This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009] See more...

Aliases for NPTN Gene

Aliases for NPTN Gene

  • Neuroplastin 2 3 4 5
  • Stromal Cell Derived Factor Receptor 1 2 3
  • Stromal Cell-Derived Receptor 1 3 4
  • SDFR1 3 4
  • SDR-1 3 4
  • SDR1 3 4
  • GP55 3
  • GP65 3
  • Np55 3
  • Np65 3

External Ids for NPTN Gene

Previous HGNC Symbols for NPTN Gene

  • SDFR1

Previous GeneCards Identifiers for NPTN Gene

  • GC15M071640
  • GC15M073852
  • GC15M050683

Summaries for NPTN Gene

Entrez Gene Summary for NPTN Gene

  • This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]

GeneCards Summary for NPTN Gene

NPTN (Neuroplastin) is a Protein Coding gene. Diseases associated with NPTN include Allergic Bronchopulmonary Aspergillosis and Retrograde Amnesia. Among its related pathways are CCR5 Pathway in Macrophages and ERK Signaling. Gene Ontology (GO) annotations related to this gene include cell adhesion molecule binding and type 1 fibroblast growth factor receptor binding. An important paralog of this gene is BSG.

UniProtKB/Swiss-Prot Summary for NPTN Gene

  • Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity).

Gene Wiki entry for NPTN Gene

Additional gene information for NPTN Gene

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

Genomics for NPTN Gene

GeneHancer (GH) Regulatory Elements for NPTN Gene

Promoters and enhancers for NPTN 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
GH15J073628 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 500.7 +2.1 2124 6.3 FOXK2 HNRNPK ZNF217 CTCF ZSCAN5C NRF1 USF1 POLR2G SP1 NCOR1 NPTN lnc-CD276-3 lnc-C15orf59-4 PML BBS4 ISLR CLK3 piR-34920-003
GH15J073682 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.8 -51.9 -51928 8 ZNF217 CTCF JUND FOS ZFX ZNF639 ZIC2 REST KDM6A ZBTB10 NONHSAG017382.2 NPTN CD276 INSYN1 GOLGA6A NONHSAG017383.2
GH15J073564 Enhancer 0.9 Ensembl ENCODE 12 +69.4 69433 1.4 CTCF JUND ZIC2 MYC NCOR1 SMC3 ZBTB17 MXI1 FOS MAX lnc-C15orf59-6 NPTN NPTN-IT1
GH15J073598 Enhancer 0.8 ENCODE 11.9 +32.6 32567 3.8 ZNF217 ZSCAN5C ZNF10 CUX1 ZEB1 CTBP1 ZNF341 SIN3A FOXA2 CEBPG NPTN ADPGK piR-34920-003 NPTN-IT1 lnc-C15orf59-4
GH15J073700 Enhancer 0.7 ENCODE 11.9 -66.0 -66041 0.2 ZNF217 CTCF ZNF639 ZBTB25 CTBP1 ZEB1 RBM25 DEK SMC3 ZNF263 NPTN HCN4 NONHSAG017383.2 CD276 NONHSAG017382.2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPTN on UCSC Golden Path with GeneCards custom track

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

Top Transcription factor binding sites by QIAGEN in the NPTN gene promoter:
  • AhR
  • AML1a
  • Arnt
  • Chx10
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • PPAR-gamma1
  • SRF
  • SRF (504 AA)

Genomic Locations for NPTN Gene

Genomic Locations for NPTN Gene
chr15:73,560,003-73,634,134
(GRCh38/hg38)
Size:
74,132 bases
Orientation:
Minus strand
chr15:73,852,344-73,926,475
(GRCh37/hg19)
Size:
74,132 bases
Orientation:
Minus strand

Genomic View for NPTN Gene

Genes around NPTN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NPTN Gene

Proteins for NPTN Gene

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

    Protein Symbol:
    Q9Y639-NPTN_HUMAN
    Recommended name:
    Neuroplastin
    Protein Accession:
    Q9Y639
    Secondary Accessions:
    • B2RAL7
    • B7Z4D3
    • B7ZLL2
    • Q17R52
    • Q59EJ9
    • Q6NVX7
    • Q9Y640

    Protein attributes for NPTN Gene

    Size:
    398 amino acids
    Molecular mass:
    44387 Da
    Quaternary structure:
    • Interacts with ATP2B1; this interaction stabilizes ATP2B1 and increases ATPase activity; this interaction controls T cell calcium homeostasis following T cell activation.
    SequenceCaution:
    • Sequence=BAD93049.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NPTN Gene

    Alternative splice isoforms for NPTN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NPTN Gene

Post-translational modifications for NPTN Gene

  • Glycosylation at Asn171, Asn197, Asn229, Asn284, Asn296, and Asn317
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for NPTN Gene

Domains & Families for NPTN Gene

Gene Families for NPTN Gene

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

Protein Domains for NPTN Gene

Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin I-set
  • Basigin signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NPTN Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ94993, Homo sapiens stromal cell derived factor receptor 1 (SDFR1),transcript variant alpha, mRNA (B2RAL7_HUMAN)
  • Stromal cell-derived receptor 1 (NPTN_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y639

UniProtKB/Swiss-Prot:

NPTN_HUMAN :
  • Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1 (By similarity).
Domain:
  • Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1 (By similarity).
genes like me logo Genes that share domains with NPTN: view

Function for NPTN Gene

Molecular function for NPTN Gene

UniProtKB/Swiss-Prot Function:
Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity).

Phenotypes From GWAS Catalog for NPTN Gene

Gene Ontology (GO) - Molecular Function for NPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005105 type 1 fibroblast growth factor receptor binding ISS --
GO:0005515 protein binding IPI 30190470
GO:0044325 ion channel binding IEA --
GO:0050839 cell adhesion molecule binding ISS --
GO:0098632 cell-cell adhesion mediator activity IBA 21873635
genes like me logo Genes that share ontologies with NPTN: view
genes like me logo Genes that share phenotypes with NPTN: view

Animal Model Products

  • Taconic Biosciences Mouse Models for NPTN

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for NPTN

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

Localization for NPTN Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPTN Gene

Cell membrane; Single-pass type I membrane protein.
[Isoform 2]: Cell junction, synapse, postsynaptic density.

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 NPTN gene
Compartment Confidence
plasma membrane 5
extracellular 3
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytoskeleton 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (2)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001772 immunological synapse ISS --
GO:0005623 cell IEA --
GO:0005886 plasma membrane IBA 21873635
GO:0009986 cell surface HDA 19581412
GO:0014069 postsynaptic density IEA --
genes like me logo Genes that share ontologies with NPTN: view

Pathways & Interactions for NPTN Gene

PathCards logo

SuperPathways for NPTN Gene

SuperPathway Contained pathways
1 Akt Signaling
.60
.60
.55
2 Transmission across Chemical Synapses
3 PAK Pathway
.56
4 CCR5 Pathway in Macrophages
.33
5 ERK Signaling
.51
genes like me logo Genes that share pathways with NPTN: view

Pathways by source for NPTN Gene

7 Qiagen pathways for NPTN Gene
  • Akt Signaling
  • Antioxidant Action of Vitamin-C
  • Chemokine Signaling
  • Molecular Mechanisms of Cancer
  • p38 Signaling

Gene Ontology (GO) - Biological Process for NPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001818 negative regulation of cytokine production ISS --
GO:0001934 positive regulation of protein phosphorylation ISS --
GO:0006874 cellular calcium ion homeostasis ISS --
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules ISS --
genes like me logo Genes that share ontologies with NPTN: view

No data available for SIGNOR curated interactions for NPTN Gene

Drugs & Compounds for NPTN Gene

No Compound Related Data Available

Transcripts for NPTN Gene

mRNA/cDNA for NPTN Gene

4 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for NPTN

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: - -
SP2: - - -
SP3: - - - -
SP4:
SP5:
SP6: - -

Relevant External Links for NPTN Gene

GeneLoc Exon Structure for
NPTN

Expression for NPTN Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NPTN Gene

This gene is overexpressed in Nasal epithelium (25.1) and Serum (18.5).

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



Protein tissue co-expression partners for NPTN Gene

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

SOURCE GeneReport for Unigene cluster for NPTN Gene:

Hs.744867

mRNA Expression by UniProt/SwissProt for NPTN Gene:

Q9Y639-NPTN_HUMAN
Tissue specificity: Isoform 1 is ubiquitously expressed. Isoform 2 is expressed in brain cortex and cerebellum (at protein level).

Evidence on tissue expression from TISSUES for NPTN Gene

  • Nervous system(4.8)
  • Liver(4.3)
  • Skin(4.3)
  • Stomach(4.3)
  • Lung(2.8)
  • Kidney(2.4)
  • Spleen(2.3)
  • Heart(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with NPTN: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPTN Gene

Orthologs for NPTN Gene

This gene was present in the common ancestor of animals.

Orthologs for NPTN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPTN 31 30
  • 99.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NPTN 31 30
  • 95.37 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nptn 30
  • 93.51 (n)
oppossum
(Monodelphis domestica)
Mammalia NPTN 31
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nptn 31
  • 80 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NPTN 31
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NPTN 31
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPTN 31 30
  • 77.72 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPTN 31
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6352 30
African clawed frog
(Xenopus laevis)
Amphibia LOC398501 30
zebrafish
(Danio rerio)
Actinopterygii nptnb 31 30
  • 69.62 (n)
OneToMany
NPTN (3 of 3) 31
  • 64 (a)
OneToMany
NPTN (1 of 3) 31
  • 38 (a)
OneToMany
wufj19g07 30
fruit fly
(Drosophila melanogaster)
Insecta Bsg 31
  • 14 (a)
OneToMany
Species where no ortholog for NPTN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NPTN Gene

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

Paralogs for NPTN Gene

Paralogs for NPTN Gene

(3) SIMAP similar genes for NPTN Gene using alignment to 6 proteins:

  • NPTN_HUMAN
  • F5GYM7_HUMAN
  • F5GZD0_HUMAN
  • H3BQ94_HUMAN
  • H3BU51_HUMAN
  • H7BXJ1_HUMAN
genes like me logo Genes that share paralogs with NPTN: view

Variants for NPTN Gene

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

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
779895 Benign: not provided 73,570,426(-) G/A INTRON_VARIANT
791101 Benign: not provided 73,570,265(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NPTN Gene

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

Variant ID Type Subtype PubMed ID
esv1006009 CNV loss 20482838
esv26087 CNV loss 19812545
esv2749873 CNV deletion 23290073
nsv1121512 CNV deletion 24896259
nsv951989 CNV duplication 24416366
nsv951990 CNV duplication 24416366

Variation tolerance for NPTN Gene

Residual Variation Intolerance Score: 24.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.66; 14.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPTN Gene

Human Gene Mutation Database (HGMD)
NPTN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPTN

SNP Genotyping and Copy Number Assay Products

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

Disorders for NPTN Gene

MalaCards: The human disease database

(4) MalaCards diseases for NPTN Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
allergic bronchopulmonary aspergillosis
  • pulmonary aspergillus disease
retrograde amnesia
  • amnesia, retrograde
erythroleukemia, familial
  • erythroleukemia, familial, susceptibility to
chromosome 15q24 deletion syndrome
  • 15q24 microdeletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search NPTN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NPTN

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NPTN: view

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

Publications for NPTN Gene

  1. Association study of putative promoter polymorphisms in the neuroplastin gene and schizophrenia. (PMID: 17123723) Saito A … Ito C (Neuroscience letters 2007) 3 23 41 54
  2. The immunolocalization of the synaptic glycoprotein neuroplastin differs substantially between the human and the rodent brain. (PMID: 17196182) Bernstein HG … Kreutz MR (Brain research 2007) 3 4 23 54
  3. Structure of the human plasma membrane Ca2+-ATPase 1 in complex with its obligatory subunit neuroplastin. (PMID: 30190470) Gong D … Zhou Q (Nature communications 2018) 3 4 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z … Henzel WJ (Protein science : a publication of the Protein Society 2004) 3 4 54

Products for NPTN Gene

  • Addgene plasmids for NPTN
  • Signalway ELISA kits for NPTN
  • Signalway Proteins for NPTN

Sources for NPTN Gene