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Variant: NM_000540.3(RYR1):c.11315G>A (p.Arg3772Gln)

CA023909

133012 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: ef497424-0087-43cb-8e11-4fb1a862a044
Approved on: 2023-04-06
Published on: 2023-04-06

HGVS expressions

NM_000540.3:c.11315G>A
NM_000540.3(RYR1):c.11315G>A (p.Arg3772Gln)
NC_000019.10:g.38534775G>A
CM000681.2:g.38534775G>A
NC_000019.9:g.39025415G>A
CM000681.1:g.39025415G>A
NC_000019.8:g.43717255G>A
NG_008866.1:g.106076G>A
ENST00000599547.6:n.11254G>A
ENST00000359596.8:c.11315G>A
ENST00000355481.8:c.11300G>A
ENST00000359596.7:n.11315G>A
ENST00000360985.7:c.11297G>A
ENST00000593322.1:n.16G>A
ENST00000594335.5:n.4702G>A
ENST00000596431.5:n.44G>A
ENST00000599547.5:n.2122G>A
ENST00000601514.5:n.596G>A
NM_000540.2:c.11315G>A
NM_001042723.1:c.11300G>A
NM_001042723.2:c.11300G>A
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Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 4
PP1_Strong BS2_Supporting PS4_Moderate PP3_Moderate
Not Met criteria codes 1
PM1

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 glutamine at codon 3772 of the RYR1 protein, p.(Arg3772Gln). The maximum allele frequency for this variant among the six major gnomAD populations is SAS: 0.000033, 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, seven 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), however, three of these individuals were homozygous for this variant and were not considered for PS4, PS4_Moderate was applied (PMID: 30236257, 17483490). This variant segregates with MHS in at least seven individuals, PP1_Strong (PMID:19645060, 22473935). This variant has been identified in an individual with a negative IVCT/CHCT result. BS2_Moderate (PMID: 30236257). No functional studies were identified for this variant. This variant does not reside in a hotspot for pathogenic variants that contribute to MHS. A REVEL score >0.85 (0.888) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Likely Pathogenic. Criteria implemented: PS4_Moderate, PP1_Strong, PP3_Moderate, BS2_Moderate.
Met criteria codes
PP1_Strong
This variant segregates with MHS in at least seven individuals, PP1_Strong (PMID:19645060, 22473935).
BS2_Supporting
This variant has been identified in an individual with a negative IVCT/CHCT result. BS2_Moderate (PMID: 30236257).
PS4_Moderate
This variant has been reported in eight unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, seven 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), however, three of these individuals were homozygous for this variant and were not considered for PS4, PS4_Moderate was applied (PMID: 30236257, 17483490).
PP3_Moderate
A REVEL score >0.85 (0.888) supports a pathogenic status for this variant, PP3_Moderate.
Not Met criteria codes
PM1
This variant does not reside in a hotspot for pathogenic variants that contribute to MHS.
Curation History
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