XPR1

Chr 1

xenotropic and polytropic retrovirus receptor 1

Also known as: IBGC6, SLC53A1, SYG1, X3

NCBI Gene: 9213ENSG00000143324UniProt: Q9UBH6

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]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtBasal ganglia calcification, idiopathic, 6

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
1
Active trials
50
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.16
LOEUF· LoF intol.
Multiple*
Mechanism· predicted
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GeneReview available — XPR1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.16LOEUF
pLI 1.000
Z-score 5.60
OE 0.05 (0.02–0.16)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
3.23Z-score
OE missense 0.55 (0.49–0.61)
218 obs / 400.0 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.05 (0.02–0.16)
0≤0.351.4
Missense OE?0.55 (0.49–0.61)
0≤0.61.4
Synonymous OE?0.92
0≤1.21.6
LoF obs/exp: 2 / 40.4Missense obs/exp: 218 / 400.0Syn Z: 0.72

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

XPR1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients