Aliases for SPNS1 Gene

Aliases for SPNS1 Gene

  • Sphingolipid Transporter 1 (Putative) 2 3 5
  • HSpin1 2 3 4
  • SPIN1 2 3 4
  • Protein Spinster Homolog 1 3 4
  • Spinster-Like Protein 1 3 4
  • SLC63A1 2 3
  • PP2030 2 3
  • SPINL 2 3
  • LAT 2 3
  • Nrs 2 3
  • SPNS Sphingolipid Transporter 1 (Putative) 3
  • Spinster Homolog 1 (Drosophila) 2
  • Spinster Homolog 1 3
  • SLC62A1 3
  • SPNS1 5

External Ids for SPNS1 Gene

Previous GeneCards Identifiers for SPNS1 Gene

  • GC16P028897
  • GC16P028986
  • GC16P026853
  • GC16P028974
  • GC16P029008

Summaries for SPNS1 Gene

GeneCards Summary for SPNS1 Gene

SPNS1 (Sphingolipid Transporter 1 (Putative)) is a Protein Coding gene. Diseases associated with SPNS1 include Ivic Syndrome and Koolen-De Vries Syndrome. Gene Ontology (GO) annotations related to this gene include transporter activity and sphingolipid transporter activity. An important paralog of this gene is SPNS2.

UniProtKB/Swiss-Prot Summary for SPNS1 Gene

  • Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPNS1 Gene

Genomics for SPNS1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPNS1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPNS1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPNS1

Top Transcription factor binding sites by QIAGEN in the SPNS1 gene promoter:
  • AhR
  • ATF-2
  • c-Jun
  • NF-kappaB

Genomic Locations for SPNS1 Gene

Latest Assembly
10,771 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
9,766 bases
Plus strand

(GRCh37/hg19 by Ensembl)
10,328 bases
Plus strand

Genomic View for SPNS1 Gene

Genes around SPNS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPNS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPNS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPNS1 Gene

Proteins for SPNS1 Gene

  • Protein details for SPNS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein spinster homolog 1
    Protein Accession:
    Secondary Accessions:
    • B5MDM9
    • Q6P182
    • Q71RB5
    • Q7L541
    • Q86VU7
    • Q8N953
    • Q8TCS5
    • Q9BRN5

    Protein attributes for SPNS1 Gene

    528 amino acids
    Molecular mass:
    56630 Da
    Quaternary structure:
    • Interacts with BCL2 and BCL2L1.
    • Sequence=AAQ15259.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAQ15259.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for SPNS1 Gene


neXtProt entry for SPNS1 Gene

Post-translational modifications for SPNS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPNS1 Gene

Domains & Families for SPNS1 Gene

Gene Families for SPNS1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SPNS1 Gene


Suggested Antigen Peptide Sequences for SPNS1 Gene

GenScript: Design optimal peptide antigens:
  • Spinster-like protein 1 (SPNS1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
genes like me logo Genes that share domains with SPNS1: view

Function for SPNS1 Gene

Molecular function for SPNS1 Gene

UniProtKB/Swiss-Prot Function:
Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death.

Phenotypes From GWAS Catalog for SPNS1 Gene

Gene Ontology (GO) - Molecular Function for SPNS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12815463
GO:0022857 transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SPNS1: view
genes like me logo Genes that share phenotypes with SPNS1: view

Animal Models for SPNS1 Gene

MGI Knock Outs for SPNS1:
  • Spns1 Spns1<tm1a(EUCOMM)Wtsi>

Animal Models for research

  • Taconic Biosciences Mouse Models for SPNS1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPNS1

Clone products for research

  • Addgene plasmids for SPNS1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SPNS1 Gene

Localization for SPNS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPNS1 Gene

Mitochondrion inner membrane. Multi-pass membrane protein. Note=Colocalizes with SDHB.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPNS1 gene
Compartment Confidence
lysosome 4
plasma membrane 3
mitochondrion 3
nucleus 2
cytosol 2
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
  • Cytosol (1)
  • Golgi apparatus (1)
  • Nucleoli fibrillar center (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPNS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005743 mitochondrial inner membrane IEA --
GO:0005765 lysosomal membrane HDA 17897319
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SPNS1: view

Pathways & Interactions for SPNS1 Gene

PathCards logo

SuperPathways for SPNS1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPNS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006869 lipid transport IEA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SPNS1: view

No data available for Pathways by source and SIGNOR curated interactions for SPNS1 Gene

Drugs & Compounds for SPNS1 Gene

No Compound Related Data Available

Transcripts for SPNS1 Gene

mRNA/cDNA for SPNS1 Gene

13 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPNS1

Clone products for research

  • Addgene plasmids for SPNS1

Alternative Splicing Database (ASD) splice patterns (SP) for SPNS1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c
SP1: -
SP3: -
SP4: - - - - - -
SP5: -
SP6: - - - - -
SP7: -
SP8: - - - - - - - -
SP9: -

Relevant External Links for SPNS1 Gene

GeneLoc Exon Structure for

Expression for SPNS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPNS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPNS1 Gene

This gene is overexpressed in Adrenal (13.0), Peripheral blood mononuclear cells (10.9), Monocytes (7.3), and Lung (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SPNS1 Gene

Protein tissue co-expression partners for SPNS1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPNS1

SOURCE GeneReport for Unigene cluster for SPNS1 Gene:


Evidence on tissue expression from TISSUES for SPNS1 Gene

  • Nervous system(4.8)
  • Skin(4.6)
  • Blood(4.6)
  • Pancreas(4.4)
  • Eye(3)
  • Lung(2.3)
genes like me logo Genes that share expression patterns with SPNS1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPNS1 Gene

Orthologs for SPNS1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPNS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SPNS1 30 31
  • 99.81 (n)
(Canis familiaris)
Mammalia SPNS1 30 31
  • 91.25 (n)
(Bos Taurus)
Mammalia SPNS1 30 31
  • 91.04 (n)
(Mus musculus)
Mammalia Spns1 30 17 31
  • 87.88 (n)
(Rattus norvegicus)
Mammalia Spns1 30
  • 87.75 (n)
(Monodelphis domestica)
Mammalia SPNS1 31
  • 86 (a)
(Ornithorhynchus anatinus)
Mammalia SPNS1 31
  • 82 (a)
(Anolis carolinensis)
Reptilia SPNS1 31
  • 71 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia spns1 30
  • 69.92 (n)
Str.16886 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.16646 30
(Danio rerio)
Actinopterygii spns1 30 31
  • 64.81 (n)
spinl 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006346 30
  • 56.05 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta spin 30 31
  • 54.4 (n)
(Caenorhabditis elegans)
Secernentea C13C4.5 30
  • 45.99 (n)
spin-2 31
  • 38 (a)
spin-1 31
  • 36 (a)
spin-3 31
  • 36 (a)
spin-4 31
  • 36 (a)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G65687 30
  • 39.16 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.5353 31
  • 33 (a)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.12624 30
Species where no ortholog for SPNS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SPNS1 Gene

Gene Tree for SPNS1 (if available)
Gene Tree for SPNS1 (if available)
Evolutionary constrained regions (ECRs) for SPNS1: view image

Paralogs for SPNS1 Gene

Paralogs for SPNS1 Gene

(2) SIMAP similar genes for SPNS1 Gene using alignment to 7 proteins:

  • H3BP14_HUMAN
  • H3BR82_HUMAN
  • H3BT44_HUMAN
genes like me logo Genes that share paralogs with SPNS1: view

Variants for SPNS1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPNS1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs113165798 Benign: not provided 28,983,890(+) C/T
NM_032038.3(SPNS1):c.1425C>T (p.Gly475=)
rs17855956 - p.Ala230Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPNS1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SPNS1 Gene

Variant ID Type Subtype PubMed ID
dgv2830n100 CNV gain 25217958
dgv2831n100 CNV gain 25217958
dgv4987n54 CNV gain 21841781
esv2758640 CNV gain+loss 17122850
esv3570454 CNV gain 25503493
esv3582129 CNV loss 25503493
esv3638351 CNV gain 21293372
esv3892826 CNV gain+loss 25118596
nsv1059555 CNV gain 25217958
nsv457480 CNV gain 19166990
nsv518648 CNV loss 19592680
nsv519100 CNV gain 19592680
nsv571805 CNV loss 21841781
nsv571808 CNV gain 21841781
nsv952964 CNV deletion 24416366

Variation tolerance for SPNS1 Gene

Residual Variation Intolerance Score: 25.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.33; 53.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPNS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPNS1 Gene

Disorders for SPNS1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SPNS1 Gene - From: COP

Disorder Aliases PubMed IDs
ivic syndrome
  • radial ray defects, hearing impairment, external ophthalmoplegia, and thrombocytopenia
koolen-de vries syndrome
  • kdvs
- elite association - COSMIC cancer census association via MalaCards
Search SPNS1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPNS1

genes like me logo Genes that share disorders with SPNS1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPNS1 Gene

Publications for SPNS1 Gene

  1. HSpin1, a transmembrane protein interacting with Bcl-2/Bcl-xL, induces a caspase-independent autophagic cell death. (PMID: 12815463) Yanagisawa H … Yamamoto D (Cell death and differentiation 2003) 2 3 4
  2. Mutations in the novel membrane protein spinster interfere with programmed cell death and cause neural degeneration in Drosophila melanogaster. (PMID: 11340170) Nakano Y … Yamamoto D (Molecular and cellular biology 2001) 2 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. (PMID: 32694731) Aregger M … Moffat J (Nature metabolism 2020) 3
  5. A trimeric Rab7 GEF controls NPC1-dependent lysosomal cholesterol export. (PMID: 33144569) van den Boomen DJH … Lehner PJ (Nature communications 2020) 3

Products for SPNS1 Gene

Sources for SPNS1 Gene