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

    Gene ID: 83985, updated on 28-Oct-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 lysophospholipid transport and transmembrane transport. Predicted to act upstream of or within phospholipid efflux and regulation of lysosomal lumen pH. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Oct 2024]
    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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    See SPNS1 in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28974778..28984765)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29255893..29265880)
    RS_2024_09 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 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. 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
    2. 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
    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 (47) 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transmembrane transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in lysophospholipid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lysophospholipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phospholipid efflux IBA
    Inferred from Biological aspect of Ancestor
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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