Variant: NM_001042723.2:c.6304G>C

CA068028

1210308 (ClinVar)

Gene: RYR1

Condition: malignant hyperthermia, susceptibility to, 1

Inheritance Mode: Autosomal dominant inheritance

UUID: 330f9155-d147-4ea4-abdf-749a86408a5c

HGVS expressions

NM_001042723.2:c.6304G>C
NC_000019.10:g.38494381G>C
CM000681.2:g.38494381G>C
NC_000019.9:g.38985021G>C
CM000681.1:g.38985021G>C
NC_000019.8:g.43676861G>C
NG_008866.1:g.65682G>C
ENST00000599547.6:n.6304G>C
ENST00000359596.8:c.6304G>C
ENST00000355481.8:c.6304G>C
ENST00000359596.7:n.6304G>C
ENST00000360985.7:c.6301G>C
NM_000540.2:c.6304G>C
NM_001042723.1:c.6304G>C
NM_000540.3:c.6304G>C
NM_000540.3(RYR1):c.6304G>C (p.Val2102Leu)

Uncertain Significance

• Met criteria codes: PM1

• Not Met criteria codes: BS1 BP4 PS4 BA1 PP1 PP3

Expert Panel

Malignant Hyperthermia Susceptibility VCEP

Criteria Specification Information

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 valine with leucine at codon 2102 of the RYR1 protein, p.Val2102Leu. The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.000018, a frequency consistent with pathogenicity for MHS. 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), however, this variant was in cis to a second RYR1 variant that has been classified as a variant of uncertain significance (p.Arg1583Cys), for that reason PS4 was not implemented (PMID:23035052). The allele containing both variants segregated with MHS in four individuals in this family, however, since the effect of the two alleles cannot be separated PP1 was not implemented for this variant (PMID:23035052). No functional studies were identified for this variant. This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704). A REVEL score of 0.515 supports neither a pathogenic nor a benign status for this variant. This variant has been classified as a Variant of Unknown Significance. Criteria implemented: PM1.

Met criteria codes

• PM1: This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704).

Not Met criteria codes

• BS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP4: A REVEL score of 0.515 supports neither a pathogenic nor a benign status for this variant.
• PS4: 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), however, this variant was in cis to a second RYR1 variant that has been classified as a variant of uncertain significance (p.Arg1583Cys), for that reason PS4 was not implemented (PMID:23035052).
• BA1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PP1: The allele containing both variants segregated with MHS in four individuals in this family, however, since the effect of the two alleles cannot be separated PP1 was not implemented for this variant (PMID:23035052).
• PP3: A REVEL score of 0.515 supports neither a pathogenic nor a benign status for this variant.

Approved on: 2023-04-06

Published on: 2023-04-06