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Variant: NM_000540.2(RYR1):c.6302T>A (p.Met2101Lys)

CA068024

544517 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia of anesthesia
Inheritance Mode: Autosomal dominant inheritance
UUID: e892ffc5-f300-4565-b5c8-406e4c65372b
Approved on: 2023-04-06
Published on: 2023-04-06

HGVS expressions

NM_000540.2:c.6302T>A
NM_000540.2(RYR1):c.6302T>A (p.Met2101Lys)
NC_000019.10:g.38494379T>A
CM000681.2:g.38494379T>A
NC_000019.9:g.38985019T>A
CM000681.1:g.38985019T>A
NC_000019.8:g.43676859T>A
NG_008866.1:g.65680T>A
ENST00000599547.6:n.6302T>A
ENST00000359596.8:c.6302T>A
ENST00000355481.8:c.6302T>A
ENST00000359596.7:n.6302T>A
ENST00000360985.7:c.6299T>A
NM_001042723.1:c.6302T>A
NM_000540.3:c.6302T>A
NM_001042723.2:c.6302T>A
NM_000540.3(RYR1):c.6302T>A (p.Met2101Lys)

Uncertain Significance

Met criteria codes 2
PM1 BP4
Not Met criteria codes 1
PS4

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 methionine with lysine at codon 2101 of the RYR1 protein, p.(Met2101Lys). The maximum minor allele frequency (MAF) for this variant among the six major gnomAD populations is NFE: 0.000087, a frequency consistent with pathogenicity for MHS. However, the MAF in the Ashkenazi Jewish population is 0.0047 which is considered to be too common for a pathogenic variant causing autosomal dominantly inherited MHS. This variant has been reported in three 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). One of these individuals had a second variant of uncertain significance in RYR1 (p.Arg1469Trp, VUS) (PMID:20681998, PMID:25735680, PMID:30236257). The high MAF in the Ashkenazi Jewish population precludes implementing PS4. No functional studies were identified for this variant. 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 <0.5 (0.392) supports a benign status for this variant, BP4. This variant has been classified as a Variant of Unknown Significance. Criteria implemented: PM1, BP4.
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).
BP4
A REVEL score <0.5 (0.392) supports a benign status for this variant, BP4.
Not Met criteria codes
PS4
This variant has been reported in three 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). One of these individuals had a second variant of uncertain significance in RYR1 (p.Arg1469Trp, VUS) (PMID:20681998, PMID:25735680, PMID:30236257). The high MAF in the Ashkenazi Jewish population precludes implementing PS4.
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