ClinVar Miner

Submissions for variant NM_000540.3(RYR1):c.1840C>T (p.Arg614Cys)

gnomAD frequency: 0.00011  dbSNP: rs118192172
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Total submissions: 33
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PharmGKB RCV001787388 SCV000925271 drug response desflurane response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB RCV001787389 SCV000925272 drug response enflurane response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB RCV001787390 SCV000925273 drug response halothane response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB RCV001787391 SCV000925274 drug response isoflurane response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB RCV001787392 SCV000925275 drug response methoxyflurane response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB RCV001787393 SCV000925276 drug response sevoflurane response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB RCV001787394 SCV000925277 drug response succinylcholine response - Toxicity 2021-03-24 reviewed by expert panel curation PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, ClinGen RCV000013830 SCV001816205 pathogenic Malignant hyperthermia, susceptibility to, 1 2021-03-17 reviewed by expert panel curation 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 Cysteine at codon 614 of the RYR1 protein, p.(Arg614Cys). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00019, a frequency consistent with pathogenicity for MHS. This variant has been reported in over 100 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, over 100 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:24433488, PMID:16163667, PMID:30236257, and others). This variant has been identified in an individual with negative IVCT/CHCT results, BS2_Moderate (PMID:10484775). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:26115329). This variant does not reside in a hotspot for pathogenic variants that contribute to MHS (PMID: 21118704). Another variant that has been assessed as pathogenic occurs at this codon, p.(Arg614Leu), PM5 (PMID:16917943). p.(Arg614Cys) segregates with MHS in 38 individuals PP1_Strong, (PMID:25960145, PMID:7586638, PMID:11493496 and others). A REVEL score >0.85 supports a pathogenic status for this variant, PP3_Moderate. Criteria implemented: PS3_Moderate, PS4, PM5, PP1_Strong, PP3_Moderate, BS2_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386).
Biesecker Lab/Clinical Genomics Section, National Institutes of Health RCV000013830 SCV000265688 pathogenic Malignant hyperthermia, susceptibility to, 1 2013-07-01 criteria provided, single submitter research
GeneDx RCV000119586 SCV000329611 pathogenic not provided 2021-02-15 criteria provided, single submitter clinical testing One of the most commonly identified RYR1 variants among individuals of Western European backgrounds (Rueffert et al., 2002; Kraeva et al., 2011); Published functional studies demonstrate a damaging effect, as the variant is sufficient to induce malignant hyperthermic episodes by causing impaired calcium and magnesium inhibition and reduced activation of the mutant protein at calcium concentrations typical of normal myotubes at rest (Tong et al., 1997; Yang et al., 2003); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21455645, 25637381, 7511586, 30325262, 12124989, 31206373, 24195946, 9334205, 21795085, 12732639, 11668625, 9873004, 23842196, 12059893, 1774074, 19648156, 8602662, 12411788, 29635721, 29382405, 30788618, 30499100, 30236257, 29730239, 30208288, 30611313, 31016048, 31447099, 33278783, 33259453, 31589614, 10352931, 33587123, 14500992, 11493496, 11553045, 32665702, 10756965, 25214167, 32528171)
Invitae RCV000538121 SCV000659874 pathogenic RYR1-related disorder 2024-01-24 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 614 of the RYR1 protein (p.Arg614Cys). This variant is present in population databases (rs118192172, gnomAD 0.02%). This missense change has been observed in individuals with malignant hyperthermia (PMID: 1774074, 8602662, 10352931, 11493496, 11668625, 12411788, 19648156, 21455645, 21795085, 23842196). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 12964). 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: 9334205, 11668625, 12732639). For these reasons, this variant has been classified as Pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000608635 SCV000711657 pathogenic Malignant hyperthermia of anesthesia 2019-08-07 criteria provided, single submitter clinical testing The p.Arg614Cys variant in RYR1 has been reported in >30 individuals with malignant hyperthermia, and segregated with disease in more than 6 affected relatives from more than 3 families (Gillard 1991, Hogan 1992, Serfas 1996, Fortunato 1999, Rueffert 2001, Girard 2001, Muniz 2003, Vladutiu 2011, Klingler 2014, LMM unpublished data). In vitro functional studies provide some evidence that the p.Arg614Cys variant may impact protein function (Tong 1999, 2003, Girard 2001). Animal models in pigs further support a contribution to malignant hyperthermia (Ostu 1991). This variant has been identified in 0.02% (24/126704) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Please note that for diseases with clinical variability or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. In summary, this variant meets criteria to be classified as pathogenic for malignant hyperthermia in an autosomal dominant manner. ACMG/AMP Criteria applied: PS3, PS4, PP1_Moderate.
Ambry Genetics RCV000624176 SCV000742007 pathogenic Inborn genetic diseases 2024-01-31 criteria provided, single submitter clinical testing The c.1840C>T (p.R614C) alteration is located in coding exon 17 of the RYR1 gene. This alteration results from a C to T substitution at nucleotide position 1840, causing the arginine (R) at amino acid position 614 to be replaced by a cysteine (C). Based on data from gnomAD, the T allele has an overall frequency of 0.011% (30/282862) total alleles studied. The highest observed frequency was 0.019% (25/129186) of European (non-Finnish) alleles. Multiple individuals with this alteration have been reported with MH (Rueffert, 2001A; Rueffert, 2001B; Carpenter, 2009; Gonsalves, 2013). Two siblings were described with this variant in trans with p.G215E with severe presentation of CCD with muliple arthryogyposis, severe hypotonia and amyotrophy, respiratory mechanical assistance, and multiple malformations including short femurs, facial dysmorphims, and bilateral clinodactyly of the second and fifth fingers (Romero, 2003). At 9 years of age the older child had delayed motor development, ptosis, strabismus, scoliosis and amyotrophy (Romero, 2003). The younger brother died at 32 weeks gestation with severe CCD congenital myopathy as well (Romero, 2003). Another alteration at the same codon, c.1841G>T (p.R614L), has been detected in individuals with a positive IVCT test and MH diagnosis (Barone, 1999). 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.
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine RCV000013830 SCV000840059 pathogenic Malignant hyperthermia, susceptibility to, 1 2017-10-16 criteria provided, single submitter clinical testing This c.1840C>T (p.Arg614Cys) variant in the RYR1 gene has been reported in multiple unrelated individuals with malignant hyperthermia (PMID: 1774074, 7762556, 10051009, 10484775, 19648156, 23842196, 11668625) or myopathy (PMID: 21795085). This variant has been shown to segregate with features of malignant hyperthermia in multiple families (PMID: 7762556, 7586638, 9520251). The c.796G>A variant is rare in the general population and arginine at position 614 of the RYR1 protein is highly evolutionarily conserved. The c.1840C>T (p.Arg614Cys) variant in the RYR1 gene is classified as pathogenic.
PreventionGenetics, part of Exact Sciences RCV000538121 SCV000852495 pathogenic RYR1-related disorder 2023-08-11 criteria provided, single submitter clinical testing The RYR1 c.1840C>T variant is predicted to result in the amino acid substitution p.Arg614Cys. This variant has been conclusively established to be causative for malignant hyperthermia (MH) (www.emhg.org; Gillard et al. 1991. PubMed ID: 1774074; Otsu et al. 1994. PubMed ID: 7511586; Quane et al. 1997. PubMed ID: 9389851; Tong et al. 1997. PubMed ID: 9334205; Robinson et al. 2006. PubMed ID: 16917943). Functional studies in HEK293 cells indicate this variant results in increased caffeine sensitivity and abnormal ryanodine receptor function (Referred to R615C in Murayama et al. 2015. PubMed ID: 26115329). A different substitution at the same amino acid has also been reported to be causative (p.Arg614Leu). An expert ClinGen MH panel has classified this variant as pathogenic for MH (www.ncbi.nlm.nih.gov/clinvar/variation/12964). This variant is reported in 0.019% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/19-38948185-C-T). This variant is interpreted as pathogenic. THIS PATIENT IS SUSCEPTIBLE TO MALIGNANT HYPERTHERMIA! Alternative anesthetics should be used. The patient should consider wearing an ID bracelet or other alert device (see www.mhaus.org).
CeGaT Center for Human Genetics Tuebingen RCV000119586 SCV001248783 pathogenic not provided 2024-04-01 criteria provided, single submitter clinical testing RYR1: PP1:Strong, PS3, PS4, PM5, PP3
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000013830 SCV001870378 pathogenic Malignant hyperthermia, susceptibility to, 1 2021-07-29 criteria provided, single submitter research ACMG codes:PS4M, PM2, PM5, PP3, PP5
Revvity Omics, Revvity RCV000119586 SCV002019925 pathogenic not provided 2023-12-29 criteria provided, single submitter clinical testing
AiLife Diagnostics, AiLife Diagnostics RCV000119586 SCV002503543 pathogenic not provided 2022-01-07 criteria provided, single submitter clinical testing
National Institute of Allergy and Infectious Diseases - Centralized Sequencing Program, National Institutes of Health RCV000608635 SCV002522201 pathogenic Malignant hyperthermia of anesthesia 2021-08-06 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV000013830 SCV002580672 pathogenic Malignant hyperthermia, susceptibility to, 1 2022-01-25 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002496349 SCV002805171 pathogenic Central core myopathy; Malignant hyperthermia, susceptibility to, 1; Congenital multicore myopathy with external ophthalmoplegia; Congenital myopathy with fiber type disproportion; King Denborough syndrome 2021-07-13 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000013830 SCV003921060 pathogenic Malignant hyperthermia, susceptibility to, 1 2024-03-18 criteria provided, single submitter clinical testing Criteria applied: PS4,PP1_STR,PS3_MOD,PM5,PP3,BS2_MOD
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV000013830 SCV004045836 pathogenic Malignant hyperthermia, susceptibility to, 1 2023-01-11 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000013830 SCV004357283 pathogenic Malignant hyperthermia, susceptibility to, 1 2023-01-17 criteria provided, single submitter clinical testing This missense variant replaces arginine with cysteine at codon 614 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). Functional studies in HEK293 cells and myotubes have shown cells expressing this variant have increased sensitivity to RYR1 agonists compared to cells expressing wild-type RYR1 (PMID: 9334205, 12732639, 26115329). This variant has been reported in more than 20 individuals and families affected with malignant hyperthermia susceptibility (PMID: 10352931, 11493496, 12411788, 25960145, 23842196, 24433488, 25268394, 25735680, 30236257). It has been shown that this variant segregates with disease in multiple families affected with malignant hyperthermia susceptibility (PMID: 10352931, 11493496, 12411788, 25960145). A different variant affecting the same codon, c.1841G>T (p.Arg614Leu), is considered to be disease-causing (ClinVar variation ID: 133108), suggesting that Arg at this position is important for the protein function. This variant has been described as a common variant associated with malignant hyperthermia in the Western European population (PMID: 11668625, 21455645). This variant has been identified in 30/282862 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
Molecular Genetics, Royal Melbourne Hospital RCV000013830 SCV004812677 pathogenic Malignant hyperthermia, susceptibility to, 1 2023-03-30 criteria provided, single submitter clinical testing This sequence change in RYR1 is predicted to replace arginine with cysteine at codon 614, p.(Arg614Cys). The arginine residue is highly conserved (100 vertebrates, UCSC), and is located in exon 17 in the N-terminal region, amino acids 1-552, which is defined as a mutational hotspot. There is a large physicochemical difference between arginine and cysteine. The highest population minor allele frequency in gnomAD v2.1 is 0.02% (25/129,186 alleles) in the European (non-Finnish) population. The prevalence of the variant in individuals with malignant hyperthermia susceptibility (MHS) is significantly increased compared with the prevalence in controls (Odds Ratio 51.1, 95% CI: 26.4-98.7) (PMID: 30236257; gnomAD v2.1 European non-Finnish). It has also been identified in cases with dominant and recessive central core disease, severe statin myopathy, and recurrent rhabdomyolysis (PMID: 14985404, 21795085, 29635721, 33458582). The variant has been reported to segregate with MHS in multiple families (PMID: 8602662, 11493496, 12411788). The variant demonstrates a gain of function effect on intracellular calcium release in a HEK293 assay indicating that this variant impacts protein function (PMID: 9334205). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (5/5 algorithms). Another missense variant c.1841G>T, p.(Arg614Leu) in the same codon has been classified as pathogenic for MHS (ClinVar Variation ID: 133108). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PS4, PP1_Strong, PS3_Moderate, PM1, PM5, PP3.
All of Us Research Program, National Institutes of Health RCV000013830 SCV004820755 pathogenic Malignant hyperthermia, susceptibility to, 1 2024-01-08 criteria provided, single submitter clinical testing This missense variant replaces arginine with cysteine at codon 614 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). Functional studies in HEK293 cells and myotubes have shown cells expressing this variant have increased sensitivity to RYR1 agonists compared to cells expressing wild-type RYR1 (PMID: 9334205, 12732639, 26115329). This variant has been reported in more than 20 individuals and families affected with malignant hyperthermia susceptibility (PMID: 10352931, 11493496, 12411788, 25960145, 23842196, 24433488, 25268394, 25735680, 30236257). It has been shown that this variant segregates with disease in multiple families affected with malignant hyperthermia susceptibility (PMID: 10352931, 11493496, 12411788, 25960145). A different variant affecting the same codon, c.1841G>T (p.Arg614Leu), is considered to be disease-causing (ClinVar variation ID: 133108), suggesting that Arg at this position is important for the protein function. This variant has been described as a common variant associated with malignant hyperthermia in the Western European population (PMID: 11668625, 21455645). This variant has been identified in 30/282862 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
OMIM RCV000013830 SCV000034077 risk factor Malignant hyperthermia, susceptibility to, 1 1996-04-01 no assertion criteria provided literature only
Leiden Muscular Dystrophy (RYR1) RCV000119586 SCV000154493 not provided not provided no assertion provided not provided
CSER _CC_NCGL, University of Washington RCV000013830 SCV000190544 pathogenic Malignant hyperthermia, susceptibility to, 1 2014-06-01 no assertion criteria provided research
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000119586 SCV001808836 pathogenic not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000119586 SCV001931444 pathogenic not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000119586 SCV001953020 pathogenic not provided no assertion criteria provided clinical testing

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