The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000540.3(RYR1):c.1589G>A (p.Arg530His)

133101 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: b2d64c99-6605-44ae-9a75-e8558a4e6604
Approved on: 2023-05-20
Published on: 2023-05-20

HGVS expressions

NM_000540.3:c.1589G>A
NM_000540.3(RYR1):c.1589G>A (p.Arg530His)

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 3
PM1 PS4_Moderate PP3_Moderate
Not Met criteria codes 3
BA1 BS1 PS3

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 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.
Met criteria codes
PM1
N-terminal hotspot
PS4_Moderate
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).
PP3_Moderate
REVEL > 0.85
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
PS3
An ex vivo functional study was published for this variant looking at acidification rates in B lymphocytes, this does not meet the criteria for PS3 which requires testing of samples from multiple unrelated individuals (PMID:27646467).
Curation History
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