rs111888148

chr19-38455463-G-Achr19-38455463-G-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM5 PP2 PP3_Moderate PP5_Very_Strong

The NM_000540.3(RYR1):c.1589G>A(p.Arg530His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,974 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. R530C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000029 (0 hom.)
• Consequence: RYR1 NM_000540.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:15 U:1 O:1
• Conservation: PhyloP100: 8.03

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
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr19-38455462-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1500771.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP2: Missense variant where missense usually causes diseases, RYR1
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.893
• PP5: Variant 19-38455463-G-A is Pathogenic according to our data. Variant chr19-38455463-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 133101.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr19-38455463-G-A is described in Lovd as [Pathogenic]. Variant chr19-38455463-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR1	NM_000540.3	c.1589G>A	p.Arg530His	missense_variant	15/106	ENST00000359596.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR1	ENST00000359596.8	c.1589G>A	p.Arg530His	missense_variant	15/106	5	NM_000540.3	A2
RYR1	ENST00000355481.8	c.1589G>A	p.Arg530His	missense_variant	15/105	1		P4
RYR1	ENST00000599547.6	c.1589G>A	p.Arg530His	missense_variant, NMD_transcript_variant	15/80	2

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 152082 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

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: 0.0000735

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000557 AC: 14 AN: 251494 Hom.: 0 AF XY: 0.0000368 AC XY: 5 AN XY: 135922

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000527

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.0000287 AC: 42 AN: 1461892 Hom.: 0 Cov.: 55 AF XY: 0.0000275 AC XY: 20 AN XY: 727248

Gnomad4 AFR exome AF: 0.0000896

Gnomad4 AMR exome AF: 0.000112

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.0000261

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000329 AC: 5 AN: 152082 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74296

Gnomad4 AFR AF: 0.00

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: 0.0000735

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000852 Hom.: 0

Bravo AF: 0.0000680

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000659 AC: 8

EpiCase AF: 0.000109

EpiControl AF: 0.00

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:15 Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:7 Other:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Oct 05, 2021	- -
not provided, no classification provided	literature only	Leiden Muscular Dystrophy (RYR1)	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2023	RYR1: PM1, PS4:Moderate, PM5:Supporting, PS3:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Dec 21, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 17, 2023	Identified in an infant with malignant hyperthermia who harbored a second pathogenic RYR1 variant on the opposite allele (in trans) (Tsutsumi et al., 2021); Published functional studies demonstrate that this variant results in higher activity and increased acidification rate compared to controls (Zullo et al., 2009); 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, 33625594, 26578207, 27646467) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jul 28, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Dec 14, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 23, 2023	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. -

Malignant hyperthermia, susceptibility to, 1 Pathogenic:4 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jul 12, 2023	Criteria applied: PS4,PS3_SUP,PM2_SUP,PP3 -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Oct 26, 2018	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. -
Pathogenic, no assertion criteria provided	research	CSER _CC_NCGL, University of Washington	Jun 01, 2014	- -
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 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 30, 2023	- -

Malignant hyperthermia of anesthesia Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2020	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 07, 2022	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. -

RYR1-Related Disorders Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 18, 2023

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. -

King Denborough syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

curation

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Jan 29, 2020

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). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.52
Cadd	Pathogenic	29
Dann	Uncertain	1.0
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.97	D;D
M_CAP	Pathogenic	0.73	D
MetaRNN	Pathogenic	0.89	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.8	M;M
MutationTaster	Benign	0.99	D;D;D
PrimateAI	Uncertain	0.73	T
PROVEAN	Uncertain	-4.2	D;D
REVEL	Pathogenic	0.93
Sift	Uncertain	0.0010	D;D
Polyphen		1.0	D;D
Vest4		0.68
MVP		1.0
MPC		1.1
ClinPred		0.92	D
GERP RS		4.0
Varity_R		0.58
gMVP		0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs111888148; hg19: chr19-38946103;