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Variant: NM_000540.3(RYR1):c.1598G>A (p.Arg533His)

CA024295

133103 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 8d6a1e52-fcc8-400e-90ae-63b202839f92

HGVS expressions

NM_000540.3:c.1598G>A
NM_000540.3(RYR1):c.1598G>A (p.Arg533His)
NC_000019.10:g.38455472G>A
CM000681.2:g.38455472G>A
NC_000019.9:g.38946112G>A
CM000681.1:g.38946112G>A
NC_000019.8:g.43637952G>A
NG_008866.1:g.26773G>A
ENST00000599547.6:n.1598G>A
ENST00000359596.8:c.1598G>A
ENST00000355481.8:c.1598G>A
ENST00000359596.7:n.1598G>A
ENST00000360985.7:c.1598G>A
NM_000540.2:c.1598G>A
NM_001042723.1:c.1598G>A
NM_001042723.2:c.1598G>A

Uncertain Significance

Met criteria codes 2
PM1 PS3_Moderate
Not Met criteria codes 5
PS4 BP4 BA1 PP3 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 533 of the RYR1 protein, p.(Arg533His). The maximum allele frequency for this variant among the six major gnomAD populations is AFR: 0.00044, a frequency consistent with pathogenicity for MHS. This variant has been reported in 3 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, 2 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), (PMID:30236257, PMID:16732084). However, the high MAF in the AFR population in gnomAD precludes the use of PS4. Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate, (PMID:23459219). 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 of 0.824 supports neither a pathogenic nor a benign status for this variant. This variant has been classified as a Variant of Unknown Significance. Criteria implemented: PS3_Moderate, PM1.
Met criteria codes
PM1
This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704).
PS3_Moderate
Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate, (PMID:23459219).
Not Met criteria codes
PS4
This variant has been reported in three unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, two 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), (PMID:30236257, PMID:16732084). However, the high MAF in the AFR population in gnomAD precludes the use of PS4.
BP4
A REVEL score of 0.824 supports neither a pathogenic nor a benign status for this variant.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
A REVEL score of 0.824 supports neither a pathogenic nor a benign status for this variant.
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-04-10
Published on: 2023-04-10
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