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Variant: NM_000540.2(RYR1):c.488G>T (p.Arg163Leu)

CA024467

133137 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: d3963666-0d28-46a5-88d3-0f7a9f6005f6

HGVS expressions

NM_000540.2:c.488G>T
NM_000540.2(RYR1):c.488G>T (p.Arg163Leu)
NC_000019.10:g.38444212G>T
CM000681.2:g.38444212G>T
NC_000019.9:g.38934852G>T
CM000681.1:g.38934852G>T
NC_000019.8:g.43626692G>T
NG_008866.1:g.15513G>T
ENST00000599547.6:n.488G>T
ENST00000359596.8:c.488G>T
ENST00000355481.8:c.488G>T
ENST00000359596.7:n.488G>T
ENST00000360985.7:c.488G>T
NM_001042723.1:c.488G>T
NM_000540.3:c.488G>T
NM_001042723.2:c.488G>T
NM_000540.3(RYR1):c.488G>T (p.Arg163Leu)

Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PS4_Moderate PS3_Moderate PM1 PP1_Moderate PP3_Moderate
Not Met criteria codes 4
PM5 BA1 BS1 BS3

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 arginine with leucine at codon 163 of the RYR1 protein p.(Arg163Leu). This variant is absent from a large population databases (gnomAD). 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 (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted), PS4_Moderate (PMID:30236257, PMID:16163667). This variant segregates with MHS in five individuals, PP1_Moderate (PMID:35718563). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:16163667, 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). Another variant assessed as pathogenic occurs at this codon, p.(Arg163Cys), however PM5 was not applied as Arg→Cys is predicted to be more disruptive based on a higher Grantham score as compared to Arg→Leu. A REVEL score > 0.85 supports pathogenicity, PP3_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID:29300386). Criteria implemented: PS4_Moderate, PS3_Moderate, PM1, PP1_Moderate, PP3_Moderate.
Met criteria codes
PS4_Moderate
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 (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted), PS4_Moderate (PMID:30236257, PMID:16163667).
PS3_Moderate
Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:16163667, PMID:26115329).

PM1
N-terminal hotspot region.
PP1_Moderate
This variant segregates with MHS in five individuals, PP1_Moderate (PMID:35718563).
PP3_Moderate
REVEL > 0.85
Not Met criteria codes
PM5
Another variant assessed as pathogenic occurs at this codon, p.(Arg163Cys), however PM5 was not applied as Arg→Cys is predicted to be more disruptive based on a higher Grantham score as compared to Arg→Leu.
BA1
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
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-05-22
Published on: 2023-05-22
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