XPR1 xenotropic and polytropic retrovirus receptor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: XPR1provided by HGNC
Official Full Name: xenotropic and polytropic retrovirus receptor 1provided by HGNC
Primary source: HGNC:HGNC:12827
See related: Ensembl:ENSG00000143324 MIM:605237; AllianceGenome:HGNC:12827
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: X3; SYG1; IBGC6; SLC53A1
Summary: The protein encoded by this gene is a receptor for the xenotropic and polytropic classes of murine leukemia viruses. The encoded protein is involved in phosphate homeostasis by mediating phosphate export from the cell. Defects in this gene have been associated with idiopathic basal ganglia calcification-6. [provided by RefSeq, Jun 2016]
Expression: Ubiquitous expression in heart (RPKM 12.0), testis (RPKM 8.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (180632022..180890279)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (179987035..180245477)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (180601158..180859415)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Human XPR1 structures reveal phosphate export mechanism.
Title: Human XPR1 structures reveal phosphate export mechanism.
Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer.
Title: Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer.
The miR-4732-5p/XPR1 axis suppresses the invasion, metastasis, and epithelial-mesenchymal transition of lung adenocarcinoma via the PI3K/Akt/GSK3beta/Snail pathway.
Title: The miR-4732-5p/XPR1 axis suppresses the invasion, metastasis, and epithelial-mesenchymal transition of lung adenocarcinoma via the PI3K/Akt/GSK3β/Snail pathway.
The genetic polymorphisms of XPR1 and SCL34A3 are associated with Fanconi syndrome in Chinese patients of tumor-induced osteomalacia.
Title: The genetic polymorphisms of XPR1 and SCL34A3 are associated with Fanconi syndrome in Chinese patients of tumor-induced osteomalacia.
Circ-XPR1 promotes osteosarcoma proliferation through regulating the miR-214-5p/DDX5 axis.
Title: Circ-XPR1 promotes osteosarcoma proliferation through regulating the miR-214-5p/DDX5 axis.
Clinical implication of xenotropic and polytropic retrovirus receptor 1 in papillary thyroid carcinoma.
Title: Clinical implication of xenotropic and polytropic retrovirus receptor 1 in papillary thyroid carcinoma.
Interplay between primary familial brain calcification-associated SLC20A2 and XPR1 phosphate transporters requires inositol polyphosphates for control of cellular phosphate homeostasis.
Title: Interplay between primary familial brain calcification-associated SLC20A2 and XPR1 phosphate transporters requires inositol polyphosphates for control of cellular phosphate homeostasis.
Characterization of XPR1/SLC53A1 variants located outside of the SPX domain in patients with primary familial brain calcification.
Title: Characterization of XPR1/SLC53A1 variants located outside of the SPX domain in patients with primary familial brain calcification.
XPR1 activity was regulated by a member of the inositol pyrophosphate (PP-InsP) signaling family: 1,5-bis-diphosphoinositol 2,3,4,6-tetrakisphosphate (InsP8).
Title: Control of XPR1-dependent cellular phosphate efflux by InsP(8) is an exemplar for functionally-exclusive inositol pyrophosphate signaling.
conclude that IP6K1 and -2 together control inositol pyrophosphate metabolism and thereby physiologically regulate phosphate export and other aspects of mammalian cellular phosphate homeostasis
Title: The inositol hexakisphosphate kinases IP6K1 and -2 regulate human cellular phosphate homeostasis, including XPR1-mediated phosphate export.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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
Basal ganglia calcification, idiopathic, 6 MedGen: C4225335 OMIM: 616413 GeneReviews: Primary Familial Brain Calcification	not available

EBI GWAS Catalog

Description
Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S308E (e-PCR)
- UniSTS:62725

AL009988 (e-PCR)
- UniSTS:73735

D1S1967E (e-PCR)
- UniSTS:151307

SHGC-75996 (e-PCR)
- UniSTS:61204

D1S2357 (e-PCR)
- UniSTS:82967

D1S2516 (e-PCR)
- UniSTS:154136

STS-N52057 (e-PCR)
- UniSTS:21540

SHGC-76010 (e-PCR)
- UniSTS:21541

D8S2279 (e-PCR)
- UniSTS:473907

XPR1_8914 (e-PCR)
- UniSTS:468795

RH91144 (e-PCR)
- UniSTS:92998

D1S2640 (e-PCR), detects polymorphism
- UniSTS:75893

AW531572 (e-PCR)
- UniSTS:245122

D11S3114 (e-PCR)
- UniSTS:152207

D1S117 (e-PCR)
- UniSTS:34197

RH93926 (e-PCR)
- UniSTS:92849

D1S3379 (e-PCR)
- UniSTS:41176

D1S2247 (e-PCR)
- UniSTS:153561

G20381 (e-PCR)
- UniSTS:66792

A005O32 (e-PCR)
- UniSTS:66793

1004 (e-PCR)
- UniSTS:37885

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables efflux transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables inositol hexakisphosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables inositol hexakisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphate transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables virus receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to phosphate starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular phosphate ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphate ion transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphate ion transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to virus	IEA Inferred from Electronic Annotation more info
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: solute carrier family 53 member 1

Names: X-receptor; phosphate exporter SLC53A1; protein SYG1 homolog; solute carrier family 53 (phosphate exporter), member 1; xenotropic and polytropic murine leukemia virus receptor X3

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_050964.1 RefSeqGene

Range

5013..263270

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001135669.2 → NP_001129141.1 solute carrier family 53 member 1 isoform 2

See identical proteins and their annotated locations for NP_001129141.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AA425354, AL162431, BC041142, DB461474

Consensus CDS

CCDS44284.1

UniProtKB/Swiss-Prot

Q9UBH6

Related

ENSP00000356561.3, ENST00000367589.3

Conserved Domains (2) summary

cd14477
Location:2 → 165

SPX_XPR1_like; SPX domain of the xenotropic and polytropic retrovirus receptor 1 (XPR1) and related proteins

pfam03124
Location:268 → 552

EXS; EXS family
NM_001328662.2 → NP_001315591.1 solute carrier family 53 member 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL358434, AL590085
NM_004736.4 → NP_004727.2 solute carrier family 53 member 1 isoform 1

See identical proteins and their annotated locations for NP_004727.2

Status: REVIEWED

Description

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

Source sequence(s)

AA425354, AF115389, AL162431, BC041142, DB461474

Consensus CDS

CCDS1340.1

UniProtKB/Swiss-Prot

O95719, Q7L8K9, Q8IW20, Q9NT19, Q9UBH6, Q9UFB9

Related

ENSP00000356562.4, ENST00000367590.9

Conserved Domains (2) summary

cd14477
Location:2 → 165

SPX_XPR1_like; SPX domain of the xenotropic and polytropic retrovirus receptor 1 (XPR1) and related proteins

pfam03124
Location:268 → 617

EXS; EXS family

RNA

NR_137330.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL162431, AL358434, AL590085