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.10348-6C>G

CA023836

132994 (ClinVar)

Gene: RYR1
Condition: RYR1-related myopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 11fa8690-5bc5-4edd-b943-8458ce033568
Approved on: 2025-05-19
Published on: 2025-06-26

HGVS expressions

NM_000540.3:c.10348-6C>G
NM_000540.3(RYR1):c.10348-6C>G
NC_000019.10:g.38523211C>G
CM000681.2:g.38523211C>G
NC_000019.9:g.39013851C>G
CM000681.1:g.39013851C>G
NC_000019.8:g.43705691C>G
NG_008866.1:g.94512C>G
ENST00000599547.6:c.10287-6C>G
ENST00000359596.8:c.10348-6C>G
ENST00000355481.8:c.10348-6C>G
ENST00000359596.7:c.10348-6C>G
ENST00000360985.7:c.10345-6C>G
ENST00000594335.5:c.3750-6C>G
ENST00000599547.5:c.1155-6C>G
ENST00000600337.1:n.50-6C>G
NM_000540.2:c.10348-6C>G
NM_001042723.1:c.10348-6C>G
NM_001042723.2:c.10348-6C>G
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Pathogenic

Met criteria codes 4
PP1 PP4 PS3_Supporting PM3_Very Strong

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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The variant NM_000540.3(RYR1):c.10348-6C>G in RYR1 is an intronic variant located in intron 68. The filtering allele frequency is 0.0003329 (34/75078 alleles, 0 homozygotes) for the African/African American population, which meets no codes. In addition, the SpliceAI Acceptor Loss value is 0.47. The variant was found in compound heterozygosity with variants of uncertain significance, likely pathogenic, or pathogenic variants in 22 patients (PM3_Very Strong; PMIDs: 18253926, 21062345, 20839240, 23553484, 28818389, 30932294, 31069529, 30611313, 34440373, 35627144, 35616356, 36939041). At least 3 patients with this variant displayed ophthalmoparesis and presence of cores on muscle biopsy, which is highly specific for RYR1-related myopathy (PP4; PMID: 20839240). This variant has been observed in at least 11 South African patients with RYR1-related myopathy, suggesting a possible founder variant (PMID: 20839240). The variant has also been reported in cis with the c.14524G>A (p.Val4842Met) variant in 17 of the 22 probands, which is part of a known haplotype and has been reported as a compound heterozygous change in individuals with RYR1-related myopathies (PMIDs: 18253926, 21062345, 20839240, 23553484, 30932294, 30611313, 35627144). The variant has been found to segregate with disease in 4 affected relatives from 2 families (PP1; PMIDs: 18253926, 21062345). Functional studies in patient cells showed that the variant resulted in a loss of splicing of intron 68 and the introduction of a premature stop codon causing the mRNA to undergo NMD (PMIDs: 18253926, 25525159) (PS3_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for autosomal recessive RYR1-related myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PM3_Very Strong, PP4, PP1, PS3_Supporting (ClinGen Congenital Myopathies VCEP specifications version 2; May 19th, 2025).
Met criteria codes
PP1
The variant has been found to segregate with disease in 4 affected relatives from 2 families (PP1; PMIDs: 18253926, 21062345).
PP4
At least 3 patients with this variant displayed ophthalmoparesis and presence of cores on muscle biopsy, which is highly specific for RYR1-related myopathy (PP4; PMID: 20839240)
PS3_Supporting
Functional studies in patient cells showed that the variant resulted in a loss of splicing of intron 68 and the introduction of a premature stop codon causing the mRNA to undergo NMD (PMIDs: 18253926, 25525159) (PS3_Supporting)
PM3_Very Strong
The variant was found in compound heterozygosity with variants of uncertain significance, likely pathogenic, or pathogenic variants in 21 patients (PM3_Very Strong; PMIDs: 18253926, 21062345, 20839240, 23553484, 28818389, 30932294, 31069529, 30611313, 34440373, 35627144, 35616356, 36939041)
Curation History
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