RYR3

protein-coding

ryanodine 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

NM_001036.6

Inheritance

AD, AR

ClinVar variants

P:4U:1147B:536

Top phenotype

Congenital myopathy 20

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr15:33,310,962-33,866,121

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~555.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

genetic developmental and epileptic encephalopathyLIMITED

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.

genetic developmental and epileptic encephalopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100062

Submitter: G2P

congenital myopathyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019952

Submitter: PanelApp Australia

congenital myopathyNO_KNOWN

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.

genetic developmental and epileptic encephalopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100062

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Congenital myopathy 20AR

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

Refs: 29498452; 31230720Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RYR3 variants in ClinVar

17 Conditions Cataloged
Epileptic encephalopathyTotal: 1309
not specifiedTotal: 631
not providedTotal: 222
RYR3-related disorderTotal: 68
Congenital myopathy 20Total: 24
RYR3-related Epileptic encephalopathyTotal: 11
Inborn genetic diseasesTotal: 7
See casesTotal: 7

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.

EffectPLPVUSLBBSum
synonymous
13
clinvar
404
clinvar
31
clinvar
448
missense
1
clinvar
3
clinvar
1109
clinvar
84
clinvar
16
clinvar
1213
nonsense
9
clinvar
9
start loss
0
frameshift
5
clinvar
5
splice donor/acceptor (+/-2bp)
11
clinvar
1
clinvar
12
Total131147489471687

Highest pathogenic variant AF is 0.00007899858

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001036.6RefSeqNP_001027.3104MANE Select
ENST00000634891.2EnsemblENSP00000489262.1104MANE Select
NM_001243996.4RefSeqNP_001230925.1103Standard
ENST00000389232.10EnsemblENSP00000373884.5104Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ryr3Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.8424012.67e+30.9000.00015532045
Missense (PolyPhen)7791055.60.73812703
Synonymous-1.9911111.03e+31.080.00006249143
Loss of Function11.4562510.2230.00001283066

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000260.00025rare
Latino/Admixed American0.000440.00043rare
Ashkenazi Jewish0.000500.00050rare
East Asian0.00430.0042notable
Finnish0.000230.00023rare
European (Non-Finnish)0.000470.00046rare
South Asian0.00120.0012notable
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighMediumHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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