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Variant: NM_000540.3(RYR1):c.11947C>T (p.Arg3983Cys)

CA405662842

650932 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 5ffcdc59-d1d4-4cc4-a189-ce1af5390baa

HGVS expressions

NM_000540.3:c.11947C>T
NM_000540.3(RYR1):c.11947C>T (p.Arg3983Cys)
NC_000019.10:g.38543810C>T
CM000681.2:g.38543810C>T
NC_000019.9:g.39034450C>T
CM000681.1:g.39034450C>T
NC_000019.8:g.43726290C>T
NG_008866.1:g.115111C>T
ENST00000688602.1:n.357C>T
ENST00000689936.1:n.339C>T
ENST00000359596.8:c.11947C>T
ENST00000355481.8:c.11932C>T
ENST00000359596.7:n.11947C>T
ENST00000360985.7:c.11929C>T
ENST00000593322.1:n.556C>T
ENST00000594335.5:n.5316C>T
NM_000540.2:c.11947C>T
NM_001042723.1:c.11932C>T
NM_001042723.2:c.11932C>T

Uncertain Significance

Met criteria codes 4
BS3_Supporting PP3_Moderate PS2_Moderate PS4_Supporting
Not Met criteria codes 3
BS1 BA1 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 cysteine at codon 3983 of the RYR1 protein, p.(Arg3983Cys). This variant is not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been reported in an individual with a personal or family history of an MH episode and 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_Supporting (PMID:21918424). In one individual the variant was determined to be de novo with confirmed parentage, PS2_Moderate (PMID:21918424). Functional studies in HEK293 cells have not shown a significant increase in sensitivity to RYR1 agonists BS3_Supporting (PMID:21918424). This variant does not reside in a hotspot for pathogenic variants that contribute to MHS. A REVEL score >0.85 (0.931) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as a Variant of Unknown Significance. Criteria implemented: PS2_Moderate, PS4_Supporting, PP3_Moderate, BS3_Supporting.
Met criteria codes
BS3_Supporting
Functional studies in HEK293 cells have not shown a significant increase in sensitivity to RYR1 agonists BS3_Supporting (PMID:21918424).
PP3_Moderate
A REVEL score >0.85 (0.931) supports a pathogenic status for this variant, PP3_Moderate.
PS2_Moderate
In one individual the variant was determined to be de novo with confirmed parentage, PS2_Moderate (PMID:21918424).
PS4_Supporting
This variant has been reported in an individual with a personal or family history of an MH episode and 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_Supporting (PMID:21918424).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-04-07
Published on: 2023-04-07
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