rs146876145

chr19-38586140-C-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PP2 PP3_Strong PP5_Very_Strong

The NM_000540.3(RYR1):c.14918C>T(p.Pro4973Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P4973S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000027 (0 hom.)
• Consequence: RYR1 NM_000540.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:19 O:2
• Conservation: PhyloP100: 7.75

Genes affected

RYR1 (HGNC:10483): (ryanodine receptor 1) This gene encodes a ryanodine receptor found in skeletal muscle. The encoded protein functions as a calcium release channel in the sarcoplasmic reticulum but also serves to connect the sarcoplasmic reticulum and transverse tubule. Mutations in this gene are associated with malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000540.3
• PP2: Missense variant where missense usually causes diseases, RYR1
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.94
• PP5: Variant 19-38586140-C-T is Pathogenic according to our data. Variant chr19-38586140-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 133098.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr19-38586140-C-T is described in Lovd as [Pathogenic]. Variant chr19-38586140-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR1	NM_000540.3	c.14918C>T	p.Pro4973Leu	missense_variant	104/106	ENST00000359596.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR1	ENST00000359596.8	c.14918C>T	p.Pro4973Leu	missense_variant	104/106	5	NM_000540.3	A2

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 152104 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000278 AC: 7 AN: 251392 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135904

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000867

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000274 AC: 40 AN: 1461872 Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21 AN XY: 727240

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000671

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000288

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152104 Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2 AN XY: 74284

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000387 Hom.: 0

Bravo AF: 0.0000189

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.0000412 AC: 5

EpiCase AF: 0.000109

EpiControl AF: 0.0000593

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:19 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:6 Other:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 19, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 11, 2023	Reported in individuals in multiple unrelated families who were either malignant hyperthermia susceptible or equivocal by contracture testing (Galli et al., 2002; Monnier et al., 2002; Monnier et al., 2005 [using incorrect nomenclature]; Miller et al., 2018); Observed with a variant on the opposite allele (in trans) in a patient with arthrogryposis multiplex congenita in published literature (Brackmann et al., 2018); 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 (Fattori et al., 2015); Published functional studies demonstrate this variant reduces the threshold for store overload-induced calcium release (Chen et al., 2017); 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, 25957634, 12411788, 16163667, 31447099, 12208234, 29169929, 33087929, 32528171, 34008892, 34904211, 35414440, 35980353, 35428369, 37510298, 33767344, 28687594) -
not provided, no classification provided	literature only	Leiden Muscular Dystrophy (RYR1)	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Sep 25, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2022	RYR1: PM1, PP1, PP3, PS3:Supporting, PS4:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Feb 21, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 26, 2019	- -

Malignant hyperthermia, susceptibility to, 1 Pathogenic:6

Likely pathogenic, no assertion criteria provided	research	CSER _CC_NCGL, University of Washington	Jun 01, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 18, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 01, 2021	- -
Likely pathogenic, reviewed by expert panel	curation	ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, ClinGen	May 20, 2023	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. -
Likely pathogenic, criteria provided, single submitter	curation	SIB Swiss Institute of Bioinformatics	May 31, 2018	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). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Oct 10, 2018	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. -

Malignant hyperthermia of anesthesia Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Mar 30, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 08, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Sep 06, 2019	- -

Central core myopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Oct 01, 2021

PM2, PM3, PP2, PP3, PP5 -

RYR1-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 05, 2023

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. -

Congenital myopathy with fiber type disproportion;C0751951:Central core myopathy;C1840365:King Denborough syndrome;C1850674:Congenital multicore myopathy with external ophthalmoplegia;C2930980:Malignant hyperthermia, susceptibility to, 1 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Mar 01, 2022

- -

Central core myopathy;C1850674:Congenital multicore myopathy with external ophthalmoplegia;C2930980:Malignant hyperthermia, susceptibility to, 1 Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.79
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.49
Cadd	Benign	21
Dann	Benign	0.80
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.48
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	1.0	D;D
M_CAP	Pathogenic	0.57	D
MetaRNN	Pathogenic	0.94	D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Pathogenic	-8.3	D;D
REVEL	Pathogenic	0.90
Sift	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.69
MVP		0.99
MPC		0.58
ClinPred		0.90	D
GERP RS		4.2
Varity_R		0.75
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs146876145; hg19: chr19-39076780; COSMIC: COSV62112669; COSMIC: COSV62112669;