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.103T>C (p.Cys35Arg)

CA023838

132995 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 8410e5b5-ba69-4c4b-a83f-f2bbb062586d
Approved on: 2021-03-18
Published on: 2021-03-31

HGVS expressions

NM_000540.3:c.103T>C
NM_000540.3(RYR1):c.103T>C (p.Cys35Arg)
NC_000019.10:g.38440802T>C
CM000681.2:g.38440802T>C
NC_000019.9:g.38931442T>C
CM000681.1:g.38931442T>C
NC_000019.8:g.43623282T>C
NG_008866.1:g.12103T>C
ENST00000355481.8:c.103T>C
ENST00000359596.7:n.103T>C
ENST00000360985.7:c.103T>C
NM_000540.2:c.103T>C
NM_001042723.1:c.103T>C
NM_001042723.2:c.103T>C
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Pathogenic

Met criteria codes 4
PS4_Moderate PP1_Strong PP3_Moderate PM1
Not Met criteria codes 5
BS3 BS1 BP4 PS3 BA1

Evidence Links 2

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 cysteine with arginine at codon 35 of the RYR1 protein, p.(Cys35Arg). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.000009, a frequency consistent with pathogenicity for MHS. This variant has been reported in three unrelated individuals who have a personal or family history of a malignant hyperthermia reaction and positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted), PS4_Moderate (PMID:17710899, PMID:20681998, PMID:9066328). Functional studies in HEK293 cells show conflicting data regarding sensitivity to RYR1 agonists, PS3/BS3 were not implemented (PMID:9334205, PMID:26115329). 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 11 individuals, PP1_Strong (PMID:9066328). A REVEL score > 0.85 supports pathogenicity, PP3_Moderate. Criteria implemented: PS4_Moderate, PM1, PP3_Moderate, PP1_Strong. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386).
Met criteria codes
PS4_Moderate
Three unrelated cases with history of MH event (personal/family history) and a positive IVCT.
PP1_Strong
Eleven co-segregation events.
PP3_Moderate
REVEL 0.947
PM1
In N-terminal RYR1 hotspot.
Not Met criteria codes
BS3
Conflicting data.

BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
Conflicting data.

BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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