The protein encoded by this gene is a transporter of sphingosine 1-phosphate, a secreted lipid that is important in cardiovascular, immunological, and neural development. Defects in this gene are a cause of early onset progressive hearing loss. [provided by RefSeq, Jul 2016] See more...

Aliases for SPNS2 Gene

Aliases for SPNS2 Gene

  • Sphingolipid Transporter 2 2 3 5
  • Protein Spinster Homolog 2 3 4
  • SPNS Sphingolipid Transporter 2 3
  • Spinster Homolog 2 (Drosophila) 2
  • Spinster Homolog 2 3
  • AC118754.1 5
  • DFNB115 3
  • SLC62A2 3

External Ids for SPNS2 Gene

Previous GeneCards Identifiers for SPNS2 Gene

  • GC17P004349
  • GC17P004402

Summaries for SPNS2 Gene

Entrez Gene Summary for SPNS2 Gene

  • The protein encoded by this gene is a transporter of sphingosine 1-phosphate, a secreted lipid that is important in cardiovascular, immunological, and neural development. Defects in this gene are a cause of early onset progressive hearing loss. [provided by RefSeq, Jul 2016]

GeneCards Summary for SPNS2 Gene

SPNS2 (Sphingolipid Transporter 2) is a Protein Coding gene. Diseases associated with SPNS2 include Deafness, Autosomal Recessive 115. Gene Ontology (GO) annotations related to this gene include transmembrane transporter activity and sphingolipid transporter activity. An important paralog of this gene is SPNS1.

UniProtKB/Swiss-Prot Summary for SPNS2 Gene

  • Sphingolipid transporter required for migration of myocardial precursors. Transports sphingosine 1-phosphate (S1P), a secreted lipid mediator that plays critical roles in cardiovascular, immunological, and neural development and function. Mediates the export of S1P from cells in the extraembryonic yolk syncytial layer (YSL), thereby regulating myocardial precursor migration.

Additional gene information for SPNS2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPNS2 Gene

Genomics for SPNS2 Gene

GeneHancer (GH) Regulatory Elements for SPNS2 Gene

Promoters and enhancers for SPNS2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J004498 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 754.3 +1.5 1467 4.2 MYC MAX ZSCAN21 GLIS2 ZIC2 ZBTB8A PRDM10 ZEB2 SP1 PATZ1 SPNS2 ENSG00000229782 SPNS3 DHX33 lnc-MYBBP1A-3
GH17J004536 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 762.2 +37.9 37927 2.1 POLR2A ZNF148 PRDM1 GLIS2 ZIC2 PRDM10 PATZ1 KLF8 NR2F2 CREM SPNS2 lnc-MYBBP1A-3 GGT6 ENSG00000229782 MYBBP1A C17orf107 KIF1C
GH17J004497 Enhancer 0.7 ENCODE dbSUPER 750.6 -1.3 -1313 0.2 SP1 FOS YY1 RAD21 HNF4A VEZF1 REST RXRA TAF1 SPNS2 ENSG00000229782 ENSG00000262823
GH17J004496 Enhancer 0.3 dbSUPER 750.6 -1.9 -1888 0.5 ZIC2 VEZF1 SPNS2 CTNS ENSG00000262823
GH17J004433 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 12.1 -65.0 -64960 1.5 CEBPB MAX POLR2A GLIS2 RUNX3 CEBPG GABPA SPNS3 SPNS2 ENSG00000229782 HSALNG0114010
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPNS2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPNS2 gene promoter:
  • AREB6
  • ARP-1
  • c-Myb
  • ER-alpha
  • FAC1
  • GATA-1
  • Pax-5
  • RP58
  • Zic3

Genomic Locations for SPNS2 Gene

Genomic Locations for SPNS2 Gene
chr17:4,498,834-4,539,933
(GRCh38/hg38)
Size:
41,100 bases
Orientation:
Plus strand
chr17:4,402,129-4,443,228
(GRCh37/hg19)
Size:
41,100 bases
Orientation:
Plus strand

Genomic View for SPNS2 Gene

Genes around SPNS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPNS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPNS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPNS2 Gene

Proteins for SPNS2 Gene

  • Protein details for SPNS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IVW8-SPNS2_HUMAN
    Recommended name:
    Protein spinster homolog 2
    Protein Accession:
    Q8IVW8
    Secondary Accessions:
    • B9A1T3

    Protein attributes for SPNS2 Gene

    Size:
    549 amino acids
    Molecular mass:
    58044 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SPNS2 Gene

Post-translational modifications for SPNS2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SPNS2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPNS2 Gene

Domains & Families for SPNS2 Gene

Gene Families for SPNS2 Gene

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

Protein Domains for SPNS2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPNS2 Gene

GenScript: Design optimal peptide antigens:
  • Protein spinster homolog 2 (SPNS2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IVW8

UniProtKB/Swiss-Prot:

SPNS2_HUMAN :
  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
Family:
  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
genes like me logo Genes that share domains with SPNS2: view

Function for SPNS2 Gene

Molecular function for SPNS2 Gene

UniProtKB/Swiss-Prot Function:
Sphingolipid transporter required for migration of myocardial precursors. Transports sphingosine 1-phosphate (S1P), a secreted lipid mediator that plays critical roles in cardiovascular, immunological, and neural development and function. Mediates the export of S1P from cells in the extraembryonic yolk syncytial layer (YSL), thereby regulating myocardial precursor migration.

Phenotypes From GWAS Catalog for SPNS2 Gene

Gene Ontology (GO) - Molecular Function for SPNS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046624 sphingolipid transporter activity IDA,IEA 21084291
genes like me logo Genes that share ontologies with SPNS2: view
genes like me logo Genes that share phenotypes with SPNS2: view

Animal Models for SPNS2 Gene

MGI Knock Outs for SPNS2:
  • Spns2 Spns2<tm1b(KOMP)Wtsi>
  • Spns2 Spns2<tm1a(KOMP)Wtsi>
  • Spns2 Spns2<tm1.2Nmoc>
  • Spns2 Spns2<tm1Tni>

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SPNS2 Gene

Localization for SPNS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPNS2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 SPNS2 gene
Compartment Confidence
plasma membrane 1
extracellular 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for SPNS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SPNS2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPNS2 Gene

Pathways & Interactions for SPNS2 Gene

PathCards logo

SuperPathways for SPNS2 Gene

No Data Available

Interacting Proteins for SPNS2 Gene

Gene Ontology (GO) - Biological Process for SPNS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001782 B cell homeostasis IEA --
GO:0002260 lymphocyte homeostasis IEA --
GO:0002920 regulation of humoral immune response IEA --
GO:0003376 sphingosine-1-phosphate receptor signaling pathway IEA --
GO:0006665 sphingolipid metabolic process IEA --
genes like me logo Genes that share ontologies with SPNS2: view

No data available for Pathways by source and SIGNOR curated interactions for SPNS2 Gene

Drugs & Compounds for SPNS2 Gene

No Compound Related Data Available

Transcripts for SPNS2 Gene

mRNA/cDNA for SPNS2 Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPNS2 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e
SP1: - - - - -
SP2: - -
SP3: - - - - -
SP4: - - -
SP5: -
SP6: - - -
SP7:

Relevant External Links for SPNS2 Gene

GeneLoc Exon Structure for
SPNS2
ECgene alternative splicing isoforms for
SPNS2

Expression for SPNS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPNS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPNS2 Gene

This gene is overexpressed in Esophagus - Mucosa (x4.9).

Protein differential expression in normal tissues from HIPED for SPNS2 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SPNS2 Gene



Protein tissue co-expression partners for SPNS2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SPNS2 Gene:

SPNS2

SOURCE GeneReport for Unigene cluster for SPNS2 Gene:

Hs.22824

Evidence on tissue expression from TISSUES for SPNS2 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with SPNS2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPNS2 Gene

Orthologs for SPNS2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPNS2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPNS2 33
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SPNS2 33 32
  • 91.8 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPNS2 32
  • 90.03 (n)
mouse
(Mus musculus)
Mammalia Spns2 17 33 32
  • 88.69 (n)
rat
(Rattus norvegicus)
Mammalia Spns2 32
  • 88.68 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SPNS2 33
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SPNS2 33
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPNS2 33 32
  • 79.54 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia spns2 32
  • 73.7 (n)
Str.18139 32
zebrafish
(Danio rerio)
Actinopterygii spns2 33 32
  • 69.9 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta spin 33
  • 32 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea spin-1 33
  • 35 (a)
ManyToMany
spin-4 33
  • 35 (a)
ManyToMany
spin-2 33
  • 34 (a)
ManyToMany
spin-3 33
  • 33 (a)
ManyToMany
wheat
(Triticum aestivum)
Liliopsida Ta.28328 32
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5353 33
  • 28 (a)
OneToMany
Species where no ortholog for SPNS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • lizard (Anolis carolinensis)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SPNS2 Gene

ENSEMBL:
Gene Tree for SPNS2 (if available)
TreeFam:
Gene Tree for SPNS2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPNS2: view image

Paralogs for SPNS2 Gene

Paralogs for SPNS2 Gene

(2) SIMAP similar genes for SPNS2 Gene using alignment to 2 proteins:

  • SPNS2_HUMAN
  • I3L4N9_HUMAN
genes like me logo Genes that share paralogs with SPNS2: view

Variants for SPNS2 Gene

Sequence variations from dbSNP and Humsavar for SPNS2 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1555537637 likely-pathogenic, pathogenic, Inborn genetic diseases, DEAFNESS, AUTOSOMAL RECESSIVE 115 4,533,107(+) CC/T coding_sequence_variant, frameshift
rs749994718 uncertain-significance, pathogenic, Inborn genetic diseases, DEAFNESS, AUTOSOMAL RECESSIVE 115 4,532,992(+) CTCCTCC/CTCC coding_sequence_variant, inframe_deletion
rs1000028433 -- 4,515,164(+) G/C intron_variant
rs1000084097 -- 4,524,110(+) C/T intron_variant
rs1000178303 -- 4,523,848(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SPNS2 Gene

Variant ID Type Subtype PubMed ID
esv1003136 CNV gain 20482838
esv3639784 CNV gain 21293372
esv3639785 CNV gain 21293372
nsv1058176 CNV gain 25217958
nsv1116184 CNV deletion 24896259
nsv1144787 CNV deletion 24896259
nsv574269 CNV gain 21841781
nsv574272 CNV loss 21841781
nsv833345 CNV loss 17160897
nsv952109 CNV deletion 24416366

Variation tolerance for SPNS2 Gene

Residual Variation Intolerance Score: 12.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.41; 42.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPNS2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPNS2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPNS2 Gene

Disorders for SPNS2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SPNS2 Gene - From: OMIM, ClinVar, GTR, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 115
  • dfnb115
- elite association - COSMIC cancer census association via MalaCards
Search SPNS2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPNS2

genes like me logo Genes that share disorders with SPNS2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPNS2 Gene

Publications for SPNS2 Gene

  1. Spinster 2, a sphingosine-1-phosphate transporter, plays a critical role in inflammatory and autoimmune diseases. (PMID: 26324848) Donoviel MS … Spiegel S (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2015) 2 3 56
  2. The sphingolipid transporter spns2 functions in migration of zebrafish myocardial precursors. (PMID: 19074308) Kawahara A … Mochizuki N (Science (New York, N.Y.) 2009) 3 4 56
  3. 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 56
  4. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. (PMID: 30575818) Tiemann K … Kani K (Oncogene 2019) 3 56
  5. Biological function of SPNS2: From zebrafish to human. (PMID: 30196234) Zhu X … Yi GH (Molecular immunology 2018) 3 56

Products for SPNS2 Gene

Sources for SPNS2 Gene