rs587784375
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_000540.3(RYR1):c.4094del(p.Gly1365GlufsTer33) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. A1363A) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RYR1
NM_000540.3 frameshift
NM_000540.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.650
Genes affected
RYR1 (HGNC:10483): (ryanodine receptor 1) This gene encodes a ryanodine receptor found in skeletal muscle. The encoded protein functions as a calcium release channel in the sarcoplasmic reticulum but also serves to connect the sarcoplasmic reticulum and transverse tubule. Mutations in this gene are associated with malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 19-38473699-CG-C is Pathogenic according to our data. Variant chr19-38473699-CG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 524049.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.4094del | p.Gly1365GlufsTer33 | frameshift_variant | 28/106 | ENST00000359596.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.4094del | p.Gly1365GlufsTer33 | frameshift_variant | 28/106 | 5 | NM_000540.3 | A2 | |
RYR1 | ENST00000355481.8 | c.4094del | p.Gly1365GlufsTer33 | frameshift_variant | 28/105 | 1 | P4 | ||
RYR1 | ENST00000599547.6 | c.4094del | p.Gly1365GlufsTer33 | frameshift_variant, NMD_transcript_variant | 28/80 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1393192Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 686610
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
1393192
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Cov.:
33
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0
AN XY:
686610
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GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2018 | The c.4094delG variant in the RYR1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.4094delG variant causes a frameshift starting with codon Glycine 1365, changes this amino acid to a Glutamic Acid residue, and creates a premature Stop codon at position 33 of the new reading frame, denoted p.Gly1365GlufsX33. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.4094delG variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.4094delG as a likely pathogenic variant. - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at