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Variant: NM_000540.2(RYR1):c.7358T>C (p.Ile2453Thr)

CA024775

65953 (ClinVar)

Gene: RYR1
Condition: malignant hyperthermia, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: d0fc3f38-e5d9-4f69-b1e0-b6c0a98bfbbf
Approved on: 2023-04-06
Published on: 2023-04-06

HGVS expressions

NM_000540.2:c.7358T>C
NM_000540.2(RYR1):c.7358T>C (p.Ile2453Thr)
NC_000019.10:g.38500640T>C
CM000681.2:g.38500640T>C
NC_000019.9:g.38991280T>C
CM000681.1:g.38991280T>C
NC_000019.8:g.43683120T>C
NG_008866.1:g.71941T>C
ENST00000599547.6:n.7358T>C
ENST00000359596.8:c.7358T>C
ENST00000355481.8:c.7358T>C
ENST00000359596.7:n.7358T>C
ENST00000360985.7:c.7355T>C
ENST00000594335.5:n.810T>C
NM_001042723.1:c.7358T>C
NM_000540.3:c.7358T>C
NM_001042723.2:c.7358T>C
NM_000540.3(RYR1):c.7358T>C (p.Ile2453Thr)
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Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 4
PM1 PP3_Moderate PS4_Supporting PS2_Moderate
Not Met criteria codes 1
PS3

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 isoleucine with threonine at codon 2453 of the RYR1 protein, p.(Ile2453Thr). This variant was not present in a large population database (gnomAD) at the time it was interpreted. This variant has been reported in an individual with a personal history of an MH episode and a positive in vitro contracture test (IVCT), PS4_Supporting (PMID:12434264). The mother was positive for the variant and was determined to be IVCT positive, and the variant was determined to be de novo in the mother with confirmed parentage, PS2_Moderate. A functional study using sarcoplasmic reticulum membrane vesicles was published for this variant; this assay is not considered a standard assay by the ClinGen RYR1 VCEP for MHS and PS3 was not applied (PMID:16958617). 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 >0.85 (0.891) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Likely Pathogenic. Criteria implemented: PS2_Moderate, PS4_Supporting, PM1, PP3_Moderate.
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).
PP3_Moderate
A REVEL score >0.85 (0.891) supports a pathogenic status for this variant, PP3_Moderate.
PS4_Supporting
This variant has been reported in an individual with a personal history of an MH episode and a positive in vitro contracture test (IVCT), PS4_Supporting (PMID:12434264).
PS2_Moderate
This variant has been reported in an individual with a personal history of an MH episode and a positive in vitro contracture test (IVCT), PS4_Supporting (PMID:12434264). The mother was positive for the variant and was determined to be IVCT positive, as well the variant was determined to be de novo in the mother with confirmed parentage, PS2_Moderate
Not Met criteria codes
PS3
A functional study using sarcoplasmic reticulum membrane vesicles was published for this variant, this assay is not considered a standard assay by the ClinGen RYR1 VCEP for MHS and PS3 was not applied (PMID:16958617).
Curation History
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