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_000540.3(RYR1):c.6961A>G (p.Ile2321Val)

CA024659

133173 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 0edf33d7-7e9e-41a8-988b-c2f21bde9e8a

HGVS expressions

NM_000540.3:c.6961A>G
NM_000540.3(RYR1):c.6961A>G (p.Ile2321Val)
NC_000019.10:g.38499177A>G
CM000681.2:g.38499177A>G
NC_000019.9:g.38989817A>G
CM000681.1:g.38989817A>G
NC_000019.8:g.43681657A>G
NG_008866.1:g.70478A>G
ENST00000355481.8:c.6961A>G
ENST00000359596.7:n.6961A>G
ENST00000360985.7:c.6958A>G
NM_000540.2:c.6961A>G
NM_001042723.1:c.6961A>G
NM_001042723.2:c.6961A>G

Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 4
BS2 BS1 BS3_Supporting PM1
Not Met criteria codes 5
BA1 BP4 PS3 PS4 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 isoleucine with valine at codon 2321 of the RYR1 protein p.(Ile2321Val). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00081, this is considered to be more common than expected for a pathogenic variant causing autosomal dominant MHS, BS1. 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 (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted) (PMID:30236257; PMID:23558838). However, the high MAF in the NFE population in gnomAD precludes the use of PS4. This variant has been identified in families with genotype positive/ phenotype negative individuals (IVCT) supporting a benign status, BS2 (PMID:30236257, personal communications). Variant did not show increased sensitivity to RYR1 agonists in HEK293 assay (personal communication), BS3_Supporting. 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 0.712 does not support pathogenic or a benign status. This variant has been classified as Benign. Criteria implemented: BS1, BS2, BS3_Supporting, PM1.
Met criteria codes
BS2
This variant has been identified in families with genotype positive/ phenotype negative individuals (IVCT) supporting a benign status, BS2 (PMID:30236257, personal communications).
BS1
NFE maf=0.00081
BS3_Supporting
Variant did not show increased sensitivity to RYR1 agonists in HEK293 assay (personal communication).
PM1
Central hotspot region
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL 0.712
PS3
Variant did not show increased sensitivity to RYR1 agonists in HEK293 assay (personal communication).
PS4
Four cases with MH published but high maf in NFE population of gnomAD.
PP3
REVEL 0.712
Approved on: 2021-03-18
Published on: 2021-03-31
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