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Variant: NM_000540.2(RYR1):c.11953T>C (p.Trp3985Arg)

CA023949

133025 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: f12e20b6-f3f3-481e-a426-b7e63cb4c86a

HGVS expressions

NM_000540.2:c.11953T>C
NM_000540.2(RYR1):c.11953T>C (p.Trp3985Arg)
NC_000019.10:g.38543816T>C
CM000681.2:g.38543816T>C
NC_000019.9:g.39034456T>C
CM000681.1:g.39034456T>C
NC_000019.8:g.43726296T>C
NG_008866.1:g.115117T>C
ENST00000688602.1:n.363T>C
ENST00000689936.1:n.345T>C
ENST00000359596.8:c.11953T>C
ENST00000355481.8:c.11938T>C
ENST00000359596.7:n.11953T>C
ENST00000360985.7:c.11935T>C
ENST00000593322.1:n.562T>C
ENST00000594335.5:n.5322T>C
NM_001042723.1:c.11938T>C
NM_000540.3:c.11953T>C
NM_001042723.2:c.11938T>C
NM_000540.3(RYR1):c.11953T>C (p.Trp3985Arg)

Uncertain Significance

Met criteria codes 2
PS4_Moderate PP3_Moderate
Not Met criteria codes 1
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 tryptophan with arginine at codon 3985 of the RYR1 protein, p.(Trp3985Arg). This variant was not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been reported in two unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, both 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:18719443, PMID:23558838). An ex vivo assay using muscle cells from mutation positive relatives showed an increased sensitivity to RYR1 agonists, this did not meet PS3 which requires multiple unrelated samples to be tested (PMID:18719443). This variant does not reside in a hotspot for pathogenic variants that contribute to MHS. A REVEL score >0.85 (0.941) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as a Variant of Unknown Significance. Criteria implemented: PS4_Moderate, 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, both 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:18719443, PMID:23558838).
PP3_Moderate
A REVEL score >0.85 (0.941) supports a pathogenic status for this variant, PP3_Moderate.
Not Met criteria codes
PS3
An ex vivo assay using muscle cells from mutation positive relatives showed an increased sensitivity to RYR1 agonists, this did not meet PS3 which requires multiple unrelated samples to be tested (PMID:18719443).
Approved on: 2023-04-06
Published on: 2023-04-06
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