ITPR1 inositol 1,4,5-trisphosphate receptor type 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ITPR1provided by HGNC
Official Full Name: inositol 1,4,5-trisphosphate receptor type 1provided by HGNC
Primary source: HGNC:HGNC:6180
See related: Ensembl:ENSG00000150995 MIM:147265; AllianceGenome:HGNC:6180
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: ACV; CLA4; IP3R; IP3R1; SCA15; SCA16; SCA29; INSP3R1; PPP1R94
Summary: This gene encodes an intracellular receptor for inositol 1,4,5-trisphosphate. Upon stimulation by inositol 1,4,5-trisphosphate, this receptor mediates calcium release from the endoplasmic reticulum. Mutations in this gene cause spinocerebellar ataxia type 15, a disease associated with an heterogeneous group of cerebellar disorders. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
Expression: Ubiquitous expression in thyroid (RPKM 15.8), brain (RPKM 10.9) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p26.1

Exon count:: 62

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (4493348..4847506)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (4487354..4841309)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (4535032..4889190)

Chromosome 3 - NC_000003.12 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?

Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design.
Title: Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design.
Identification of ITPR1 gene as a novel target for hsa-miR-34b-5p in non-obstructive azoospermia: a Ca[2+]/apoptosis pathway cross-talk.
Title: Identification of ITPR1 gene as a novel target for hsa-miR-34b-5p in non-obstructive azoospermia: a Ca(2+)/apoptosis pathway cross-talk.
The Complex Effects of PKM2 and PKM2:IP3R Disruption on Intracellular Ca[2+] Handling and Cellular Functions.
Title: The Complex Effects of PKM2 and PKM2:IP(3)R Disruption on Intracellular Ca(2+) Handling and Cellular Functions.
Two unrelated fetuses with ITPR1 missense variants and fetal hydrops.
Title: Two unrelated fetuses with ITPR1 missense variants and fetal hydrops.
Inositol 1,4,5-trisphosphate receptor gene variants are related to the risk of breast cancer in a Chinese population.
Title: Inositol 1,4,5-trisphosphate receptor gene variants are related to the risk of breast cancer in a Chinese population.
KRAP is required for diffuse and punctate IP3-mediated Ca(2+) liberation and determines the number of functional IP3R channels within clusters.
Title: KRAP is required for diffuse and punctate IP(3)-mediated Ca(2+) liberation and determines the number of functional IP(3)R channels within clusters.
Decreased GZMB, NRP1, ITPR1, and SERPINB9 Transcripts Lead to Reduced Regulatory T Cells Suppressive Capacity in Generalized Vitiligo Patients.
Title: Decreased GZMB, NRP1, ITPR1, and SERPINB9 Transcripts Lead to Reduced Regulatory T Cells Suppressive Capacity in Generalized Vitiligo Patients.
A gain-of-function mutation in the ITPR1 gating domain causes male infertility in mice.
Title: A gain-of-function mutation in the ITPR1 gating domain causes male infertility in mice.
Identification of ITPR1 as a Hub Gene of Group 3 Medulloblastoma and Coregulated Genes with Potential Prognostic Values.
Title: Identification of ITPR1 as a Hub Gene of Group 3 Medulloblastoma and Coregulated Genes with Potential Prognostic Values.
Upregulation of IP3 receptor mediates APP-induced defects in synaptic downscaling and sleep homeostasis.
Title: Upregulation of IP(3) receptor mediates APP-induced defects in synaptic downscaling and sleep homeostasis.

Submit: New GeneRIF Correction See all GeneRIFs (127)

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
Gillespie syndrome MedGen: C0431401 OMIM: 206700 GeneReviews: Not available	Compare labs
Spinocerebellar ataxia type 15/16 MedGen: C1847725 OMIM: 606658 GeneReviews: Hereditary Ataxia Overview, Spinocerebellar Ataxia Type 15	Compare labs
Spinocerebellar ataxia type 29 MedGen: C1861732 OMIM: 117360 GeneReviews: Hereditary Ataxia Overview	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2023-10-12) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2023-10-12) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic 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
Nef	nef	HIV-1 Nef interacts with inositol 1,4,5-triphosphate receptor (IP3R) to trigger the activation of plasma membrane calcium influx channels	PubMed
Pr55(Gag)	gag	IP3R differentially associates with HIV-1 wild-type Gag and P7L-Gag, indicating that Gag and IP3R are in proximity at the plasma membrane	PubMed
	gag	Inositol (1,4,5)-triphosphate receptor (IP3R) function is required for efficient release of HIV-1 Gag	PubMed
	gag	SPRY-mediated inhibition of HIV-1 Gag release is repressed by IP3R	PubMed
Tat	tat	HIV-1 Tat induces release of calcium from inositol 1,4,5-triphosphate receptor-regulated stores in neurons and astrocytes, an effect that plays an important role in Tat-induced TNF-alpha production	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-59934 (e-PCR)
- UniSTS:20993

D3S3340 (e-PCR)
- UniSTS:25345

SHGC-76664 (e-PCR)
- UniSTS:78111

D3S1560 (e-PCR)
- UniSTS:47923

ha3079 (e-PCR)
- UniSTS:515639

D8S1804 (e-PCR), detects polymorphism
- UniSTS:5944

D3S1304 (e-PCR), detects polymorphism
- UniSTS:78656

ITPR1 (e-PCR)
- UniSTS:479831

SHGC-112572 (e-PCR)
- UniSTS:183651

SHGC-147293 (e-PCR)
- UniSTS:175725

D3S3630 (e-PCR), detects polymorphism
- UniSTS:4724

SHGC-153500 (e-PCR)
- UniSTS:177787

IB262 (e-PCR)
- UniSTS:61846

RH68059 (e-PCR)
- UniSTS:46758

RH104411 (e-PCR)
- UniSTS:98736

RH121104 (e-PCR)
- UniSTS:134099

RH102411 (e-PCR)
- UniSTS:96745

G19634 (e-PCR)
- UniSTS:9965

A001T36 (e-PCR)
- UniSTS:9966

SHGC-50648 (e-PCR)
- UniSTS:13811

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium channel inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables inositol 1,4,5 trisphosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels	IEA Inferred from Electronic Annotation more info
enables inositol 1,4,5-trisphosphate-gated calcium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables inositol 1,4,5-trisphosphate-gated calcium channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables inositol 1,4,5-trisphosphate-gated calcium channel activity	TAS Traceable Author Statement more info	PubMed
enables intracellularly gated calcium channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylinositol binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in calcium ion transport	NAS Non-traceable Author Statement more info	PubMed
involved_in calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in epithelial fluid transport	IEA Inferred from Electronic Annotation more info
involved_in intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	ISS Inferred from Sequence or Structural Similarity more info
involved_in ion channel modulating, G protein-coupled receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in ligand-gated ion channel signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of calcium-mediated signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of insulin secretion	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in regulation of autophagy	TAS Traceable Author Statement more info	PubMed
involved_in regulation of postsynaptic cytosolic calcium ion concentration	IEA Inferred from Electronic Annotation more info
involved_in release of sequestered calcium ion into cytosol	IBA Inferred from Biological aspect of Ancestor more info
involved_in release of sequestered calcium ion into cytosol	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to hypoxia	IDA Inferred from Direct Assay more info	PubMed
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed
involved_in voluntary musculoskeletal movement	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
part_of calcineurin complex	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum	NAS Non-traceable Author Statement more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in nuclear inner membrane	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in platelet dense granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in platelet dense tubular network	IDA Inferred from Direct Assay more info	PubMed
located_in platelet dense tubular network membrane	TAS Traceable Author Statement more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
is_active_in sarcoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
is_active_in secretory granule membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: inositol 1,4,5-trisphosphate receptor type 1

Names: IP3 receptor; IP3R 1; inositol 1,4,5-triphosphate receptor, type 1; protein phosphatase 1, regulatory subunit 94; type 1 InsP3 receptor; type 1 inositol 1,4,5-trisphosphate 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_016144.2 RefSeqGene

Range

5002..359160

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001099952.4 → NP_001093422.2 inositol 1,4,5-trisphosphate receptor type 1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AC018816, AC024168, AC069248, AC090944

Consensus CDS

CCDS46740.2

UniProtKB/TrEMBL

A0A3B3IU04

Related

ENSP00000349597.4, ENST00000357086.10

Conserved Domains (6) summary

smart00472
Location:231 → 287

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

pfam00520
Location:2302 → 2561

Ion_trans; Ion transport protein

pfam01365
Location:476 → 665

RYDR_ITPR; RIH domain

pfam02815
Location:232 → 433

MIR; MIR domain

pfam08454
Location:1925 → 2030

RIH_assoc; RyR and IP3R Homology associated

pfam08709
Location:4 → 225

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
NM_001168272.2 → NP_001161744.1 inositol 1,4,5-trisphosphate receptor type 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon, uses an alternate in-frame splice site and includes three additional exons in the central coding region, compared to variant 1, resulting in an isoform (3) that is longer than isoform 1.

Source sequence(s)

AC018816, AC024168, AC069248, AC090944, U23850

Consensus CDS

CCDS54551.1

UniProtKB/TrEMBL

A0A3B3ITU8

Related

ENSP00000401671.2, ENST00000443694.5

Conserved Domains (6) summary

smart00472
Location:231 → 287

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

pfam00520
Location:2335 → 2594

Ion_trans; Ion transport protein

pfam01365
Location:461 → 650

RYDR_ITPR; RIH domain

pfam02815
Location:232 → 418

MIR; MIR domain

pfam08454
Location:1958 → 2063

RIH_assoc; RyR and IP3R Homology associated

pfam08709
Location:4 → 225

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
NM_001378452.1 → NP_001365381.1 inositol 1,4,5-trisphosphate receptor type 1 isoform 4

Status: REVIEWED

Source sequence(s)

AC018816, AC024168, AC069248, AC090944

Consensus CDS

CCDS93191.1

UniProtKB/Swiss-Prot

E7EPX7, E9PDE9, Q14643, Q14660, Q99897

UniProtKB/TrEMBL

A0A3B3IU04

Related

ENSP00000497605.1, ENST00000649015.2

Conserved Domains (5) summary

pfam00520
Location:2359 → 2609

Ion_trans; Ion transport protein

pfam01365
Location:474 → 670

RYDR_ITPR; RIH domain

pfam02815
Location:232 → 433

MIR; MIR domain

pfam08454
Location:1971 → 2078

RIH_assoc; RyR and IP3R Homology associated

pfam08709
Location:4 → 229

Ins145_P3_rec; Inositol 1,4,5-trisphosphate/ryanodine receptor
NM_002222.7 → NP_002213.5 inositol 1,4,5-trisphosphate receptor type 1 isoform 2

See identical proteins and their annotated locations for NP_002213.5

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in a shorter isoform (2), compared to isoform 1.

Source sequence(s)

AC018816, AC024168, AC069248, AC090944

Consensus CDS

CCDS54550.1

UniProtKB/TrEMBL

A0A3B3ITU8

Related

ENSP00000397885.2, ENST00000456211.8

Conserved Domains (6) summary

smart00472
Location:231 → 287

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

pfam00520
Location:2287 → 2546

Ion_trans; Ion transport protein

pfam01365
Location:461 → 650

RYDR_ITPR; RIH domain

pfam02815
Location:232 → 418

MIR; MIR domain

pfam08454
Location:1910 → 2015

RIH_assoc; RyR and IP3R Homology associated

pfam08709
Location:4 → 225

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