The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000540.3(RYR1):c.7373G>A (p.Arg2458His)

CA024787

12972 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 3778fd48-227a-4d54-b8c6-095bf4d41315

HGVS expressions

NM_000540.3:c.7373G>A
NM_000540.3(RYR1):c.7373G>A (p.Arg2458His)
NC_000019.10:g.38500655G>A
CM000681.2:g.38500655G>A
NC_000019.9:g.38991295G>A
CM000681.1:g.38991295G>A
NC_000019.8:g.43683135G>A
NG_008866.1:g.71956G>A
ENST00000359596.8:c.7373G>A
ENST00000355481.8:c.7373G>A
ENST00000359596.7:n.7373G>A
ENST00000360985.7:c.7370G>A
ENST00000594335.5:n.825G>A
NM_000540.2:c.7373G>A
NM_001042723.1:c.7373G>A
NM_001042723.2:c.7373G>A

Pathogenic

Met criteria codes 5
PP1_Strong PS3_Moderate PP3_Moderate PS4 PM1
Not Met criteria codes 2
BA1 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Malignant Hyperthermia Susceptibility VCEP
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 2458 of the RYR1 protein, p.(Arg2458His). The maximum allele frequency for this variant among the six major gnomAD populations is EAS: 0.000054, a frequency consistent with pathogenicity for MHS. This variant has been reported in 26 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, 23 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, 16163667, 22415532, 9450902, 16732084, 21157159 and others). This variant segregates with MHS in 10 individuals, PP1_Strong (PMID:30236257). Functional studies in HEK293 cells and dyspedic myotubes show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:27586648, 12732639). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704). A REVEL score >0.85 (0.959) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Pathogenic. Criteria implemented: PS3_Moderate, PS4, PM1, PP1_Strong, PP3_Moderate.
Met criteria codes
PP1_Strong
This variant segregates with MHS in 10 individuals, PP1_Strong (PMID:30236257).
PS3_Moderate
Functional studies in HEK293 cells and dyspedic myotubes show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:27586648, 12732639).
PP3_Moderate
A REVEL score >0.85 (0.959) supports a pathogenic status for this variant, PP3_Moderate.
PS4
This variant has been reported in 26 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, 23 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, 16163667, 22415532, 9450902, 16732084, 21157159 and others).
PM1
This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-01-04
Published on: 2022-01-04
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