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Variant: NM_000540.2(RYR1):c.8026C>T (p.Arg2676Trp)

CA024883

133217 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia of anesthesia
Inheritance Mode: Autosomal dominant inheritance
UUID: 149af01b-aeeb-4b3b-8053-07b981dc2ff1

HGVS expressions

NM_000540.2:c.8026C>T
NM_000540.2(RYR1):c.8026C>T (p.Arg2676Trp)
NC_000019.10:g.38504319C>T
CM000681.2:g.38504319C>T
NC_000019.9:g.38994959C>T
CM000681.1:g.38994959C>T
NC_000019.8:g.43686799C>T
NG_008866.1:g.75620C>T
ENST00000599547.6:n.8026C>T
ENST00000359596.8:c.8026C>T
ENST00000355481.8:c.8026C>T
ENST00000359596.7:n.8026C>T
ENST00000360985.7:c.8023C>T
ENST00000594335.5:n.1478C>T
NM_001042723.1:c.8026C>T
NM_000540.3:c.8026C>T
NM_001042723.2:c.8026C>T
NM_000540.3(RYR1):c.8026C>T (p.Arg2676Trp)

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 2
PS4_Moderate PP1_Strong
Not Met criteria codes 3
PP3 PM1 BP4

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 tryptophan at codon 2676 of the RYR1 protein, p.(Arg2676Trp). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.0000259, a frequency consistent with pathogenicity for MHS. This variant has been reported in eight 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). Two individuals were reported to have a second variant in RYR1 and were not considered for PS4, PS4_Moderate was applied (PMID:30236257, PMID:16163667, PMID:19191329, PMID:25960145, PMID:21157159, Stowell Laboratory personal communication). No functional studies were identified for this variant. This variant does not reside in a hotspot for pathogenic variants that contribute to MHS. This variant segregates with MHS in more than ten individuals, PP1_Strong (PMID:30236257, PMID:25960145, PMID:14732627). A REVEL score of 0.601 supports neither a pathogenic nor a benign status for this variant. This variant has been classified as a Likely Pathogenic. Criteria implemented: PS4_Moderate, PP1_Strong.
Met criteria codes
PS4_Moderate
This variant has been reported in eight 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). Two individuals were reported to have a second variant in RYR1 and were not considered for PS4, PS4_Moderate was applied (PMID:30236257, PMID:16163667, PMID:19191329, PMID:25960145, PMID:21157159, Stowell Laboratory personal communication).
PP1_Strong
This variant segregates with MHS in more than ten individuals, PP1_Moderate (PMID:30236257, PMID:25960145, PMID:14732627).
Not Met criteria codes
PP3
A REVEL score of 0.601 supports neither a pathogenic nor a benign status for this variant.
PM1
This variant does not reside in a hotspot for pathogenic variants that contribute to MHS.
BP4
A REVEL score of 0.601 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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