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Variant: NM_000540.3(RYR1):c.130C>T (p.Arg44Cys)

CA024034

133045 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 1eca410d-5681-4ef6-a109-45927d4ba949

HGVS expressions

NM_000540.3:c.130C>T
NM_000540.3(RYR1):c.130C>T (p.Arg44Cys)
NC_000019.10:g.38440829C>T
CM000681.2:g.38440829C>T
NC_000019.9:g.38931469C>T
CM000681.1:g.38931469C>T
NC_000019.8:g.43623309C>T
NG_008866.1:g.12130C>T
ENST00000599547.6:n.130C>T
ENST00000359596.8:c.130C>T
ENST00000355481.8:c.130C>T
ENST00000359596.7:n.130C>T
ENST00000360985.7:c.130C>T
NM_000540.2:c.130C>T
NM_001042723.1:c.130C>T
NM_001042723.2:c.130C>T

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 4
PP3_Moderate PS3_Moderate PS4_Moderate PM1
Not Met criteria codes 4
BA1 BP4 BS3 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 cysteine at codon 44 of the RYR1 protein, p.(Arg44Cys). The maximum allele frequency for this variant among the six major gnomAD populations is AMR: 0.000029, 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 and a 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:12709367, PMID:24433488). 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 > 0.85 supports pathogenicity, PP3_Moderate. For these reasons, this variant has been classified as Likely Pathogenic. Criteria implemented: PS4_Moderate, PS3_Moderate, PM1, PP3_Moderate.
Met criteria codes
PP3_Moderate
REVEL > 0.85
PS3_Moderate
Decreased EC50 as compared to WT, 4-CmC
PS4_Moderate
Two unrelated individuals, MH reactions and diagnostics tests.
PM1
N-terminal hotspot region.
Not Met criteria codes
BA1
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
BS3
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
Approved on: 2023-04-06
Published on: 2023-04-06
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