RYR3
protein-codingryanodine receptor 3, the group of Ryanodine receptors|EF-hand domain containing
Gene summary
The protein encoded by this gene is a ryanodine receptor, which functions to release calcium from intracellular storage for use in many cellular processes. For example, the encoded protein is involved in skeletal muscle contraction by releasing calcium from the sarcoplasmic reticulum followed by depolarization of T-tubules. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~555.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0100062
Submitter: ClinGen
*RYR3* was first reported in relation to autosomal dominant developmental and epileptic encephalopathy in 2014 (EuroEPINOMICS-RES Consortium et al., PMID: 25262651). Of note, there is currently an additional assertion for autosomal recessive congenital myopathies resulting from biallelic RYR3 variants (OMIM: 620310). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in phenotype and inheritance pattern. Therefore, these assertions have been split into separate curations; the curation for autosomal recessive congenital myopathies has been completed by the ClinGen Congenital Myopathies GCEP. This curation only includes individuals with developmental and epileptic encephalopathy. Two missense variants, reported in two probands in one publication are included in this curation (PMID: 25262651). Additional publications were reviewed, but no scorable evidence was identified. In summary, there is limited evidence to support the gene-disease relationship between *RYR3* and autosomal dominant developmental and epileptic encephalopathy (MONDO:0100062). Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This gene-disease pair was originally evaluated by the Epilepsy GCEP on June 19th, 2018. It was recurated on October 3rd, 2023. Several new papers were reviewed, but no new evidence was scored (PMIDs: 33557955, 29667327, 33994118). As a result of this reevaluation, the classification did not change.
Inheritance Pattern: AD
Disease ID:MONDO:0100062
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0019952
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0019952
Submitter: ClinGen
*RYR3* was first reported in relation to autosomal recessive congenital myopathy in 2018 (Nilipour *et al.*, 2018; PMID 29498452) in an affected individual with nemaline myopathy and harboring two unique *RYR3* missense variants, however, the impact of these variants on protein function is unclear. In 2019, Pehlivan *et al.* reported bi-allelic *RYR3* variants in three unrelated individuals among a large cohort of arthrogryposis patients (PMID: 31230720). However, those probands were not considered as evidence due to either high minor allele frequency of the *RYR3* variant, involvement of variants from other genes, lack of muscle biopsy, and/or unclear impact of the variants to RYR3 protein function. To our knowledge, there are no current reports in the literature of additional individuals with *RYR3*-related autosomal recessive congenital myopathy. In addition, there is some functional evidence in support of this *RYR3*-autosomal recessive congenital myopathy relationship exists, including protein expression data (PMID: 29498452) and functional alteration data from ryr3 knockout mice (PMIDs: 9384575 and 17412417) and RyR3-depleted zebrafish (PMID: 25667412). In summary, no convincing evidence of a causal role for *RYR3* in autosomal recessive congenital myopathy has been reported. Although this gene-disease association is supported by relevant experimental evidence, the single report implicating *RYR3* in autosomal recessive congenital myopathy in humans is not sufficient to be scored as genetic evidence and the relationship between *RYR3* and autosomal recessive congenital myopathy is Disputed. More evidence is needed to either support or entirely refute the role *RYR3* plays in this disease. This gene-disease pair was originally evaluated by the ClinGen Congenital Myopathies GCEP on August 28, 2023. It was reevaluated on October 27, 2025. As a result of this reevaluation, the classification did not change. This classification was approved by the ClinGen Congenital Myopathies GCEP on meeting date October 27, 2025.
Inheritance Pattern: AD
Disease ID:MONDO:0100062
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RYR3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001036.6. 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 | 13 | 404 | 31 | 448 | ||
| missense | 1 | 3 | 1109 | 84 | 16 | 1213 |
| nonsense | 9 | 9 | ||||
| start loss | 0 | |||||
| frameshift | 5 | 5 | ||||
| splice donor/acceptor (+/-2bp) | 11 | 1 | 12 | |||
| Total | 1 | 3 | 1147 | 489 | 47 | 1687 |
Highest pathogenic variant AF is 0.00007899858
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001027.3 | 104 | MANE Select | |
| Ensembl | ENSP00000489262.1 | 104 | MANE Select | |
| RefSeq | NP_001230925.1 | 103 | Standard | |
| Ensembl | ENSP00000373884.5 | 104 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ryr3 | Danio rerio | Structure: slow muscle cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Oxytocin signaling pathway - Homo sapiens (human)
- Alzheimer,s disease - Homo sapiens (human)
- Circadian entrainment - Homo sapiens (human)
- Calcium signaling pathway - Homo sapiens (human)
- Apelin signaling pathway - Homo sapiens (human)
Biological Process
- calcium ion transport
- ion transmembrane transport
- release of sequestered calcium ion into cytosol
- protein homotetramerization
- negative regulation of cytosolic calcium ion concentration
Molecular Function
- ryanodine-sensitive calcium-release channel activity
- calcium ion binding
- calmodulin binding
- calcium-release channel activity
- calcium-induced calcium release activity
Cellular Component
- smooth endoplasmic reticulum
- plasma membrane
- integral component of membrane
- sarcoplasmic reticulum
- Z disc
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000389232
- Coding exons
- 104
- Length
- 555141
- Individuals with no LoFs
- 125160
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 197
- Defined
- 125357
- p
- 0.000786
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.84 | 2401 | 2.67e+3 | 0.900 | 0.000155 | 32045 |
| Missense (PolyPhen) | 779 | 1055.6 | 0.738 | 12703 | ||
| Synonymous | -1.99 | 1111 | 1.03e+3 | 1.08 | 0.0000624 | 9143 |
| Loss of Function | 11.4 | 56 | 251 | 0.223 | 0.0000128 | 3066 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00025 | rare |
| Latino/Admixed American | 0.00044 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.0043 | 0.0042 | notable |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00047 | 0.00046 | rare |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm in muscle and thereby plays a role in triggering muscle contraction. May regulate Ca(2+) release by other calcium channels. Calcium channel that mediates Ca(2+)-induced Ca(2+) release from the endoplasmic reticulum in non-muscle cells. Contributes to cellular calcium ion homeostasis (By similarity). Plays a role in cellular calcium signaling. {ECO:0000250, ECO:0000269|PubMed:12354756}.;
Recessive Scores
- pRec
- 0.170
Intolerance Scores
- LoFtool
- 0.0351
- RVIS EVS
- -5.87
- RVIS percentile EVS
- 0.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.746
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |