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Variant: NM_000540.3(RYR1):c.7048G>A (p.Ala2350Thr)

CA024690

133182 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: efb7116e-4296-4306-a153-395080a0a23e
Approved on: 2021-03-17
Published on: 2021-03-31

HGVS expressions

NM_000540.3:c.7048G>A
NM_000540.3(RYR1):c.7048G>A (p.Ala2350Thr)
NC_000019.10:g.38499655G>A
CM000681.2:g.38499655G>A
NC_000019.9:g.38990295G>A
CM000681.1:g.38990295G>A
NC_000019.8:g.43682135G>A
NG_008866.1:g.70956G>A
ENST00000355481.8:c.7048G>A
ENST00000359596.7:n.7048G>A
ENST00000360985.7:c.7045G>A
NM_000540.2:c.7048G>A
NM_001042723.1:c.7048G>A
NM_001042723.2:c.7048G>A
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Pathogenic

Met criteria codes 5
PS4 PP3_Moderate PP1_Strong PM1 PS3_Moderate
Not Met criteria codes 2
BA1 BS1

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 2350 of the RYR1 protein, p.(Ala2350Thr). This variant was not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been reported in 19 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, 17 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), PS4, (PMID:30236257, PMID:16163667, PMID:11525881, PMID:12434264, and others). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:11525881). An ex vivo study in myotubes from a single patient also showed increased sensitivity to RYR1 agonists, (PMID:15210166). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704). This variant segregates with MHS in 7 individuals PP1_Strong (PMID:11525881, PMID:25960145). A REVEL score >0.85 (0.952) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Pathogenic. Criteria implemented: PS3_Moderate, PS4, PM1, PP1_Strong, PP3_Moderate.
Met criteria codes
PS4
This variant has been reported in 19 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, 17 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), PS4, (PMID:30236257, PMID:16163667, PMID:11525881, PMID:12434264, and others).
PP3_Moderate
A REVEL score >0.85 (0.952) supports a pathogenic status for this variant, PP3_Moderate.
PP1_Strong
This variant segregates with MHS in 7 individuals PP1_Strong (PMID:11525881, PMID:25960145).
PM1
Central hotspot region.
PS3_Moderate
Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:11525881). An ex vivo study in myotubes from a single patient also showed increased sensitivity to RYR1 agonists, (PMID:15210166).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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