ClinVar Genomic variation as it relates to human health
NM_000540.3(RYR1):c.10616G>A (p.Arg3539His)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000540.3(RYR1):c.10616G>A (p.Arg3539His)
Variation ID: 132997 Accession: VCV000132997.68
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 19q13.2 19: 38525492 (GRCh38) [ NCBI UCSC ] 19: 39016132 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 9, 2014 Oct 8, 2024 Nov 10, 2021 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000540.3:c.10616G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000531.2:p.Arg3539His missense NM_001042723.2:c.10601G>A NP_001036188.1:p.Arg3534His missense NC_000019.10:g.38525492G>A NC_000019.9:g.39016132G>A NG_008866.1:g.96793G>A LRG_766:g.96793G>A LRG_766t1:c.10616G>A LRG_766p1:p.Arg3539His P21817:p.Arg3539His - Protein change
- R3539H, R3534H
- Other names
- p.R3539H:CGT>CAT
- NM_000540.3(RYR1):c.10616G>A
- Canonical SPDI
- NC_000019.10:38525491:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00060 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.00047
1000 Genomes Project 0.00060
Trans-Omics for Precision Medicine (TOPMed) 0.00144
The Genome Aggregation Database (gnomAD), exomes 0.00155
The Genome Aggregation Database (gnomAD) 0.00171
Exome Aggregation Consortium (ExAC) 0.00179
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00185
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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RYR1 | No evidence available | No evidence available |
GRCh38 GRCh37 |
8909 | 9223 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Conflicting interpretations of pathogenicity (16) |
criteria provided, conflicting classifications
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Mar 1, 2024 | RCV000119414.57 | |
Likely benign (1) |
no assertion criteria provided
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Jun 1, 2014 | RCV000148796.5 | |
Conflicting interpretations of pathogenicity (4) |
criteria provided, conflicting classifications
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Jan 7, 2022 | RCV000203202.19 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Aug 18, 2022 | RCV000209955.9 | |
Likely benign (2) |
criteria provided, single submitter
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Jan 29, 2024 | RCV001085699.9 | |
Likely benign (1) |
reviewed by expert panel
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Nov 10, 2021 | RCV001802859.3 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely benign
(Nov 10, 2021)
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reviewed by expert panel
Method: curation
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Malignant hyperthermia of anesthesia
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
|
ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, ClinGen
FDA Recognized Database
Accession: SCV002047661.1 First in ClinVar: Jan 08, 2022 Last updated: Jan 08, 2022 |
Comment:
This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies … (more)
This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions. This sequence variant predicts a substitution of arginine with histidine at codon 3539 of the RYR1 protein, p.(Arg3539His). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00305, this is considered to be more common than expected for a pathogenic variant causing autosomal dominantly inherited MHS, BS1. This variant has been reported in 10 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, all of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted) (PMID:30236257; PMID:23460944; PMID:23558838; PMID:24433488; PMID:25960145), however, the high MAF in the NFE population precludes the use of PS4. This variant has been identified in multiple individuals with negative IVCT/CHCT results, BS2 (PMID:18253926, PMID:22473935). No functional studies were identified for this variant. This variant does not reside in a hotspot for pathogenic variants that contribute to MHS. A REVEL score >0.85 (0.877) supports a pathogenic status for this variant, PP3_Moderate. Based on using Bayes to combine criteria this variant is assessed as Likely Benign, (PMID: 29300386). Criteria implemented: PP3_Moderate, BS1, BS2. (less)
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Uncertain significance
(Jun 18, 2015)
|
criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
unknown
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Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000257708.2
First in ClinVar: Dec 27, 2015 Last updated: Dec 27, 2015 |
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Uncertain significance
(Jul 01, 2013)
|
criteria provided, single submitter
Method: research
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Malignant hyperthermia, susceptibility to, 1
Affected status: unknown
Allele origin:
unknown
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Biesecker Lab/Clinical Genomics Section, National Institutes of Health
Study: ClinSeq
Accession: SCV000265737.1 First in ClinVar: Mar 12, 2016 Last updated: Mar 12, 2016
Comment:
The study set was not selected for affection status in relation to any myopathy. Pathogenicity categories were based on literature curation. See Pubmed ID: 24195946 … (more)
The study set was not selected for affection status in relation to any myopathy. Pathogenicity categories were based on literature curation. See Pubmed ID: 24195946 for details. (less)
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Number of individuals with the variant: 1
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Uncertain significance
(Jan 24, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000540251.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant is classified in HGMD as DM relating to central core disease and is reported in 10 papers, with comments suggesting VUS/LB. This variant has a Max MAF of 0.30% in ExAC (384/126200 European chrs including 1 homozygote - high for central core disease prevalence of 6/100,000). It is classified in ClinVar as VUS by 4 submitters (Emory, GeneDx, CHOP, Biesecker), and Likely benign by U Wash. (less)
Method: Genome/Exome Filtration
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Likely benign
(Jan 07, 2022)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002074555.1
First in ClinVar: Feb 12, 2022 Last updated: Feb 12, 2022 |
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Uncertain significance
(Sep 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003820576.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Likely benign
(Nov 07, 2023)
|
criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV004563935.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
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Uncertain significance
(Feb 02, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: no
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV000596887.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
|
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Uncertain significance
(May 25, 2016)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV000852216.1
First in ClinVar: Mar 01, 2018 Last updated: Mar 01, 2018 |
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Benign
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Malignant hyperthermia, susceptibility to, 1
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001141071.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Likely benign
(Aug 16, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000234974.13
First in ClinVar: Jul 05, 2015 Last updated: Mar 04, 2023 |
Comment:
See Variant Classification Assertion Criteria.
|
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Likely benign
(Aug 18, 2022)
|
criteria provided, single submitter
Method: clinical testing
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Malignant hyperthermia, susceptibility to, 1
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV004358187.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
|
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Likely benign
(Mar 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV000575180.31
First in ClinVar: Dec 06, 2016 Last updated: Oct 08, 2024 |
Comment:
RYR1: BS1
Number of individuals with the variant: 12
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Uncertain significance
(Aug 01, 2016)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000232393.5
First in ClinVar: Jun 29, 2015 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 4
Sex: mixed
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Uncertain significance
(Jun 03, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: unknown
Allele origin:
germline
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV002541636.1
First in ClinVar: Jul 09, 2022 Last updated: Jul 09, 2022 |
|
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Uncertain significance
(Jun 22, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV001474664.2
First in ClinVar: Jan 26, 2021 Last updated: Dec 31, 2022 |
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Likely benign
(Jan 29, 2024)
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criteria provided, single submitter
Method: clinical testing
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RYR1-related disorder
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000659754.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 28, 2024 |
|
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Likely benign
(-)
|
criteria provided, single submitter
Method: not provided
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
|
Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005207182.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
|
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Likely benign
(Jun 01, 2014)
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no assertion criteria provided
Method: research
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Central core disease
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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CSER _CC_NCGL, University of Washington
Study: ESP 6500 variant annotation
Accession: SCV000190534.1 First in ClinVar: Dec 06, 2014 Last updated: Dec 06, 2014
Comment:
Variants classified for the Actionable exomic incidental findings in 6503 participants: challenges of variant classification manuscript
|
|
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Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002037066.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
|
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Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
unknown
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Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001552609.1 First in ClinVar: Apr 13, 2021 Last updated: Apr 13, 2021 |
|
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Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001806817.1 First in ClinVar: Aug 25, 2021 Last updated: Aug 25, 2021 |
|
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Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001953585.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
|
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Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001980081.1 First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
|
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Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001744337.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
|
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not provided
(-)
|
no classification provided
Method: not provided
|
not provided
Affected status: not provided
Allele origin:
unknown
|
Leiden Muscular Dystrophy (RYR1)
Accession: SCV000154321.1
First in ClinVar: Jun 09, 2014 Last updated: Jun 09, 2014 |
|
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not provided
(-)
|
no classification provided
Method: phenotyping only
|
RYR1-related disorder
Affected status: unknown
Allele origin:
unknown
|
GenomeConnect, ClinGen
Accession: SCV002075091.1
First in ClinVar: Feb 12, 2022 Last updated: Feb 12, 2022 |
Comment:
Variant interpreted as Uncertain significance and reported on 05-17-2017 by Lab or GTR ID 303161. GenomeConnect assertions are reported exactly as they appear on the … (more)
Variant interpreted as Uncertain significance and reported on 05-17-2017 by Lab or GTR ID 303161. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less)
Clinical Features:
Melanoma (present) , Abnormality of vision (present) , Abnormal retinal morphology (present) , Tinnitus (present) , Hyperacusis (present) , Vertigo (present) , Cognitive impairment (present) … (more)
Melanoma (present) , Abnormality of vision (present) , Abnormal retinal morphology (present) , Tinnitus (present) , Hyperacusis (present) , Vertigo (present) , Cognitive impairment (present) , Abnormality of coordination (present) , Hypertonia (present) , Memory impairment (present) , Anxiety (present) , Depression (present) , Atrophic scars (present) , Cutaneous photosensitivity (present) , Joint hypermobility (present) , Abnormal muscle physiology (present) , Abnormality of the musculature of the limbs (present) , Cardiac arrhythmia (present) , Abnormality of the cardiovascular system (present) , Abnormal pattern of respiration (present) , Abnormal esophagus morphology (present) , Abnormal intestine morphology (present) , Gingivitis (present) (less)
Indication for testing: Diagnostic
Age: 30-39 years
Sex: female
Testing laboratory: MNG Laboratories (Medical Neurogenetics, LLC.)
Date variant was reported to submitter: 2017-05-17
Testing laboratory interpretation: Uncertain significance
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Diagnostic power and clinical impact of exome sequencing in a cohort of 500 patients with rare diseases. | Quaio CRDC | American journal of medical genetics. Part C, Seminars in medical genetics | 2020 | PMID: 33258288 |
Investigating the genetic susceptibility to exertional heat illness. | Gardner L | Journal of medical genetics | 2020 | PMID: 32054689 |
Bayesian modeling to predict malignant hyperthermia susceptibility and pathogenicity of RYR1, CACNA1S and STAC3 variants. | Sadhasivam S | Pharmacogenomics | 2019 | PMID: 31559918 |
The histopathological spectrum of malignant hyperthermia and rhabdomyolysis due to RYR1 mutations. | Knuiman GJ | Journal of neurology | 2019 | PMID: 30788618 |
'Dusty core disease' (DuCD): expanding morphological spectrum of RYR1 recessive myopathies. | Garibaldi M | Acta neuropathologica communications | 2019 | PMID: 30611313 |
RYR1 and CACNA1S genetic variants identified with statin-associated muscle symptoms. | Isackson PJ | Pharmacogenomics | 2018 | PMID: 30325262 |
Genetic epidemiology of malignant hyperthermia in the UK. | Miller DM | British journal of anaesthesia | 2018 | PMID: 30236257 |
Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. | Maxwell KN | American journal of human genetics | 2016 | PMID: 27153395 |
Malignant hyperthermia testing in probands without adverse anesthetic reaction. | Timmins MA | Anesthesiology | 2015 | PMID: 26068069 |
RYR1-related myopathies: a wide spectrum of phenotypes throughout life. | Snoeck M | European journal of neurology | 2015 | PMID: 25960145 |
Functional and genetic characterization of clinical malignant hyperthermia crises: a multi-centre study. | Klingler W | Orphanet journal of rare diseases | 2014 | PMID: 24433488 |
Using exome data to identify malignant hyperthermia susceptibility mutations. | Gonsalves SG | Anesthesiology | 2013 | PMID: 24195946 |
Actionable, pathogenic incidental findings in 1,000 participants' exomes. | Dorschner MO | American journal of human genetics | 2013 | PMID: 24055113 |
Ryanodine receptor type 1 gene variants in the malignant hyperthermia-susceptible population of the United States. | Brandom BW | Anesthesia and analgesia | 2013 | PMID: 23558838 |
CASQ1 gene is an unlikely candidate for malignant hyperthermia susceptibility in the North American population. | Kraeva N | Anesthesiology | 2013 | PMID: 23460944 |
Congenital myopathy with focal loss of cross-striations revisited. | Voermans NC | Neuromuscular disorders : NMD | 2013 | PMID: 23127960 |
Clinical and genetic findings in a large cohort of patients with ryanodine receptor 1 gene-associated myopathies. | Klein A | Human mutation | 2012 | PMID: 22473935 |
The role of CACNA1S in predisposition to malignant hyperthermia. | Carpenter D | BMC medical genetics | 2009 | PMID: 19825159 |
Biochemical and genetic analysis of 3-methylglutaconic aciduria type IV: a diagnostic strategy. | Wortmann SB | Brain : a journal of neurology | 2009 | PMID: 19015156 |
Null mutations causing depletion of the type 1 ryanodine receptor (RYR1) are commonly associated with recessive structural congenital myopathies with cores. | Monnier N | Human mutation | 2008 | PMID: 18253926 |
Gene symbol: RYR1. Disease: malignant hyperthermia. | Dekomien G | Human genetics | 2005 | PMID: 16521288 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=RYR1 | - | - | - | - |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/8c7855ea-b508-4ae1-87a3-d3a34fa2a209 | - | - | - | - |
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Text-mined citations for rs143987857 ...
HelpRecord last updated Oct 08, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.