RYR3 ryanodine receptor 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RYR3provided by HGNC
Official Full Name: ryanodine receptor 3provided by HGNC
Primary source: HGNC:HGNC:10485
See related: Ensembl:ENSG00000198838 MIM:180903; AllianceGenome:HGNC:10485
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RYR-3; CMYP20
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]
Expression: Broad expression in brain (RPKM 1.5), endometrium (RPKM 1.4) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q13.3-q14

Exon count:: 107

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (33310967..33866102)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (31107439..31663747)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (33603168..34158303)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The genomic and clinical landscape of fetal akinesia.
Title: The genomic and clinical landscape of fetal akinesia.
RYR3 variants are associated with risk of and age of onset for hypertension, diabetes, and Alzheimer disease.
Title: Polymorphisms Within RYR3 Gene Are Associated With Risk and Age at Onset of Hypertension, Diabetes, and Alzheimer's Disease.
The Ryr Ca2+ release channel is central to cytoplasmic Ca2+ signalling in skeletal muscle, the heart, and many other tissues, playing a vital role in muscular contraction.
Title: Altered ryanodine receptor gene expression in Hirschsprung's disease.
Mutations in RYR3 Gene is associated with Gender Dysphoria.
Title: Genomic Characteristics of Gender Dysphoria Patients and Identification of Rare Mutations in RYR3 Gene.
a genome-wide linkage scan and regional association fine-mapping identified variants in the RYR3 gene as a quantitative trail locus for plasma adiponectin levels in Chinese population
Title: Genome-wide linkage analysis and regional fine mapping identified variants in the RYR3 gene as a novel quantitative trait locus for circulating adiponectin in Chinese population.
Studies indicate that the ryanodine receptors (RyRs: RyR1, RyR2, RyR3) and inositol 1,4,5-trisphosphate receptors (IP3Rs: IP3R1, IP3R2, IP3R3) are the major Ca(2+) release channels (CRCs) on the endo/sarcoplasmic reticulum (ER/SR).
Title: Essential Roles of Intracellular Calcium Release Channels in Muscle, Brain, Metabolism, and Aging.
Data show that the common variant single-nucleotide polymorphism rs2229116 of the ryanodine receptor 3 gene (RYR3) was significantly associated with carotid intima-media thickness (cIMT).
Title: Deep sequencing of RYR3 gene identifies rare and common variants associated with increased carotid intima-media thickness (cIMT) in HIV-infected individuals.
SNPs within the RYR3 region were associated with subclinical atherosclerosis among HIV-infected women. Allelic heterogeneity observed across the three races suggests that the contribution of the RYR3 gene to CCA cIMT is complex.
Title: RYR3 gene variants in subclinical atherosclerosis among HIV-infected women in the Women's Interagency HIV Study (WIHS).
rs877087 and rs2229116 of RYR3 gene are associated with atherosclerosis severity in Japanese.
Title: Association of the RYR3 gene polymorphisms with atherosclerosis in elderly Japanese population.
a genetic interaction between the RYR3 and CACNA1C genes explained variance in amyloid deposition above and beyond other major known risk factors for late-onset Alzheimer's disease
Title: Genetic interactions found between calcium channel genes modulate amyloid load measured by positron emission tomography.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital myopathy 20 MedGen: C5830393 OMIM: 620310 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study of carotid atherosclerosis in HIV-infected men. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat activates RyRs via a calcium- and calpain-mediated mechanism that upregulates DAT trafficking to the PM	PubMed
	tat	Neurons exposed to HIV-1 Tat induces calcium loss from the endoplasmic reticulum via ryanodine receptor (RyR) and increases the phosphorylated levels of PERK, eIF2a, and XBP1	PubMed
	tat	RYR3 gene regulated by HIV-1 Tat is associated with common and internal carotid intima-media thicknesses (cIMT) in HARRT-treated HIV-infected persons	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-89207 (e-PCR)
- UniSTS:170520

SHGC-84456 (e-PCR)
- UniSTS:104751

G60145 (e-PCR)
- UniSTS:137264

G66865 (e-PCR)
- UniSTS:166704

RH121729 (e-PCR)
- UniSTS:134471

RH122298 (e-PCR)
- UniSTS:137825

RH94176 (e-PCR)
- UniSTS:88939

RYR3 (e-PCR)
- UniSTS:254065

SHGC-77736 (e-PCR)
- UniSTS:100991

RYR3 (e-PCR)
- UniSTS:503171

RH123440 (e-PCR)
- UniSTS:135828

SHGC-77979 (e-PCR)
- UniSTS:101527

D15S224E (e-PCR)
- UniSTS:51096

SHGC-145281 (e-PCR)
- UniSTS:174491

RH123450 (e-PCR)
- UniSTS:135838

D15S995 (e-PCR), detects polymorphism
- UniSTS:27567

RH120387 (e-PCR)
- UniSTS:132530

D13S284 (e-PCR)
- UniSTS:42934

RYR3__6899 (e-PCR)
- UniSTS:471747

D15S1040 (e-PCR), detects polymorphism
- UniSTS:73677

SHGC-142044 (e-PCR)
- UniSTS:171214

RH120621 (e-PCR)
- UniSTS:132562

D15S1355 (e-PCR)
- UniSTS:51671

D15S1007 (e-PCR), detects polymorphism
- UniSTS:54234

G09850 (e-PCR)
- UniSTS:65245

SHGC-81739 (e-PCR)
- UniSTS:103909

RH98244 (e-PCR)
- UniSTS:89589

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium-induced calcium release activity	ISS Inferred from Sequence or Structural Similarity more info
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables intracellularly gated calcium channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ryanodine-sensitive calcium-release channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables ryanodine-sensitive calcium-release channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables ryanodine-sensitive calcium-release channel activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium ion transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in cellular response to ATP	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to caffeine	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to calcium ion	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to magnesium ion	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in protein homotetramerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in release of sequestered calcium ion into cytosol	ISS Inferred from Sequence or Structural Similarity more info
involved_in release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
involved_in striated muscle contraction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
part_of calcium channel complex	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in sarcolemma	IBA Inferred from Biological aspect of Ancestor more info
is_active_in sarcoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in sarcoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in sarcoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in sarcoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in smooth endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: ryanodine receptor 3

Names: brain ryanodine receptor-calcium release channel; brain-type ryanodine receptor; type 3 ryanodine receptor

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_047076.1 RefSeqGene

Range

5185..560320

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001036.6 → NP_001027.3 ryanodine receptor 3 isoform 1

See identical proteins and their annotated locations for NP_001027.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC010809, AC011938, AC055874, AC067793, AC087638

Consensus CDS

CCDS45210.1

UniProtKB/Swiss-Prot

O15175, Q15412, Q15413

UniProtKB/TrEMBL

A0A0X1KG73

Related

ENSP00000489262.1, ENST00000634891.2

Conserved Domains (12) summary

smart00472
Location:275 → 368

MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases

cd12877
Location:641 → 792

SPRY1_RyR; SPRY domain 1 (SPRY1) of ryanodine receptor (RyR)

cd12878
Location:1072 → 1204

SPRY2_RyR; SPRY domain 2 (SPRY2) of ryanodine receptor (RyR)

pfam00520
Location:4621 → 4781

Ion_trans; Ion transport protein

pfam01365
Location:442 → 621

RYDR_ITPR; RIH domain

pfam02026
Location:849 → 937

RyR; RyR domain

pfam02815
Location:216 → 397

MIR; MIR domain

pfam06459
Location:4234 → 4504

RR_TM4-6; Ryanodine Receptor TM 4-6

pfam08454
Location:3731 → 3844

RIH_assoc; RyR and IP3R Homology associated

pfam13833
Location:3935 → 3983

EF-hand_8; EF-hand domain pair

cd12879
Location:1324 → 1462

SPRY3_RyR; SPRY domain 3 (SPRY3) of ryanodine receptor (RyR)

cl19745
Location:12 → 207

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
NM_001243996.4 → NP_001230925.1 ryanodine receptor 3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (2) is shorter than isoform 1.

Source sequence(s)

AB001025, AC011938, AC087638, AJ001515

Consensus CDS

CCDS58351.1

UniProtKB/TrEMBL

A0A0X1KG73

Related

ENSP00000399610.3, ENST00000415757.7

Conserved Domains (12) summary

smart00472
Location:275 → 368

MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases

cd12877
Location:641 → 792

SPRY1_RyR; SPRY domain 1 (SPRY1) of ryanodine receptor (RyR)

cd12878
Location:1072 → 1204

SPRY2_RyR; SPRY domain 2 (SPRY2) of ryanodine receptor (RyR)

pfam00520
Location:4616 → 4776

Ion_trans; Ion transport protein

pfam01365
Location:442 → 621

RYDR_ITPR; RIH domain

pfam02026
Location:849 → 937

RyR; RyR domain

pfam02815
Location:216 → 397

MIR; MIR domain

pfam06459
Location:4229 → 4499

RR_TM4-6; Ryanodine Receptor TM 4-6

pfam08454
Location:3726 → 3839

RIH_assoc; RyR and IP3R Homology associated

pfam13833
Location:3930 → 3978

EF-hand_8; EF-hand domain pair

cd12879
Location:1324 → 1462

SPRY3_RyR; SPRY domain 3 (SPRY3) of ryanodine receptor (RyR)

cl19745
Location:12 → 207

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

33310967..33866102

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047432931.1 → XP_047288887.1 ryanodine receptor 3 isoform X10
XM_017022468.2 → XP_016877957.1 ryanodine receptor 3 isoform X1

UniProtKB/TrEMBL

A0A0X1KG73
XM_017022475.2 → XP_016877964.1 ryanodine receptor 3 isoform X11

UniProtKB/TrEMBL

A0A0X1KG73
XM_017022473.2 → XP_016877962.1 ryanodine receptor 3 isoform X7

UniProtKB/TrEMBL

A0A0X1KG73
XM_047432932.1 → XP_047288888.1 ryanodine receptor 3 isoform X12
XM_017022469.2 → XP_016877958.1 ryanodine receptor 3 isoform X2

UniProtKB/TrEMBL

A0A0X1KG73
XM_011521880.3 → XP_011520182.1 ryanodine receptor 3 isoform X8

UniProtKB/TrEMBL

A0A0U1RRH1, A0A0X1KG73

Related

ENSP00000489529.1, ENST00000634418.1

Conserved Domains (12) summary

smart00472
Location:275 → 368

MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases

cd12877
Location:641 → 792

SPRY1_RyR; SPRY domain 1 (SPRY1) of ryanodine receptor (RyR)

cd12878
Location:1072 → 1204

SPRY2_RyR; SPRY domain 2 (SPRY2) of ryanodine receptor (RyR)

pfam00520
Location:4610 → 4770

Ion_trans; Ion transport protein

pfam01365
Location:442 → 621

RYDR_ITPR; RIH domain

pfam02026
Location:849 → 937

RyR; RyR domain

pfam02815
Location:216 → 397

MIR; MIR domain

pfam06459
Location:4223 → 4493

RR_TM4-6; Ryanodine Receptor TM 4-6

pfam08454
Location:3720 → 3833

RIH_assoc; RyR and IP3R Homology associated

pfam13833
Location:3924 → 3972

EF-hand_8; EF-hand domain pair

cd12879
Location:1324 → 1462

SPRY3_RyR; SPRY domain 3 (SPRY3) of ryanodine receptor (RyR)

cl19745
Location:12 → 207

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
XM_017022472.2 → XP_016877961.1 ryanodine receptor 3 isoform X5

UniProtKB/TrEMBL

A0A0X1KG73
XM_017022471.2 → XP_016877960.1 ryanodine receptor 3 isoform X4

UniProtKB/TrEMBL

A0A0X1KG73
XM_024450015.2 → XP_024305783.1 ryanodine receptor 3 isoform X6

UniProtKB/TrEMBL

A0A0X1KG73

Conserved Domains (11) summary

cd12877
Location:641 → 792

SPRY1_RyR; SPRY domain 1 (SPRY1) of ryanodine receptor (RyR)

cd12878
Location:1072 → 1204

SPRY2_RyR; SPRY domain 2 (SPRY2) of ryanodine receptor (RyR)

cd12879
Location:1318 → 1461

SPRY3_RyR; SPRY domain 3 (SPRY3) of ryanodine receptor (RyR)

pfam00520
Location:4615 → 4775

Ion_trans; Ion transport protein

pfam01365
Location:440 → 621

RYDR_ITPR; RIH domain

pfam02026
Location:849 → 937

RyR; RyR domain

pfam02815
Location:216 → 397

MIR; MIR domain

pfam06459
Location:4228 → 4498

RR_TM4-6; Ryanodine Receptor TM 4-6

pfam08454
Location:3725 → 3838

RIH_assoc; RyR and IP3R Homology associated

pfam13499
Location:3922 → 3977

EF-hand_7; EF-hand domain pair

cl19745
Location:12 → 207

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
XM_024450016.2 → XP_024305784.1 ryanodine receptor 3 isoform X16

UniProtKB/TrEMBL

A0A0X1KG73

Conserved Domains (11) summary

cd12877
Location:641 → 792

SPRY1_RyR; SPRY domain 1 (SPRY1) of ryanodine receptor (RyR)

cd12878
Location:1072 → 1204

SPRY2_RyR; SPRY domain 2 (SPRY2) of ryanodine receptor (RyR)

cd12879
Location:1318 → 1461

SPRY3_RyR; SPRY domain 3 (SPRY3) of ryanodine receptor (RyR)

pfam00520
Location:4614 → 4774

Ion_trans; Ion transport protein

pfam01365
Location:440 → 621

RYDR_ITPR; RIH domain

pfam02026
Location:849 → 937

RyR; RyR domain

pfam02815
Location:216 → 397

MIR; MIR domain

pfam06459
Location:4227 → 4497

RR_TM4-6; Ryanodine Receptor TM 4-6

pfam08454
Location:3724 → 3837

RIH_assoc; RyR and IP3R Homology associated

pfam13499
Location:3921 → 3976

EF-hand_7; EF-hand domain pair

cl19745
Location:12 → 207

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
XM_017022476.2 → XP_016877965.1 ryanodine receptor 3 isoform X13

UniProtKB/TrEMBL

A0A0X1KG73
XM_047432933.1 → XP_047288889.1 ryanodine receptor 3 isoform X14
XM_017022477.2 → XP_016877966.1 ryanodine receptor 3 isoform X15
XM_017022474.2 → XP_016877963.1 ryanodine receptor 3 isoform X9

UniProtKB/TrEMBL

A0A0X1KG73
XM_017022470.3 → XP_016877959.1 ryanodine receptor 3 isoform X3

UniProtKB/TrEMBL

A0A0X1KG73