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.14582G>A (p.Arg4861His)

CA024187

12982 (ClinVar)

Gene: RYR1
Condition: RYR1-related myopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 5e84bf47-8862-4e7e-8f15-e4df3ba0715e
Approved on: 2024-08-27
Published on: 2025-01-03

HGVS expressions

NM_000540.3:c.14582G>A
NM_000540.3(RYR1):c.14582G>A (p.Arg4861His)
NC_000019.10:g.38580440G>A
CM000681.2:g.38580440G>A
NC_000019.9:g.39071080G>A
CM000681.1:g.39071080G>A
NC_000019.8:g.43762920G>A
NG_008866.1:g.151741G>A
ENST00000593677.2:c.1518G>A
ENST00000688602.1:c.2915G>A
ENST00000689936.1:c.2887G>A
ENST00000359596.8:c.14582G>A
ENST00000355481.8:c.14567G>A
ENST00000359596.7:c.14582G>A
ENST00000360985.7:c.14564G>A
NM_000540.2:c.14582G>A
NM_001042723.1:c.14567G>A
NM_001042723.2:c.14567G>A
More

Pathogenic

Met criteria codes 7
PS4 PS2 PM2_Supporting PP3 PP1 PM5 PS3_Supporting
Not Met criteria codes 16
PS1 PP4 PVS1 PM6 PM1 PM3 PM4 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3

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 NM_000540.3:c.14582G>A variant in RYR1 is a missense variant predicted to cause substitution of arginine by histidine at amino acid 4861 (p.Arg4861His). The highest population minor allele frequency in gnomAD v4.1 is 0.0000008475 (1/1180004 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Congenital Myopathies VCEP threshold (absent with 1 allele allowed) for PM2_Supporting, meeting this criterion (PM2_Supporting). The REVEL computational prediction analysis tool gives a score of 0.912, which is above the threshold necessary to apply PP3. Four different missense variants, c.14581C>A (p.Arg4861Ser), c.14581C>G (p.Arg4861Gly), c.14581C>T (p.Arg4861Cys), c.14582G>C (p.Arg4861Pro) (ClinVar IDs: 2027376, 943431, 65986, 1066439), in the same codon have been classified as pathogenic/likely pathogenic for RYR1-related myopathy (PM5). This variant has been reported in at least five probands with RYR1-related myopathy which meets the criteria for PS4, two of which were confirmed to be de novo occurrences meeting PS2 (PMIDs:11709545, 35428369, 35081925). The variant has also been reported to segregate in one affected sibling from a family (PP1, PMID:11709545). Calcium homeostasis analysis of immortalized B-lymphocytes from patients showed significantly smaller thapsigargin-sensitive intracellular calcium stores, compared to lymphoblasts from control individuals, indicating that this variant may impact protein function (PS3_Supporting, PMID:11741831). In summary, the variant meets the criteria to be classified as pathogenic for autosomal dominant RYR1-related myopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PS4, PS2, PS3_Supporting, PM5, PM2_Supporting, PP1, PP3 (ClinGen Congenital Myopathies VCEP specifications version 2; 8/27/2024).
Met criteria codes
PS4
The variant was identified in at least 5 probands in 3 publications (PMIDs:11709545, 35428369, 35081925). More probands available in the literature but were not scored in this curation.
PS2
The variant was confirmed to be de novo occurrences in two probands (PMIDs:11709545, 35081925)
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1 is 0.0000008475 (1/1180004 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Congenital Myopathies VCEP threshold (absent with 1 allele allowed) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of 0.912, which is above the threshold of 0.7, evidence that correlates with impact to RYR1 function (PP3).
PP1
The variant segregated in one affected female sibling with childhood onset of myopathy, difficulty running and climbing stairs, at 31 yrs showed proximal muscle weakness and myogenic EMG (PMID:11709545)
PM5
Four different missense variants reported as pathogenic/likely pathogenic on ClinVar: c.14581C>A (p.Arg4861Ser), c.14581C>G (p.Arg4861Gly), c.14581C>T (p.Arg4861Cys), c.14582G>C (p.Arg4861Pro) (ClinVar IDs: 2027376, 943431, 65986, 1066439)
PS3_Supporting
Calcium homeostasis analysis of immortalized B-lymphocytes from patients showed significantly smaller thapsigargin-sensitive intracellular calcium stores, compared to lymphoblasts from control individuals
Not Met criteria codes
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The variant is absent from gnomAD v2.1.1 meeting PM2_Supporting.
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The variant is absent from gnomAD v2.1.1 meeting PM2_Supporting.
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.