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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Variant: NM_000540.3(RYR1):c.13013_13032del (p.Ala4338fs)

CA024029

12996 (ClinVar)

Gene: RYR1
Condition: RYR1-related myopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 6ee3f66b-5a25-42a5-a7cd-c833bc95b647
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_000540.3:c.13013_13032del
NM_000540.3(RYR1):c.13013_13032del (p.Ala4338fs)
NC_000019.10:g.38565347_38565366del
CM000681.2:g.38565347_38565366del
NC_000019.9:g.39055987_39056006del
CM000681.1:g.39055987_39056006del
NC_000019.8:g.43747827_43747846del
NG_008866.1:g.136648_136667del
ENST00000688602.1:c.1423_1442del
ENST00000689936.1:c.1405_1424del
ENST00000359596.8:c.13013_13032del
ENST00000355481.8:c.12998_13017del
ENST00000359596.7:c.13013_13032del
ENST00000360985.7:c.12995_13014del
NM_000540.2:c.13013_13032del
NM_001042723.1:c.12998_13017del
NM_001042723.2:c.12998_13017del
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Pathogenic

Met criteria codes 4
PM2_Supporting PM3_Supporting PP4 PVS1

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 NM_000540.3:c.13013_13032del p.(Ala4338Glyfs*238) variant in RYR1 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 91/106 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). The highest population minor allele frequency in gnomAD v4.1 is 0.000004965 (5/1006982 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Congenital Myopathies VCEP threshold (≤ 0.00000697) for PM2_Supporting, meeting this criterion (PM2_Supporting). This variant was found in trans with an RYR1 VUS NM_000540.3:c.1559T>C p.(Leu520Pro), in an adult woman affected with centronuclear myopathy which is highly compatible with recessive RYR1-related myopathy (PM3_Supporting, PP4, Internal VCEP contributors). 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: PVS1, PM2_Supporting, PM3_Supporting, PP4 (Congenital Myopathies VCEP specifications Version 1: 8/7/2024)
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1 is 0.000004965 (5/1006982 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Congenital Myopathies VCEP threshold (≤ 0.00000697) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PM3_Supporting
This variant was found in trans with an RYR1 VUS NM_000540.3:c.1559T>C p.(Leu520Pro), in an adult woman affected with centronuclear myopathy which is highly compatible with recessive RYR1-related myopathy (PM3_Supporting, PP4, Internal VCEP contributors).
PP4
This variant was found in trans with an RYR1 VUS NM_000540.3:c.1559T>C p.(Leu520Pro), in an adult woman affected with centronuclear myopathy which is highly compatible with recessive RYR1-related myopathy (PM3_Supporting, PP4, Internal VCEP contributors).
PVS1
The c.13013_13032del p.(Ala4338Glyfs*238)(NM_000540.3) variant in RYR1 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 91/106 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Curation History
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