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 proline with leucine at codon 4973 of the RYR1 protein, p.(Pro4973Leu). The maximum allele frequency for this variant among the six major gnomAD populations is AMR: 0.0000870, 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: 30236257, 16163667, 20681998). This variant segregates with MHS in 3 individuals, PP1 (PMID: 30236257). A functional study assessing store overload-induced calcium release was published for this variant and showed a reduced threshold for spontaneous calcium release compared to the wild type protein. This assay is not considered a standard assay by the ClinGen RYR1 VCEP for MHS (PMID: 28687594). 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 (0.898) supports a pathogenic status for this variant, PP3_Moderate. Based on using Bayes to combine criteria this variant is assessed as Likely Pathogenic, (PMID: 29300386). Criteria implemented: PS4_Moderate, PM1_Supporting, PP1, PP3_Moderate.

This variant is interpreted as a Likely Pathogenic, for Malignant hyperthermia 1, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PMID:12411788) (PMID:12208234). PM2 => Present in ExAC with allele frequency compatible with incidence of malignant hyperthermia in the general population. PS3 => Well-established functional studies show a deleterious effect (PMID:28687594).

This c.14918C>T (p.Pro4973Leu) variant in the RYR1 gene has been reported in multiple individuals with susceptibility to malignant hyperthermia and segregates with disease in several families (PMID 12208234, 12411788, 23558838). This variant was also reported in trans with another pathogenic RYR1 variant in one individual affected with centronuclear myopathy (PMID 25957634). In silico analyses of this conserved variant predict damaging consequences on the RYR1 protein. Therefore, this c.14918C>T (p.Pro4973Leu) variant in the RYR1 gene is classified as likely pathogenic.

PM2, PM3, PP2, PP3, PP5

Variant summary: RYR1 c.14918C>T (p.Pro4973Leu) results in a non-conservative amino acid change located in the Ryanodine/Inositol 1,4,5-trisphosphate receptor (IPR015925) 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 2.8e-05 in 251392 control chromosomes. c.14918C>T has been reported in the literature in multiple individuals affected with Malignant Hyperthermia Susceptibility or Equivalent (Galli_2002, Monnier_2002, Monnier_2005, Tammaro_2011, Miller_2018). The variant was observed to segregate with Malignant Hyperthermia in several families (Galli2002, Monnier 2002), however one affected individual also carried a second variant in CACNA1S, segregating in two affected relatives without this variant (Monnier 2002). At least one publication reports experimental evidence evaluating an impact on protein function indicating that the variant results in reduced threshold for store overload-induced Ca2+ release (Chen_2008). The following publications have been ascertained in the context of this evaluation (PMID: 23558838, 28687594, 12208234, 30236257, 12411788, 16163667, 20681998). Multiple clinical diagnostic laboratories and a ClinGen expert panel have submitted clinical-significance assessments for this variant to ClinVar after 2014 citing overlapping evidence utilized in the context of this evaluation and classified the variant as Pathogenic/likely pathogenic (n=15) and VUS (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 4973 of the RYR1 protein (p.Pro4973Leu). This variant is present in population databases (rs146876145, gnomAD 0.009%). This missense change has been observed in individual(s) with autosomal dominant malignant hyperthermia susceptibility and/or autosomal recessive RYR1-related myopathy (PMID: 12411788, 25957634, 29169929, 30236257). 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: 133098). 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: 28687594). For these reasons, this variant has been classified as Pathogenic.

Reported in individuals in multiple unrelated families who were either malignant hyperthermia susceptible or equivocal by contracture testing (PMID: 12208234, 12411788, 16163667, 30236257); Observed with a variant on the opposite allele (in trans) in a patient with arthrogryposis multiplex congenita in published literature (PMID: 29169929); Found to be on the same chromsome (in cis) as another RYR1 variant and in trans with a third RYR1 variant in an individual with centronuclear myopathy (PMID: 25957634); Published functional studies demonstrate this variant reduces the threshold for store overload-induced calcium release (PMID: 28687594); Not observed at significant frequency in large population cohorts (gnomAD); 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: 23558838, 20681998, 28008009, 30236257, 25637381, 12411788, 16163667, 33087929, 31447099, 32528171, 34008892, 34904211, 35428369, 37919205, 35980353, 28687594, 12208234, 33767344, 25957634, 29169929, 35414440, 37510298)

The c.14918C>T (p.P4973L) alteration is located in exon 104 (coding exon 104) of the RYR1 gene. This alteration results from a C to T substitution at nucleotide position 14918, causing the proline (P) at amino acid position 4973 to be replaced by a leucine (L). Based on data from gnomAD, the T allele has an overall frequency of 0.003% (7/251392) total alleles studied. The highest observed frequency was 0.009% (3/34586) of Latino alleles. This variant was reported in multiple individuals and families with a clinical reaction suggestive of malignant hyperthermia (MH), MH susceptibility confirmed by IVCT, and/or a family member with one or both of these clinical findings (Galli, 2002; Monnier, 2002; Miller, 2018; Andrade, 2022). 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.

This missense variant replaces proline with leucine at codon 4973 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 have shown this variant reduces the threshold for store overload-induced Ca2+ release after exposure to caffeine, compared to cells expressing wild-type RYR1 (PMID: 28687594). This variant has been reported in 6 families and individuals affected with malignant hyperthermia susceptibility (PMID: 12208234, 12411788, 12411788, 16163667, 23558838, 30236257, 34904211). It has been shown that this variant segregates with malignant hyperthermia susceptibility in two families (PMID: 12208234, 12411788). This variant has been identified in 7/251392 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

This sequence change is predicted to replace proline with leucine at codon 4973 of the RYR1 protein (p.(Pro4973Leu)). The proline residue is highly conserved (100 vertebrates, UCSC), and is located in exon 104 in the RYR1 channel and activation core. There is a moderate physicochemical difference between proline and leucine. The variant is present in a large population cohort at a frequency of 0.003% (rs146876145, 7/251,392 alleles, 0 homozygotes in gnomAD v2.1). The prevalence of the variant in individuals with malignant hyperthermia susceptibility (MHS) is significantly increased compared with the prevalence in the population (PMID: 30236257). It has been identified in multiple individuals with a clinical reaction consistent with malignant hyperthermia (MH) under anaesthesia confirmed by positive in vitro contracture test, and segregates with MH susceptibility in multiple families (PMID: 12208234, 12411788, 30236257). The variant demonstrates a gain of function effect on intracellular calcium release in well-established in vitro functional studies (PMID: 28687594). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (5/5 algorithms). Based on the classification scheme RMH Modified ACMG Guidelines v1.3.2, this variant is classified as PATHOGENIC. Following criteria are met: PS3, PS4, PP1, PP3, PP4.

The p.Pro4973Leu variant in RYR1 has been reported in 4 heterozygous individuals with malignant hyperthermia susceptible or equivalent, 1 compound heterozygous individual with centronuclear myopathy, and 1 compound heterozygous individual with arthrogryposis multiplex congenita (Galli 2002 PMID: 12208234, Monnier 2002 PMID: 12411788, Monnier 2005 PMID: 16163667, Robinson 2006 PMID: 16917943, Carpenter 2009 PMID: 19825159, Brandom 2013 PMID: 23558838, Fattori 2015 PMID: 25957634, Brackmann 2018 PMID: 29169929, Miller 2018 PMID: 30236257). The variant segregated with disease in at least four affected relatives from at least two families, although one affected relative also carried a second variant, p.Arg1086His in CACNA1S, that segregated in two affected relatives without the p.Pro4973Leu variant in RYR1 (Galli 2002 PMID: 12208234, Monnier 2002 PMID: 12411788). This variant has been reported in ClinVar (Variation ID 133098). The p.Pro4973Leu variant has also been identified in 0.009% (3/34586) of Latino chromosomes by gnomAD (http://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis suggest that the p.Pro4973Leu variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies assaying store overload-induced Ca2+ release (SOICR) from inducible expression of the RYR1 protein with the p.Pro4973Leu substitution in HEK293 cells support that the variant may impact protein function (Chen 2017 PMID: 28687594). Furthermore, this variant is located within one of the RYR1 regions that are considered critical functional domains. 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 malignant hyperthermia. ACMG/AMP criteria applied: PM2_Supporting, PP1, PP3, PS3_Supporting, PS4_Supporting, PM1.

RYR1: PM1, PP1, PP3, PS3:Supporting, PS4:Supporting

The RYR1 c.14918C>T variant is predicted to result in the amino acid substitution p.Pro4973Leu. The c.14918C>T variant has been reported to be causative for malignant hyperthermia (MH) in several different families (Galli et al. 2002. PubMed ID: 12208234; Monnier et al. 2002. PubMed ID: 12411788; Tammaro et al. 2011. PubMed ID: 20681998; Brandom et al. 2013. PubMed ID: 23558838; Miller et al. 2018. PubMed ID: 30236257). In all of the families where it was examined, the c.14918C>T variant segregated with abnormal in vitro muscle contraction. This variant has also been reported in the compound heterozygous state in individuals with autosomal recessive RYR1-related myopathy (Fattori F et al 2015. PubMed ID: 25957634; Brackmann F et al 2017. PubMed ID: 29169929). Miller et al. reported that this variant was significantly more frequent in cases than controls.  In a model system functional study, it was reported that this variant resulted in a reduced threshold for Ca++ release (Chen et al. 2017. PubMed ID: 28687594).  This variant is reported in 0.0087% of alleles in individuals of Latino descent in gnomAD. This variant has been interpreted by the ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel as likely pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/133098/). This variant is interpreted as likely pathogenic. This patient is susceptible to malignant hyperthermia!  Alternative anesthetics should be carefully considered.  The patient should consider wearing an ID-bracelet or other medical alert (see www.mhaus.org).

Variant interpretted as Likely pathogenic and reported on 10-03-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.