919814, 12668474)

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 2206 of the RYR1 protein (p.Thr2206Met). This variant is present in population databases (rs118192177, gnomAD 0.003%). This missense change has been observed in individual(s) with malignant hyperthermia susceptibility and/or RYR1-related myopathy (PMID: 9497245, 12220451, 16835904, 19648156, 19919814, 23558838, 23919265, 24433488, 25960145; 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. ClinVar contains an entry for this variant (Variation ID: 12977). 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: 12220451, 16084090, 27586648). For these reasons, this variant has been classified as Pathogenic.

Variant summary: RYR1 c.6617C>T (p.Thr2206Met) 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 2e-05 in 251224 control chromosomes (gnomAD). c.6617C>T has been reported in the literature in numerous individuals affected with Malignant Hyperthermia Susceptibility and was also shown to co-segregate with disease in families (e.g. Manning_1998, Carpenter_2009, Brandom_2013, Klinger_2014). Functional studies have shown the variant to disrupt cellular calcium homeostasis (e.g. Wehner_2002). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The c.6617C>T (p.Thr2206Met) variant in the RYR1 gene has been reported in multiple unrelated individuals affected with malignant hyperthermia (PMID 9497245, 12220451, 19648156) and is extremely rare in general population databases. Multiple independent in vitro experiments showed this variant is functionally damaging (PMID 12220451, 19648156, 27586648). Multiple in silico algorithms also predicted this p.Thr2206Met change to be deleterious. Therefore, this c.6617C>T (p.Thr2206Met) variant in the RYR1 gene is classified as pathogenic.

The p.Thr2206Met variant in RYR1 has been reported in the heterozygous state in >30 individuals with malignant hyperthermia (MH) and segregated with disease in 6 relatives from 3 families (Manning 1998 PMID: 9497245, Rueffert 2002 PMID: 19919814, Carpenter 2009 PMID: 19648156, Sambuughin 2001 PMID: 11575529, Wehner 2002 PMID: 12220451, Alazami 2015 PMID: 25558065, Miller 2018 PMID: 30236257, Ibarra Moreno 2019 PMID: 31206373). It was also reported in the heterozygous state in at least 1 individual with multi-minicore myopathy and in the homozygous state in 1 individual with muscular dystrophy (Amburgey 2013 PMID: 23919265). Additionally, it has been reported by other clinical laboratories in ClinVar (Variation ID: 12977) and has been identified in 0.004% (5/129110) of European chromosomes and 0.005% (1/19446) of East Asian by gnomAD (http://gnomad.broadinstitute.org). In vitro functional studies provide some evidence that the p.Thr2206Met variant may impact RYR1 protein function (Wehner 2002 PMID: 12220451, Murayama 2016 PMID: 27586648), and computational prediction tools and conservation analysis suggest that this variant may impact the protein. This variant lies in the central region of the protein and missense variants in this region are statistically more likely to be disease-associated (Maclennan 2011 PMID: 21118704). In summary, this variant meets criteria to be classified as pathogenic for MH in an autosomal dominant manner. ACMG/AMP Criteria applied: PS4, PM1, PP1_Moderate, PM2_Supporting, PP3, PS3_Supporting.

Criteria applied: PS4,PS3_MOD,PM5,PP3,PP4

This missense variant replaces threonine with methionine at codon 2206 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). A functional study in HEK293 cells showed that cells expressing this variant are more sensitive to the RYR1 agonist caffeine than cells expressing wild-type RYR1 (PMID: 27586648). This variant has been reported in multiple individuals and families affected with malignant hyperthermia susceptibility (PMID: 30236257, 31206373), and it has been shown that this variant segregates with malignant hyperthermia susceptibility in several families (PMID: 9497245, 19919814, 25960145). This variant has been identified in 6/282614 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

The c.6617C>T (p.Thr2206Met) variant in the RYR1 gene, that encodes ryanodine receptor 1, has been identified in numerous unrelated individuals (>50) with personal or family history of a malignant hyperthermia reaction and a positive in-vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (PMID: 30236257, 12059893, 24433488, 23558838, 10484775, 25735680, 25960145, 16163667, 11575529, 12220451, 12434264, 15731587, 17081152, 18505122, 22696611, 9497245, 25268394, 31559918, ClinGen Review [ClinVar ID:12977]). This variant segregates with malignant hyperthermia syndrome (MHS) in nine individuals (PMID: 12059893, 25960145).This missense variant resides in a mutational hot spot region that contributes to MHS (PMID: 21118704). A functional study in HEK293 cells shows an increased sensitivity to RYR1 agonists (PMID: 27586648). In-silico computational prediction tools suggest that the p.Thr2206Met variant may have deleterious effect on the protein function (REVEL score: 0.95). This variant has been interpreted as pathogenic by several submitters in ClinVar database including the ClinGen expert panel (ClinVar ID: 12977). Therefore, the c.6617C>T (p.Thr2206Met) variant in the RYR1 gene is classified as pathogenic.

The c.6617C>T (p.Thr2206Met) variant in the RYR1 gene, that encodes ryanodine receptor 1, has been identified in numerous unrelated individuals (>50) with personal or family history of a malignant hyperthermia reaction and a positive in-vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (PMID: 30236257, 12059893, 24433488, 23558838, 10484775, 25735680, 25960145, 16163667, 11575529, 12220451, 12434264, 15731587, 17081152, 18505122, 22696611, 9497245, 25268394, 31559918, ClinGen Review [ClinVar ID:12977]). This variant segregates with malignant hyperthermia syndrome (MHS) in nine individuals (PMID: 12059893, 25960145).This missense variant resides in a mutational hot spot region that contributes to MHS (PMID: 21118704). A functional study in HEK293 cells shows an increased sensitivity to RYR1 agonists (PMID: 27586648). In-silico computational prediction tools suggest that the p.Thr2206Met variant may have deleterious effect on the protein function (REVEL score: 0.95). This variant has been interpreted as pathogenic by several submitters in ClinVar database including the ClinGen expert panel (ClinVar ID: 12977). Therefore, the c.6617C>T (p.Thr2206Met) variant in the RYR1 gene is classified as pathogenic.

The c.6617C>T (p.T2206M) alteration is located in exon 40 (coding exon 40) of the RYR1 gene. This alteration results from a C to T substitution at nucleotide position 6617, causing the threonine (T) at amino acid position 2206 to be replaced by a methionine (M). Based on data from gnomAD, the T allele has an overall frequency of 0.002% (6/282614) total alleles studied. The highest observed frequency was 0.005% (1/19946) of East Asian alleles. This variant was reported in multiple unrelated individuals, as well as shown to segregate with disease in two large families, with a positive in vitro contracture test (IVCT) and/or a reported malignant hyperthermia event (Manning, 1998; Wang, 2008; Brandom, 2013; Klingler, 2014; Wehner, 2002). Another alteration at the same codon, c.6617C>G (p.T2206R), has been detected in individuals with clinical features of malignant hyperthermia susceptibility (Brandt, 1999; Yeh, 2005). 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 pathogenic.

RYR1: PP1:Strong, PM5, PS4:Moderate, PP3, PS3:Supporting

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with RYR1-related disorders (OMIM). Gain of function mechanism has been described in the context of malignant hyperthermia susceptibility 1 (MIM#145600) and autosomal dominant congenital myopathy 1A with susceptibility to malignant hyperthermia (MIM#117000). Autosomal recessive congenital myopathy 1B (MIM#255320) is associated with a loss of function mechanism (PMID: 27855725, 23919265). The mechanism of King-Denborough syndrome (MIM#619542) is unclear. (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from threonine to methionine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 (v2: 6 heterozygotes, 0 homozygotes). (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: 30406384). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been identified in patients with a known positive malignant hyperthermia reaction (PMID: 31206373) and has a 3 star rating from the ClinGen MH expert panel in ClinVar. This variant has also been identified by the European Malignant Hyperthermia Group (EMHG) as causative for Malignant Hyperthermia. (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. In vitro studies demonstrated increased sensitivity to 4-chloro-m-cresol and caffeine (PMID: 12220451). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign