RYR1
protein-codingryanodine receptor 1, the group of Ryanodine receptors|Protein phosphatase 1 regulatory subunits
Gene summary
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]
- MHS
- MHS1
- CCO
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~161.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0100150
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009712
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0007294
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0100150
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0100150
Submitter: ClinGen
RYR1 was reported in relation to autosomal recessive RYR1-related myopathy in 2002 (Ferreiro et al., PMID:12112081). At least 14 unique variants (missense, frameshift, nonsense, splice) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Variants in this gene have been reported in at least 7 probands in 4 publications (PMIDs: 12112081, 12136074, 12719381, 18253926). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) and experimental evidence (6 pts) has been reached. Of note, this gene has also been implicated in autosomal dominant malignant hyperthermia and autosomal dominant RYR1-related myopathy. These will be assessed separately. This gene-disease association is supported by expression studies and animal models. In summary, RYR1 is definitively associated with autosomal recessive RYR1-related myopathy.
Inheritance Pattern: AD
Disease ID:MONDO:0007783
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007783
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007294
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0018528
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0015705
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0017936
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009712
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0007783
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0020485
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007294
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0007783
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0007294
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007783
Submitter: ClinGen
RYR1 has been reported in relation to autosomal dominant malignant hyperthermia susceptibility as early as 1991 by Gillard et al. (PMID:1774074). Malignant hyperthermia is a pharmacogenetic disorder of skeletal muscle calcium regulation associated with uncontrolled skeletal muscle metabolism with significant morbidity in response to specific anesthetics. Numerous unique missense variants have been reported in humans and the mechanism for disease is heterozygous gain-of-function. Evidence supporting this gene-disease relationship includes case-level, segregation, and experimental data. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. Of note, this gene has also been implicated in autosomal dominant and autosomal recessive congenital myopathies. These associations have been assessed separately by the ClinGen Congenital Myopathies GCEP. In summary, RYR1 is definitively associated with autosomal dominant malignant hyperthermia susceptibility. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen General GCEP on 11/25/2020. (SOP Version 8).
Inheritance Pattern: AD
Disease ID:MONDO:0100150
Submitter: ClinGen
RYR1 was reported in relation to autosomal dominant RYR1-related myopathy in 1993. At least 7 unique variants (missense) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Variants in this gene have been reported in at least 7 probands in 6 publications (PMIDs: 8220422, 12136074, 20888934, 17376685, 28527222, 25960145). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. This gene-disease association is supported by knock-in mouse models, in vitro functional assays, and expression studies. In summary, RYR1 is definitively associated with autosomal dominant RYR1-related myopathy. Of note, this gene has also been implicated in autosomal recessive RYR1-related myopathy and autosomal dominant malignant hyperthermia susceptibility.
Inheritance Pattern: AD
Disease ID:MONDO:0018493
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009668
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007294
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Renal
Intervention: Cardiovascular; Musculoskeletal; Renal; Pharmacogenomic
Rationale: Individuals with recessive inheritance have been described; Invididuals are susceptible to malignant hyperthermic crisis (which can affect both skeletal muscle and cardiac function) in a number of situations, including when exposed to specific agents such as certain agents used in anesthesia (eg, halothane) or depolarizing muscle relaxants (eg, succinyl choline), and to treat or prevent acute crises, dantrolene can be effective; Individuals may also suffer from exertional rhabdomyolysis or have attacks triggered by tachycardia or acidosis, and precautions may be beneficial; For Minicore myopathy with external ophthalmoplegia, Centronuclear myopathy, individuals with these conditions may also be at risk of malignant hyperthermia, and appropriate precautions may be beneficial
Comments: Individuals with RYR1-related conditions may be at risk of malignant hyperthermia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RYR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000540.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 6 | 82 | 2573 | 19 | 2682 |
| missense | 80 | 336 | 4490 | 122 | 19 | 5047 |
| nonsense | 108 | 48 | 25 | 181 | ||
| start loss | 1 | 1 | ||||
| frameshift | 159 | 117 | 52 | 1 | 329 | |
| splice donor/acceptor (+/-2bp) | 23 | 142 | 29 | 3 | 197 | |
| Total | 372 | 649 | 4679 | 2699 | 38 | 8437 |
Highest pathogenic variant AF is 0.00021201343
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000531.2 | 106 | MANE Select | |
| Ensembl | ENSP00000352608.2 | 106 | MANE Select | |
| RefSeq | NP_001036188.1 | 105 | Standard | |
| Ensembl | ENSP00000347667.3 | 105 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ryr1b | Danio rerio | Structure: fast muscle cell Quality: disorganized abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Oxytocin signaling pathway - Homo sapiens (human)
- Long-term depression - Homo sapiens (human)
- Circadian entrainment - Homo sapiens (human)
- Calcium signaling pathway - Homo sapiens (human)
- Apelin signaling pathway - Homo sapiens (human)
Biological Process
- response to hypoxia
- outflow tract morphogenesis
- calcium ion transport
- muscle contraction
- release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
Molecular Function
- protease binding
- ryanodine-sensitive calcium-release channel activity
- voltage-gated calcium channel activity
- calcium channel activity
- calcium ion binding
Cellular Component
- cytoplasm
- smooth endoplasmic reticulum
- plasma membrane
- integral component of plasma membrane
- cell cortex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359596
- Coding exons
- 106
- Length
- 153866
- Individuals with no LoFs
- 125404
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 344
- Defined
- 125748
- p
- 0.00137
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.92 | 2698 | 2.99e+3 | 0.901 | 0.000218 | 32806 |
| Missense (PolyPhen) | 524 | 603.91 | 0.86768 | 6389 | ||
| Synonymous | -2.17 | 1365 | 1.27e+3 | 1.08 | 0.0000972 | 9980 |
| Loss of Function | 9.05 | 97 | 252 | 0.385 | 0.0000139 | 2847 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0010 | 0.00098 | rare |
| Latino/Admixed American | 0.0014 | 0.0014 | notable |
| Ashkenazi Jewish | 0.0043 | 0.0043 | notable |
| East Asian | 0.00088 | 0.00087 | rare |
| Finnish | 0.0011 | 0.0011 | notable |
| European (Non-Finnish) | 0.0016 | 0.0016 | notable |
| South Asian | 0.00039 | 0.00039 | rare |
| Other | 0.0016 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules (PubMed:11741831, PubMed:16163667). Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm (PubMed:18268335). Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity). {ECO:0000250|UniProtKB:E9PZQ0, ECO:0000269|PubMed:18268335, ECO:0000305|PubMed:11741831, ECO:0000305|PubMed:16163667}.;
- Disease
- DISEASE: Malignant hyperthermia 1 (MHS1) [MIM:145600]: Autosomal dominant pharmacogenetic disorder of skeletal muscle and is one of the main causes of death due to anesthesia. In susceptible people, an MH episode can be triggered by all commonly used inhalational anesthetics such as halothane and by depolarizing muscle relaxants such as succinylcholine. The clinical features of the myopathy are hyperthermia, accelerated muscle metabolism, contractures, metabolic acidosis, tachycardia and death, if not treated with the postsynaptic muscle relaxant, dantrolene. Susceptibility to MH can be determined with the 'in vitro' contracture test (IVCT): observing the magnitude of contractures induced in strips of muscle tissue by caffeine alone and halothane alone. Patients with normal response are MH normal (MHN), those with abnormal response to caffeine alone or halothane alone are MH equivocal (MHE(C) and MHE(H) respectively). {ECO:0000269|PubMed:10051009, ECO:0000269|PubMed:10484775, ECO:0000269|PubMed:10612851, ECO:0000269|PubMed:10823104, ECO:0000269|PubMed:10888602, ECO:0000269|PubMed:11241852, ECO:0000269|PubMed:11389482, ECO:0000269|PubMed:11525881, ECO:0000269|PubMed:11575529, ECO:0000269|PubMed:11928716, ECO:0000269|PubMed:12059893, ECO:0000269|PubMed:12066726, ECO:0000269|PubMed:12123492, ECO:0000269|PubMed:12208234, ECO:0000269|PubMed:12411788, ECO:0000269|PubMed:12709367, ECO:0000269|PubMed:12883402, ECO:0000269|PubMed:1354642, ECO:0000269|PubMed:14732627, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:15221887, ECO:0000269|PubMed:15448513, ECO:0000269|PubMed:16163667, ECO:0000269|PubMed:1774074, ECO:0000269|PubMed:19191329, ECO:0000269|PubMed:19685112, ECO:0000269|PubMed:20142353, ECO:0000269|PubMed:20681998, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24013571, ECO:0000269|PubMed:26115329, ECO:0000269|PubMed:26381711, ECO:0000269|PubMed:26631338, ECO:0000269|PubMed:27586648, ECO:0000269|PubMed:7751854, ECO:0000269|PubMed:7849712, ECO:0000269|PubMed:7881417, ECO:0000269|PubMed:8012359, ECO:0000269|PubMed:8220423, ECO:0000269|PubMed:9066328, ECO:0000269|PubMed:9138151, ECO:0000269|PubMed:9389851, ECO:0000269|PubMed:9450902, ECO:0000269|PubMed:9497245}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Central core disease of muscle (CCD) [MIM:117000]: Autosomal dominant congenital myopathy, but a severe autosomal recessive form also exists. Both clinical and histological variability is observed. Affected individuals typically display hypotonia and proximal muscle weakness in infancy, leading to the delay of motor milestones. The clinical course of the disorder is usually slow or nonprogressive in adulthood, and the severity of the symptoms may vary from normal to significant muscle weakness. Microscopic examination of CCD-affected skeletal muscle reveals a predominance of type I fibers containing amorphous-looking areas (cores) that do not stain with oxidative and phosphorylase histochemical techniques. {ECO:0000269|PubMed:10097181, ECO:0000269|PubMed:11113224, ECO:0000269|PubMed:11709545, ECO:0000269|PubMed:11741831, ECO:0000269|PubMed:12112081, ECO:0000269|PubMed:12136074, ECO:0000269|PubMed:12565913, ECO:0000269|PubMed:12566385, ECO:0000269|PubMed:12937085, ECO:0000269|PubMed:14670767, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:17204054, ECO:0000269|PubMed:17226826, ECO:0000269|PubMed:18253926, ECO:0000269|PubMed:18312400, ECO:0000269|PubMed:20142353, ECO:0000269|PubMed:21674524, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24561095, ECO:0000269|PubMed:26381711, ECO:0000269|PubMed:27234031, ECO:0000269|PubMed:27586648, ECO:0000269|PubMed:7829078, ECO:0000269|PubMed:8220422, ECO:0000269|PubMed:8220423, ECO:0000269|PubMed:9497245}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiminicore disease with external ophthalmoplegia (MMDO) [MIM:255320]: Clinically heterogeneous neuromuscular disorder. General features include neonatal hypotonia, delayed motor development, and generalized muscle weakness and amyotrophy, which may progress slowly or remain stable. Muscle biopsy shows multiple, poorly circumscribed, short areas of sarcomere disorganization and mitochondria depletion (areas termed minicores) in most muscle fibers. Typically, no dystrophic signs, such as muscle fiber necrosis or regeneration or significant endomysial fibrosis, are present in multiminicore disease. {ECO:0000269|PubMed:12719381, ECO:0000269|PubMed:16380615, ECO:0000269|PubMed:20583297}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in RYR1 may be a cause of Samaritan myopathy, a congenital myopathy with benign course. Patients display severe hypotonia and respiratory distress at birth. Unlike other congenital myopathies, the health status constantly improves and patients are minimally affected at adulthood.;
Intolerance Scores
- LoFtool
- 0.00248
- RVIS EVS
- -8.29
- RVIS percentile EVS
- 0.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.872
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |