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.6670C>T (p.Arg2224Cys)

CA068565

224387 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: fbe0116f-58bd-4caf-8b91-572acc551b1e
Approved on: 2021-03-18
Published on: 2021-03-31

HGVS expressions

NM_000540.2:c.6670C>T
NM_000540.2(RYR1):c.6670C>T (p.Arg2224Cys)
NC_000019.10:g.38496415C>T
CM000681.2:g.38496415C>T
NC_000019.9:g.38987055C>T
CM000681.1:g.38987055C>T
NC_000019.8:g.43678895C>T
NG_008866.1:g.67716C>T
ENST00000355481.8:c.6670C>T
ENST00000359596.7:n.6670C>T
ENST00000360985.7:c.6667C>T
NM_001042723.1:c.6670C>T
NM_000540.3:c.6670C>T
NM_001042723.2:c.6670C>T
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Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 2
BS1 PM1
Not Met criteria codes 6
BP4 BA1 PS4 PS1 PM5 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 arginine with cysteine at codon 2224 of the RYR1 protein p.(Arg2224Cys). The maximum allele frequency for this variant among the six major gnomAD populations is SAS: 0.00091, this is considered to be more common than expected for a pathogenic variant causing autosomal dominant MHS, BS1. This variant has been reported in one individual who has a personal or family history of a malignant hyperthermia reaction, this individual 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) (PMID:30236257). The high maf in the SAS population in gnomAD precludes the use of 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 0.728 supports neither a pathogenic or a benign status. Based on using Bayes to combine criteria this variant is assessed as Likely Benign, (PMID: 29300386). Criteria implemented: BS1, PM1.
Met criteria codes
BS1
based on gnomAD SAS population may, 0.00091
PM1
Variant falls in central hotspot for MHS pathogenic variants.
Not Met criteria codes
BP4
REVEL 0.728
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
One reported case PMID:30236257
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL 0.728
Curation History
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