The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000540.3(RYR1):c.14690G>A (p.Gly4897Asp)

CA405690291

582126 (ClinVar)

Gene: RYR1
Condition: RYR1-related myopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 0964ac83-ed0e-48d3-ad6f-64f95e9ea1f6
Approved on: 2024-08-07
Published on: 2024-10-02

HGVS expressions

NM_000540.3:c.14690G>A
NM_000540.3(RYR1):c.14690G>A (p.Gly4897Asp)
NC_000019.10:g.38584986G>A
CM000681.2:g.38584986G>A
NC_000019.9:g.39075626G>A
CM000681.1:g.39075626G>A
NC_000019.8:g.43767466G>A
NG_008866.1:g.156287G>A
ENST00000593677.2:c.1626G>A
ENST00000688602.1:c.3023G>A
ENST00000689936.1:c.2995G>A
ENST00000692547.1:n.83G>A
ENST00000359596.8:c.14690G>A
ENST00000355481.8:c.14675G>A
ENST00000359596.7:c.14690G>A
ENST00000360985.7:c.14672G>A
NM_000540.2:c.14690G>A
NM_001042723.1:c.14675G>A
NM_001042723.2:c.14675G>A
More

Likely Pathogenic

Met criteria codes 4
PS4_Moderate PP3 PM1 PM2_Supporting
Not Met criteria codes 2
BA1 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Congenital Myopathies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RYR1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The c.14690G>A variant in RYR1 is a missense variant predicted to cause substitution of glycine by aspartic acid at amino acid 4897. This variant is absent from gnomAD v4.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.835, which is above the threshold of 0.7, evidence that correlates with impact to RYR1 function (PP3). This variant resides within the pore region (amino acids 4800-4950), of RYR1 that is defined as a mutation hotspot/critical functional domain by the ClinGen Congenital Myopathies VCEP (PM1). This variant has been reported in 2 probands with RYR1-related myopathy (PS4_Moderate; PMIDs: 24561095, 35428369). Additionally, the variant was identified in a third individual with c.9989A>G (p.Asp3330Gly) likely in cis, although variants phasing could not be confirmed at this time (PMID: 23919265, SCV000852450.1). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant RYR1-related myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PS4_Moderate, PM1, PM2_Supporting, PP3. (Congenital Myopathies VCEP specifications version 1; 8/7/2024)
Met criteria codes
PS4_Moderate
This variant has been reported in 2 probands with RYR1-related myopathy (PS4_Moderate; PMIDs: 24561095, 35428369). Additionally, the variant was identified in a third individual with c.9989A>G (p.Asp3330Gly) likely in cis, although variants phasing could not be confirmed at this time (PMID: 23919265, SCV000852450.1).
PP3
The computational predictor REVEL gives a score of 0.835, which is above the threshold of 0.7, evidence that correlates with impact to RYR1 function (PP3).
PM1
This variant resides within the pore region (amino acids 4800-4950), of RYR1 that is defined as a mutation hotspot/critical functional domain by the ClinGen Congenital Myopathies VCEP (PM1).
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
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
Curation History
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