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SPNS1 SPNS lysolipid transporter 1, lysophospholipid [ Homo sapiens (human) ]

Gene ID: 83985, updated on 3-Apr-2024

Summary

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Official Symbol
SPNS1provided by HGNC
Official Full Name
SPNS lysolipid transporter 1, lysophospholipidprovided by HGNC
Primary source
HGNC:HGNC:30621
See related
Ensembl:ENSG00000169682 MIM:612583; AllianceGenome:HGNC:30621
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LAT; nrs; SPIN1; SPINL; HSpin1; PP2030; SLC62A1; SLC63A1
Summary
Predicted to enable transmembrane transporter activity. Predicted to be involved in lipid transport and transmembrane transport. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lung (RPKM 11.3), placenta (RPKM 11.2) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
16p11.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28974778..28984765)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29255893..29265880)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28986099..28995864)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NFATC2IP antisense RNA 1 Neighboring gene nuclear factor of activated T cells 2 interacting protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:28973628-28973836 Neighboring gene microRNA 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7324 Neighboring gene MPRA-validated peak2553 silencer Neighboring gene linker for activation of T cells Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29036345-29036846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7325 Neighboring gene nuclear pore complex interacting protein family, member B10, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. L-leucine and SPNS1 coordinately ameliorate dysfunction of autophagy in mouse and human Niemann-Pick type C disease. Yanagisawa H, et al. Sci Rep, 2017 Nov 21. PMID 29162837, Free PMC Article
  2. Polymorphisms in sh2b1 and spns1 loci are associated with triglyceride levels in a healthy population in northern Sweden. Västermark Å, et al. J Genet, 2012 Aug. PMID 22942098
  3. Spns1 is a lysophospholipid transporter mediating lysosomal phospholipid salvage. He M, et al. Proc Natl Acad Sci U S A, 2022 Oct 4. PMID 36161949, Free PMC Article
  4. HSpin1, a transmembrane protein interacting with Bcl-2/Bcl-xL, induces a caspase-independent autophagic cell death. Yanagisawa H, et al. Cell Death Differ, 2003 Jul. PMID 12815463
  5. Mutations in the novel membrane protein spinster interfere with programmed cell death and cause neural degeneration in Drosophila melanogaster. Nakano Y, et al. Mol Cell Biol, 2001 Jun. PMID 11340170, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Spns1 is a lysosomal proton-dependent lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) transporter mediating phospholipid salvage pathway
    Title: Spns1 is a lysophospholipid transporter mediating lysosomal phospholipid salvage.
  2. SPNS1-dependent L-leucine export across the lysosomal membrane is a key step for triggering autophagy, and that this mechanism is impaired in Niemann-Pick type C disease-1.
    Title: L-leucine and SPNS1 coordinately ameliorate dysfunction of autophagy in mouse and human Niemann-Pick type C disease.
  3. Spindlin 1 (SPIN1) sequesters ribosomal protein uL18 in the nucleolus, preventing it from interacting with c-mdm2 Proto-oncogene protein (MDM2), and alleviating uL18-mediated inhibition of MDM2 ubiquitin ligase activity toward p53 tumor suppressor protein (p53).
    Title: SPIN1 promotes tumorigenesis by blocking the uL18 (universal large ribosomal subunit protein 18)-MDM2-p53 pathway in human cancer.
  4. A single nucleotide polymorphism located within the spns1 gene is associated with plasma triglyceride levels.
    Title: Polymorphisms in sh2b1 and spns1 loci are associated with triglyceride levels in a healthy population in northern Sweden.
  5. Spinster protein interferes with programmed cell death in Drosophila melanogaster and has orthologs in nematode, mouse, and human.
    Title: Mutations in the novel membrane protein spinster interfere with programmed cell death and cause neural degeneration in Drosophila melanogaster.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ38358

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in lysophospholipid transport IEA
Inferred from Electronic Annotation
more info
  
involved_in phospholipid efflux IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of lysosomal lumen pH IEA
Inferred from Electronic Annotation
more info
  
involved_in transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in lysosomal membrane HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein spinster homolog 1
Names
SPNS sphingolipid transporter 1 (putative)
solute carrier family 63 member 1
sphingolipid transporter 1 (putative)
spinster homolog 1
spinster-like protein 1

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.

mRNA and Protein(s)

  1. NM_001142448.2 → NP_001135920.1  protein spinster homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_001135920.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode isoform 1.
    Source sequence(s)
    BC008325, BC065235, BG771918, CD368853
    Consensus CDS
    CCDS10646.1
    UniProtKB/Swiss-Prot
    B5MDM9, Q6P182, Q71RB5, Q7L541, Q86VU7, Q8N953, Q8TCS5, Q9BRN5, Q9H2V7
    Related
    ENSP00000454360.1, ENST00000565975.5
    Conserved Domains (1) summary
    cd17328
    Location:62 → 479
    MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters

  2. NM_001142449.2 → NP_001135921.1  protein spinster homolog 1 isoform 4

    See identical proteins and their annotated locations for NP_001135921.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AL390215, BG771918, CD368853
    Consensus CDS
    CCDS45453.1
    UniProtKB/Swiss-Prot
    Q9H2V7
    Related
    ENSP00000306050.10, ENST00000352260.11
    Conserved Domains (2) summary
    cd06174
    Location:62 → 376
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    pfam07690
    Location:79 → 337
    MFS_1; Major Facilitator Superfamily

  3. NM_001142450.2 → NP_001135922.1  protein spinster homolog 1 isoform 2

    See identical proteins and their annotated locations for NP_001135922.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AL524908, BC008325, BG771918, CD368853
    Consensus CDS
    CCDS45454.1
    Related
    ENSP00000318228.8, ENST00000323081.12
    Conserved Domains (1) summary
    cd17328
    Location:1 → 406
    MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters

  4. NM_001142451.2 → NP_001135923.1  protein spinster homolog 1 isoform 3

    See identical proteins and their annotated locations for NP_001135923.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    BC047741, BG771918
    Consensus CDS
    CCDS45452.1
    UniProtKB/Swiss-Prot
    Q9H2V7
    Related
    ENSP00000335494.8, ENST00000334536.12
    Conserved Domains (2) summary
    cd06174
    Location:62 → 398
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    pfam07690
    Location:65 → 359
    MFS_1; Major Facilitator Superfamily

  5. NM_032038.3 → NP_114427.1  protein spinster homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_114427.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 2 both encode isoform 1.
    Source sequence(s)
    BC008325, BG771918, CD368853
    Consensus CDS
    CCDS10646.1
    UniProtKB/Swiss-Prot
    B5MDM9, Q6P182, Q71RB5, Q7L541, Q86VU7, Q8N953, Q8TCS5, Q9BRN5, Q9H2V7
    Related
    ENSP00000309945.11, ENST00000311008.16
    Conserved Domains (1) summary
    cd17328
    Location:62 → 479
    MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters

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

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    28974778..28984765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434739.1 → XP_047290695.1  protein spinster homolog 1 isoform X1

    Related
    ENSP00000456119.1, ENST00000566059.5

  2. XM_047434741.1 → XP_047290697.1  protein spinster homolog 1 isoform X4

  3. XM_006721096.5 → XP_006721159.1  protein spinster homolog 1 isoform X3

    Conserved Domains (2) summary
    cd06174
    Location:107 → 472
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    pfam07690
    Location:110 → 404
    MFS_1; Major Facilitator Superfamily

  4. XM_047434740.1 → XP_047290696.1  protein spinster homolog 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29255893..29265880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314109.1 → XP_054170084.1  protein spinster homolog 1 isoform X1

  2. XM_054314112.1 → XP_054170087.1  protein spinster homolog 1 isoform X4

  3. XM_054314111.1 → XP_054170086.1  protein spinster homolog 1 isoform X3

  4. XM_054314110.1 → XP_054170085.1  protein spinster homolog 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H2V7.1 GenPept UniProtKB/Swiss-Prot:Q9H2V7

Gene LinkOut

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