The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • See Evidence submitted by expert panel for details.

Variant: NM_001042723.2:c.5033A>G

CA066616

1214007 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 89c61653-3803-4e54-9278-d1ea8093993f

HGVS expressions

NM_001042723.2:c.5033A>G
NC_000019.10:g.38485688A>G
CM000681.2:g.38485688A>G
NC_000019.9:g.38976328A>G
CM000681.1:g.38976328A>G
NC_000019.8:g.43668168A>G
NG_008866.1:g.56989A>G
ENST00000599547.6:n.5033A>G
ENST00000359596.8:c.5033A>G
ENST00000355481.8:c.5033A>G
ENST00000359596.7:n.5033A>G
ENST00000360985.7:c.5030A>G
NM_000540.2:c.5033A>G
NM_001042723.1:c.5033A>G
NM_000540.3:c.5033A>G
NM_000540.3(RYR1):c.5033A>G (p.Asn1678Ser)

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 5
BA1 BS1 PS4 PP3 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 asparagine with serine at codon 1678 of the RYR1 protein p.(Asn1678Ser). 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 one individual who had a personal or family history of a malignant hyperthermia reaction and a positive in vitro contracture test (IVCT) result (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted) (PMID:30236257), this individual was also reported to have a pathogenic variant in RYR1, p.Gly2434Arg, and was not considered for PS4 (personal communication, The UK (Leeds) MH Unit). No functional studies were identified for this variant. This variant does not reside in a hotspot for pathogenic variants that contribute to MHS (PMID: 21118704). A REVEL score <0.5 supports a benign status, BP4. Based on using Bayes to combine criteria this variant is assessed to be a Variant of Uncertain Significance, (PMID: 29300386). Criteria implemented: BP4.
Met criteria codes
BP4
REVEL 0.371
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
PS4
This variant has been reported in one individual who had a personal or family history of a malignant hyperthermia reaction and a positive in vitro contracture test (IVCT) result (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted) (PMID:30236257), this individual was also reported to have a pathogenic variant in RYR1, p.Gly2434Arg, and was not considered for PS4 (personal communication, The UK (Leeds) MH Unit).
PP3
REVEL 0.371
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-04-06
Published on: 2023-04-06
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