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Variant: NM_000540.2(RYR1):c.641C>T (p.Thr214Met)

CA024581

167614 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia of anesthesia
Inheritance Mode: Autosomal dominant inheritance
UUID: 52083721-82d7-4413-a279-27c7e0f626b3

HGVS expressions

NM_000540.2:c.641C>T
NM_000540.2(RYR1):c.641C>T (p.Thr214Met)
NC_000019.10:g.38446481C>T
CM000681.2:g.38446481C>T
NC_000019.9:g.38937121C>T
CM000681.1:g.38937121C>T
NC_000019.8:g.43628961C>T
NG_008866.1:g.17782C>T
ENST00000599547.6:n.641C>T
ENST00000359596.8:c.641C>T
ENST00000355481.8:c.641C>T
ENST00000359596.7:n.641C>T
ENST00000360985.7:c.641C>T
NM_001042723.1:c.641C>T
NM_000540.3:c.641C>T
NM_001042723.2:c.641C>T
NM_000540.3(RYR1):c.641C>T (p.Thr214Met)

Uncertain Significance

Met criteria codes 5
PM1 BS3_Supporting PS4_Moderate BS2 PP1
Not Met criteria codes 2
BP4 PP3

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 threonine with methionine at codon 214 of the RYR1 protein, p.(Thr214Met). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00017, a frequency consistent with pathogenicity for MHS. This variant has been reported in four unrelated individuals who have a personal or family history of a malignant hyperthermia reaction; all 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:30236257). This variant has been reported in a fifth individual with a second variant in RYR1 classified as Likely Pathogenic (p.Glu2348del), this individual was not counted toward PS4 (PMID:27857962), the mother of this individual shared the p.Thr214Met variant and was MHN by IVCT, BS2_Moderate. Functional studies in HEK293 cells do not show a significant increase in sensitivity to RYR1 agonists, BS3_Supporting (PMID:27857962). This variant segregates with MHS in three individuals, PP1 (PMID:25658027, PMID:30236257). 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 of 0.533 supports neither a pathogenic nor a benign status for this variant. Based on using Bayes to combine criteria this variant is assessed as a Variant of Uncertain Significance, (PMID: 29300386). Criteria implemented: PS4_Moderate, PM1, PP1, BS2_Moderate, BS3_Supporting.
Met criteria codes
PM1
This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704).
BS3_Supporting
Functional studies in HEK293 cells do not show a significant increase in sensitivity to RYR1 agonists, BS3_Supporting (PMID:27857962).
PS4_Moderate
This variant has been reported in five unrelated individuals who have a personal or family history of a malignant hyperthermia reaction; all 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:30236257, PMID:27857962).
BS2
This variant has been reported in a fifth individual with a second variant in RYR1 classified as Likely Pathogenic (p.Glu2348del), this individual was not counted toward PS4 (PMID:27857962), the mother of this individual shared the p.Thr214Met variant and was MHN by IVCT, BS2_Moderate.
PP1
This variant segregates with MHS in four individuals, PP1_Supporting (PMID:25658027, PMID:30236257).
Not Met criteria codes
BP4
A REVEL score of 0.533 supports neither a pathogenic nor a benign status for this variant.
PP3
A REVEL score of 0.533 supports neither a pathogenic nor a benign status for this variant.
Approved on: 2023-04-06
Published on: 2023-04-06
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