The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000540.2(RYR1):c.418G>A (p.Ala140Thr)

CA065638

544412 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 20ee66b5-e6bf-4915-a71e-d26fee9f1823
Approved on: 2021-03-18
Published on: 2021-03-31

HGVS expressions

NM_000540.2:c.418G>A
NM_000540.2(RYR1):c.418G>A (p.Ala140Thr)
NC_000019.10:g.38443790G>A
CM000681.2:g.38443790G>A
NC_000019.9:g.38934430G>A
CM000681.1:g.38934430G>A
NC_000019.8:g.43626270G>A
NG_008866.1:g.15091G>A
ENST00000355481.8:c.418G>A
ENST00000359596.7:n.418G>A
ENST00000360985.7:c.418G>A
NM_001042723.1:c.418G>A
NM_000540.3:c.418G>A
NM_001042723.2:c.418G>A

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 3
BP4 PM1 BS2_Supporting
Not Met criteria codes 2
PP3 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 alanine with threonine at codon 140 of the RYR1 protein, p.(Ala140Thr). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.0002, a frequency consistent with pathogenicity for MHS. This variant has been reported in an individual with a personal or family history of an MH episode without 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), this does not meet the requirement for PS4 (PMID:21455645). This variant has been identified in one individual with a negative IVCT/CHCT results, BS2_Moderate (PMID:21455645). 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 >0.85 (0.261) supports a benign status for this variant, BP4. Based on using Bayes to combine criteria this variant is classified as Likely Benign (PMID: 29300386). Criteria implemented: BS2_Moderate, PM1, BP4.
Met criteria codes
BP4
A REVEL score >0.85 (0.261) supports a benign status for this variant, BP4.
PM1
This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704).
BS2_Supporting
This variant has been identified in one individual with a negative IVCT/CHCT results, BS2_Moderate (PMID:21455645).
Not Met criteria codes
PP3
A REVEL score >0.85 (0.261) supports a benign status for this variant, BP4.
PS4
This variant has been reported in an individual with a personal or family history of an MH episode without 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), this does not meet the requirement for PS4 (PMID:21455645).
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