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.14510del (p.Gln4837fs)

CA024161

133073 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia of anesthesia
Inheritance Mode: Autosomal dominant inheritance
UUID: c8d232df-329c-4f12-8557-db6ecde5e496

HGVS expressions

NM_000540.2:c.14510delA
NM_000540.2:c.14510del
NM_000540.2(RYR1):c.14510del (p.Gln4837fs)
NC_000019.10:g.38580127del
CM000681.2:g.38580127del
NC_000019.9:g.39070767del
CM000681.1:g.39070767del
NC_000019.8:g.43762607del
NG_008866.1:g.151428del
ENST00000359596.8:c.14510del
ENST00000355481.8:c.14495del
ENST00000359596.7:n.14510del
ENST00000360985.7:c.14492del
NM_001042723.1:c.14495del
NM_000540.3:c.14510del
NM_001042723.2:c.14495del
NM_000540.3(RYR1):c.14510del (p.Gln4837fs)

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 3
PS4_Supporting BS2_Supporting BS3_Supporting
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 frameshift variant, p.Gln4837Argfs*3, predicts the substitution of glutamine with arginine at codon 4837 and a premature stop codon at position 3 of the new reading frame. This variant was not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been reported in an individual with a personal or family history of an MH episode and 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_Supporting (PMID:17293538). Two relatives of this individual were shown to be heterozygous for the variant and IVCT negative, BS2_Moderate was implemented. This variant predicts a loss of function due to nonsense mediated decay, loss of function variants are not expected to cause MH. Experiments expressing this variant in HEK293 cells did not demonstrate NMD as determined by protein expression on a Western blot. Expression of this variant alone showed no calcium release upon stimulation with caffeine, when the variant was transfected with wild-type RYR1 the EC50 was comparable to that observed in cells expressing wild-type RYR1 alone, BS3_Supporting was applied (PMID:17293538). Based on using Bayes to combine criteria this variant is assessed as Likely Benign, (PMID: 29300386), (relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern). Criteria implemented: PS4_Supporting, BS2_Moderate, BS3_Supporting.
Met criteria codes
PS4_Supporting
This variant has been reported in an individual with a personal or family history of an MH episode and 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_Supporting (PMID:17293538).
BS2_Supporting
This variant has been reported in an individual with a personal or family history of an MH episode and 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_Supporting (PMID:17293538). Two relatives of this individual were shown to be heterozygous for the variant and IVCT negative, BS2_Moderate was implemented.
BS3_Supporting
This variant predicts a loss of function due to nonsense mediated decay, loss of function variants are not expected to cause MH. Experiments expressing this variant in HEK293 cells did not demonstrate NMD as determined by protein expression on a Western blot. Expression of this variant alone showed no calcium release upon stimulation with caffeine, when the variant was transfected with wild-type RYR1 the EC50 was comparable to that observed in cells expressing wild-type RYR1 alone, BS3_Supporting was applied (PMID:17293538).
Not Met criteria codes
PM1
Only applies to missense variants
Approved on: 2022-03-14
Published on: 2022-03-14
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