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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SPNS1
SPNS lysolipid transporter 1, lysophospholipid
Chromosome 16 · 16p11.2
NCBI Gene: 83985Ensembl: ENSG00000169682.18HGNC: HGNC:30621UniProt: Q9H2V7
52PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transporter
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
lysophospholipid transportprotein bindinglysosomelysophospholipid:sodium symporter activityatrial fibrillationAlzheimer diseaseosteosarcomaovarian neoplasm
✦AI Summary

SPNS1 functions as a critical lysosomal transporter mediating the rate-limiting, proton-dependent efflux of lysophospholipids from lysosomes to the cytosol 12. The protein selectively transports zwitterionic lysophospholipids including lysophosphatidylcholine (LPC), lysophosphatidylethanolamine (LPE), and lysoplasmalogen, facilitating phospholipid salvage through subsequent reacylation by cytosolic acyltransferases 12. Mechanistically, SPNS1 utilizes a five-residue network for proton sensing and specific transmembrane domains for substrate recognition, with LPC binding within a luminal-open cavity 3. Disease relevance is significant, as SPNS1 deficiency causes lysosomal storage disease characterized by accumulation of sphingosines and lysoglycerophospholipids, leading to embryonic lethality, liver dysfunction, and altered PI3K/AKT signaling in mouse models 4. Human patients with biallelic SPNS1 variants present with multiorgan disease including progressive liver injury, striated muscle damage, and neurological impairment 54. Clinically, SPNS1 dysfunction affects mTOR-regulated lipid homeostasis, reduces triglyceride synthesis, and impairs cellular energy storage under nutrient limitation 5. Additionally, SPNS1 serves as an essential factor for enterovirus infections by transporting viral pocket factors 6.

Sources cited
1
SPNS1 mediates proton-dependent lysosomal efflux of lysophospholipids and selects for zwitterionic headgroups
PMID: 36161949
2
SPNS1 plays critical role in phospholipid salvage pathway and is essential for cell survival under nutrient limitation
PMID: 37075117
3
Structural basis showing LPC binding mechanism and proton-sensing network in SPNS1
PMID: 39739806
4
SPNS1 deficiency causes lysosomal storage disease with accumulation of sphingosines and lysoglycerophospholipids
PMID: 38451736
5
Human SPNS1 variants cause multiorgan disease and affect mTOR-regulated lipid homeostasis
PMID: 40608416
6
SPNS1 serves as essential factor for enterovirus infection by transporting viral pocket factors
PMID: 41385544
Disease Associationsⓘ20
atrial fibrillationOpen Targets
0.11Weak
Alzheimer diseaseOpen Targets
0.09Suggestive
osteosarcomaOpen Targets
0.08Suggestive
ovarian neoplasmOpen Targets
0.07Suggestive
neoplasmOpen Targets
0.07Suggestive
cancerOpen Targets
0.06Suggestive
lung cancerOpen Targets
0.05Suggestive
risk-taking behaviourOpen Targets
0.05Suggestive
rheumatoid arthritisOpen Targets
0.05Suggestive
infectionOpen Targets
0.05Suggestive
sinusitisOpen Targets
0.04Suggestive
obesityOpen Targets
0.04Suggestive
hepatocellular carcinomaOpen Targets
0.04Suggestive
metabolic diseaseOpen Targets
0.04Suggestive
liver diseaseOpen Targets
0.03Suggestive
AnisometropiaOpen Targets
0.03Suggestive
lysosomal storage diseaseOpen Targets
0.03Suggestive
Other metabolic diseaseOpen Targets
0.03Suggestive
Varicose veinsOpen Targets
0.03Suggestive
achalasia-alacrima syndromeOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
BCL2L1Protein interaction75%BCL2Protein interaction72%MFSD2BProtein interaction60%ABCA10Shared pathway50%ABCA9Shared pathway50%ABCA6Shared pathway50%
Tissue Expression6 tissues
Lung
100%
Bone Marrow
86%
Ovary
78%
Liver
59%
Brain
33%
Heart
16%
Gene Interaction Network
Click a node to explore
SPNS1BCL2L1BCL2MFSD2BABCA10ABCA9ABCA6
PROTEIN STRUCTURE
Preparing viewer…
PDB9BOI · 3.22 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.65LoF Tolerant
pLIⓘ
0.03Tolerant
Observed/Expected LoF0.46 [0.33–0.65]
RankingsWhere SPNS1 stands among ~20K protein-coding genes
  • #8,614of 20,598
    Most Researched52
  • #4,741of 17,882
    Most Constrained (LOEUF)0.65
Genes detectedSPNS1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
SPNS1 is an essential cellular factor for EV-A71 by acting as a transporter of viral pocket factor.
PMID: 41385544
Proc Natl Acad Sci U S A · 2025
1.00
2
Deficiency of spns1 exacerbates per- and polyfluoroalkyl substances mediated hepatic toxicity and steatosis in zebrafish (Danio rerio).
PMID: 37806615
Toxicology · 2023
0.90
3
SPNS1 variants cause multiorgan disease and implicate lysophospholipid transport as critical for mTOR-regulated lipid homeostasis.
PMID: 40608416
J Clin Invest · 2025
0.80
4
Lack of SPNS1 results in accumulation of lysolipids and lysosomal storage disease in mouse models.
PMID: 38451736
JCI Insight · 2024
0.70
5
Oseltamivir enhances 5-FU sensitivity in esophageal squamous carcinoma with high SPNS1.
PMID: 38460365
Biomed Pharmacother · 2024
0.60