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Variant: NM_000540.2(RYR1):c.7076G>A (p.Arg2359Gln)

CA405667952

573252 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 16017df4-8c9b-4fac-8831-cf7ba360b618

HGVS expressions

NM_000540.2:c.7076G>A
NM_000540.2(RYR1):c.7076G>A (p.Arg2359Gln)
NC_000019.10:g.38499683G>A
CM000681.2:g.38499683G>A
NC_000019.9:g.38990323G>A
CM000681.1:g.38990323G>A
NC_000019.8:g.43682163G>A
NG_008866.1:g.70984G>A
ENST00000599547.6:n.7076G>A
ENST00000359596.8:c.7076G>A
ENST00000355481.8:c.7076G>A
ENST00000359596.7:n.7076G>A
ENST00000360985.7:c.7073G>A
ENST00000594335.5:n.528G>A
NM_001042723.1:c.7076G>A
NM_000540.3:c.7076G>A
NM_001042723.2:c.7076G>A
NM_000540.3(RYR1):c.7076G>A (p.Arg2359Gln)

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 3
PS4_Moderate PP3_Moderate PM1

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 glutamine at codon 2359 of the RYR1 protein, p.(Arg2359Gln). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00001, a frequency consistent with pathogenicity for MHS. This variant has been reported in two 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), PS4_Moderate (PMID:24433488, PMID:30236257). No functional studies were identified for this variant. 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 (0.873) 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
PS4_Moderate
This variant has been reported in two 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), PS4_Moderate (PMID:24433488, PMID:30236257).
PP3_Moderate
A REVEL score >0.85 (0.873) supports a pathogenic status for this variant, PP3_Moderate.
PM1
This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704).
Approved on: 2023-04-06
Published on: 2023-04-06
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