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.12884C>T (p.Ala4295Val)

CA024018

133043 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: ee8cf8a1-7193-4be2-92d4-4ee287b0fdf0

HGVS expressions

NM_000540.2:c.12884C>T
NM_000540.2(RYR1):c.12884C>T (p.Ala4295Val)
NC_000019.10:g.38565218C>T
CM000681.2:g.38565218C>T
NC_000019.9:g.39055858C>T
CM000681.1:g.39055858C>T
NC_000019.8:g.43747698C>T
NG_008866.1:g.136519C>T
ENST00000355481.8:c.12869C>T
ENST00000359596.7:n.12884C>T
ENST00000360985.7:c.12866C>T
NM_001042723.1:c.12869C>T
NM_000540.3:c.12884C>T
NM_001042723.2:c.12869C>T

Benign

The Expert Panel has overridden the computationally generated classification - "Likely Benign"
Met criteria codes 4
BS2_Supporting BS1 BP2 BP4
Not Met criteria codes 4
PS4 PP3 PM1 BA1

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 Valine at codon 4295 of the RYR1 protein, p.(Ala4295Val). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.0019, this is considered to be more common than expected for a pathogenic variant causing autosomal dominantly inherited MHS, BS1. This variant has been reported in two unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, both 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), (PMID:30236257). However, the high MAF in the NFE population in gnomAD precludes the use of PS4. This variant has been identified in an individual with a negative IVCT/CHCT result, BS2_Moderate, (PMID:25658027). 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 was observed in cis with a variant assessed as pathogenic, p.(Arg2435His), BP2 (PMID:19513315). A REVEL score <0.5 (0.152) supports a benign status for this variant, BP4. Based on using Bayes to combine criteria this variant is assessed as Benign, (PMID: 29300386). Criteria implemented: BS1, BS2_Moderate, BP2, BP4.
Met criteria codes
BS2_Supporting
This variant has been identified in an individual with a negative IVCT/CHCT result, BS2_Moderate, (PMID:25658027).
BS1
The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.0019, this is considered to be more common than expected for a pathogenic variant causing autosomal dominantly inherited MHS, BS1.
BP2
This variant was observed in cis with a variant assessed as pathogenic, p.(Arg2435His), BP2 (PMID:19513315).
BP4
A REVEL score <0.5 (0.152) supports a benign status for this variant, BP4.
Not Met criteria codes
PS4
This sequence variant predicts a substitution of Alanine with Valine at codon 4295 of the RYR1 protein, p.(Ala4295Val). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.0019, this is considered to be more common than expected for a pathogenic variant causing autosomal dominantly inherited MHS, BS1. This variant has been reported in two unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, both 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), (PMID:30236257). However, the high MAF in the NFE population in gnomAD precludes the use of PS4.
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
This variant does not reside in a hotspot for pathogenic variants that contribute to MHS.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2021-03-18
Published on: 2021-03-31
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