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Aliases for CLSTN1 Gene

Aliases for CLSTN1 Gene

  • Calsyntenin 1 2 3
  • Alzheimer-Related Cadherin-Like Protein 3 4
  • Cadherin-Related Family Member 12 2 3
  • Non-Classical Cadherin XB31alpha 3 4
  • Alcadein-Alpha 3 4
  • ALC-ALPHA 3 4
  • XB31alpha 3
  • Alcalpha1 3
  • Alcalpha2 3
  • KIAA0911 4
  • CDHR12 3
  • PIK3CD 3
  • CST-1 3
  • CSTN1 3
  • CS1 4

External Ids for CLSTN1 Gene

Previous GeneCards Identifiers for CLSTN1 Gene

  • GC01M009751
  • GC01M009632
  • GC01M009398
  • GC01M009498
  • GC01M009723
  • GC01M009711
  • GC01M008945

Summaries for CLSTN1 Gene

Entrez Gene Summary for CLSTN1 Gene

  • This gene is a member of the calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

GeneCards Summary for CLSTN1 Gene

CLSTN1 (Calsyntenin 1) is a Protein Coding gene. Diseases associated with CLSTN1 include dravet syndrome and alzheimer disease. Among its related pathways are PI3K-Akt signaling pathway and PI3K/AKT Signaling in Cancer. GO annotations related to this gene include calcium ion binding and beta-amyloid binding. An important paralog of this gene is CLSTN3.

UniProtKB/Swiss-Prot for CLSTN1 Gene

  • Induces KLC1 association with vesicles and functions as a cargo in axonal anterograde transport. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. In complex with APBA2 and C99, a C-terminal APP fragment, abolishes C99 interaction with PSEN1 and thus APP C99 cleavage by gamma-secretase, most probably through stabilization of the direct interaction between APBA2 and APP. The intracellular fragment AlcICD suppresses APBB1-dependent transactivation stimulated by APP C-terminal intracellular fragment (AICD), most probably by competing with AICD for APBB1-binding. May modulate calcium-mediated postsynaptic signals (By similarity).

Gene Wiki entry for CLSTN1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLSTN1 Gene

Genomics for CLSTN1 Gene

Regulatory Elements for CLSTN1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CLSTN1 Gene

Chromosome:
1
Start:
9,729,021 bp from pter
End:
9,824,526 bp from pter
Size:
95,506 bases
Orientation:
Minus strand

Genomic View for CLSTN1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLSTN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLSTN1 Gene

Proteins for CLSTN1 Gene

  • Protein details for CLSTN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94985-CSTN1_HUMAN
    Recommended name:
    Calsyntenin-1
    Protein Accession:
    O94985
    Secondary Accessions:
    • A8K183
    • Q5SR52
    • Q5UE58
    • Q71MN0
    • Q8N4K9

    Protein attributes for CLSTN1 Gene

    Size:
    981 amino acids
    Molecular mass:
    109793 Da
    Quaternary structure:
    • Directly interacts with APBA2. Forms a tripartite complex with APBA2 and APP. The CTF1 chain interacts with PSEN1. The intracellular fragment AlcICD interacts with APBB1; this interaction stabilizes AlcICD metabolism. Interacts with KLC1 and APBB1 (By similarity).
    SequenceCaution:
    • Sequence=BAA74934.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CLSTN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLSTN1 Gene

Proteomics data for CLSTN1 Gene at MOPED

Post-translational modifications for CLSTN1 Gene

  • Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N-terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by presenilin gamma-secretase within the transmembrane domain releases the beta-Alc-alpha chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with PSEN1.
  • Glycosylation at Asn 346, Asn 366, and Asn 515
  • Modification sites at PhosphoSitePlus

Other Protein References for CLSTN1 Gene

Antibody Products

  • R&D Systems Antibodies for CLSTN1 (Calsyntenin-1)

No data available for DME Specific Peptides for CLSTN1 Gene

Domains & Families for CLSTN1 Gene

Gene Families for CLSTN1 Gene

Protein Domains for CLSTN1 Gene

Suggested Antigen Peptide Sequences for CLSTN1 Gene

Graphical View of Domain Structure for InterPro Entry

O94985

UniProtKB/Swiss-Prot:

CSTN1_HUMAN :
  • The cytoplasmic domain is involved in interaction with APBA2, as well as the binding of synaptic Ca(2+).
Domain:
  • The cytoplasmic domain is involved in interaction with APBA2, as well as the binding of synaptic Ca(2+).
  • Contains 2 cadherin domains.
genes like me logo Genes that share domains with CLSTN1: view

Function for CLSTN1 Gene

Molecular function for CLSTN1 Gene

UniProtKB/Swiss-Prot Function:
Induces KLC1 association with vesicles and functions as a cargo in axonal anterograde transport. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. In complex with APBA2 and C99, a C-terminal APP fragment, abolishes C99 interaction with PSEN1 and thus APP C99 cleavage by gamma-secretase, most probably through stabilization of the direct interaction between APBA2 and APP. The intracellular fragment AlcICD suppresses APBB1-dependent transactivation stimulated by APP C-terminal intracellular fragment (AICD), most probably by competing with AICD for APBB1-binding. May modulate calcium-mediated postsynaptic signals (By similarity).

Gene Ontology (GO) - Molecular Function for CLSTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 beta-amyloid binding IDA 17332754
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 17332754
GO:0019894 kinesin binding IPI 17332754
GO:0042988 X11-like protein binding IPI 12972431
genes like me logo Genes that share ontologies with CLSTN1: view
genes like me logo Genes that share phenotypes with CLSTN1: view

miRNA for CLSTN1 Gene

miRTarBase miRNAs that target CLSTN1

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLSTN1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for CLSTN1 Gene

Localization for CLSTN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLSTN1 Gene

Endoplasmic reticulum membrane; Single-pass type I membrane protein. Golgi apparatus membrane. Cell projection. Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein. Nucleus. Note=Neurite tips. Localized in the postsynaptic membrane of both excitatory and inhibitory synapses (By similarity). The AlcICD fragment is translocated to the nucleus upon interaction with APBB1. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLSTN1 Gene COMPARTMENTS Subcellular localization image for CLSTN1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 3
golgi apparatus 3
nucleus 3
plasma membrane 3
cytoskeleton 1
endosome 1

Gene Ontology (GO) - Cellular Components for CLSTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005576 extracellular region --
GO:0005634 nucleus IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0009986 cell surface IEA --
genes like me logo Genes that share ontologies with CLSTN1: view

Pathways & Interactions for CLSTN1 Gene

SuperPathways for CLSTN1 Gene

Superpath Contained pathways
1 Interleukin receptor SHC signaling
2 PI3K/AKT Signaling in Cancer
3 Translation Insulin regulation of translation
4 IL-7 Signaling Pathways
5 Development HGF signaling pathway
genes like me logo Genes that share pathways with CLSTN1: view

Gene Ontology (GO) - Biological Process for CLSTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001558 regulation of cell growth IEA --
GO:0007155 cell adhesion TAS 17332754
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0050806 positive regulation of synaptic transmission IEA --
GO:0051965 positive regulation of synapse assembly IEA --
genes like me logo Genes that share ontologies with CLSTN1: view

No data available for SIGNOR curated interactions for CLSTN1 Gene

Drugs & Compounds for CLSTN1 Gene

(1) Drugs for CLSTN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 0
genes like me logo Genes that share compounds with CLSTN1: view

Transcripts for CLSTN1 Gene

Unigene Clusters for CLSTN1 Gene

Calsyntenin 1:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLSTN1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLSTN1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c ^ 16 ^ 17 ^ 18a · 18b ^
SP1: - - - - - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - -
SP5: - - -
SP6: - - - - -
SP7: - - -
SP8: - - -
SP9:
SP10: -
SP11:
SP12:

ExUns: 19a · 19b ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23 ^ 24a · 24b ^ 25a · 25b
SP1: - -
SP2: - -
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -

Relevant External Links for CLSTN1 Gene

GeneLoc Exon Structure for
CLSTN1
ECgene alternative splicing isoforms for
CLSTN1

Expression for CLSTN1 Gene

mRNA expression in normal human tissues for CLSTN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLSTN1 Gene

This gene is overexpressed in Vitreous humor (42.7), Amniocyte (9.3), and Cerebrospinal fluid (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLSTN1 Gene



SOURCE GeneReport for Unigene cluster for CLSTN1 Gene Hs.29665

mRNA Expression by UniProt/SwissProt for CLSTN1 Gene

O94985-CSTN1_HUMAN
Tissue specificity: Expressed in the brain and, a lower level, in the heart, skeletal muscle, kidney and placenta. Accumulates in dystrophic neurites around the amyloid core of Alzheimer disease senile plaques (at protein level).
genes like me logo Genes that share expression patterns with CLSTN1: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CLSTN1 Gene

Orthologs for CLSTN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLSTN1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia CLSTN1 35
  • 86.04 (n)
  • 91.26 (a)
CLSTN1 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLSTN1 35
  • 87.8 (n)
  • 92.05 (a)
CLSTN1 36
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clstn1 35
  • 85.78 (n)
  • 92.56 (a)
Clstn1 16
Clstn1 36
  • 93 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CLSTN1 35
  • 99.29 (n)
  • 99.59 (a)
CLSTN1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clstn1 35
  • 85.62 (n)
  • 93.1 (a)
oppossum
(Monodelphis domestica)
Mammalia CLSTN1 36
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLSTN1 36
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLSTN1 35
  • 77.37 (n)
  • 85.68 (a)
CALSYNTENIN-1 36
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLSTN1 36
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clstn3 35
  • 68.23 (n)
  • 70.88 (a)
zebrafish
(Danio rerio)
Actinopterygii -- 35
clstn1 35
  • 74.41 (n)
  • 77.86 (a)
clstn1 36
  • 76 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta calsyntenin-1 37
  • 29 (a)
cals 36
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea casy-1 35
  • 45.71 (n)
  • 34.18 (a)
casy-1 36
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 33 (a)
ManyToMany
-- 36
  • 26 (a)
ManyToMany
Species with no ortholog for CLSTN1:
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for CLSTN1 Gene

ENSEMBL:
Gene Tree for CLSTN1 (if available)
TreeFam:
Gene Tree for CLSTN1 (if available)

Paralogs for CLSTN1 Gene

Paralogs for CLSTN1 Gene

(2) SIMAP similar genes for CLSTN1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CLSTN1: view

Variants for CLSTN1 Gene

Sequence variations from dbSNP and Humsavar for CLSTN1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs11674 -- 9,751,483(+) TTGTC(A/G)ACAGT synonymous-codon, reference
rs767762 -- 9,802,314(-) attta(A/G)ccagg intron-variant
rs935071 -- 9,814,744(-) TTTGT(A/G)GAGAC intron-variant
rs946277 -- 9,815,575(-) CCATA(A/G)TCACT intron-variant
rs946278 -- 9,815,289(-) ACTCT(A/G)CTGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLSTN1 Gene

Variant ID Type Subtype PubMed ID
nsv871610 CNV Gain 21882294
nsv832203 CNV Loss 17160897
esv2662594 CNV Deletion 23128226
esv2656500 CNV Deletion 23128226
nsv827364 CNV Loss 20364138
nsv2298 CNV Loss 18451855
esv2743630 CNV Deletion 23290073
dgv11n67 CNV Loss 20364138
nsv498662 CNV Loss 21111241
esv2669918 CNV Deletion 23128226
esv2669984 CNV Deletion 23128226

Variation tolerance for CLSTN1 Gene

Residual Variation Intolerance Score: 3.81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.57; 56.08% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLSTN1 Gene

HapMap Linkage Disequilibrium report
CLSTN1
Human Gene Mutation Database (HGMD)
CLSTN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLSTN1 Gene

Disorders for CLSTN1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLSTN1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
dravet syndrome
  • dravet syndrome, modifier of
alzheimer disease
  • alzheimer disease, late-onset
- elite association

Relevant External Links for CLSTN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLSTN1
genes like me logo Genes that share disorders with CLSTN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLSTN1 Gene

Publications for CLSTN1 Gene

  1. Calsyntenins mediate TGN exit of APP in a kinesin-1-dependent manner. (PMID: 19192245) Ludwig A. … Sonderegger P. (Traffic 2009) 23 67
  2. Neuronal pentraxin receptor in cerebrospinal fluid as a potential biomarker for neurodegenerative diseases. (PMID: 19368810) Yin G.N. … Suk K. (Brain Res. 2009) 23 67
  3. Characterization of the vitreous proteome in diabetes without diabetic retinopathy and diabetes with proliferative diabetic retinopathy. (PMID: 18433156) Gao B.B. … Feener E.P. (J. Proteome Res. 2008) 23 67
  4. Expression profile of the cadherin family in the developing Drosophila brain. (PMID: 18041774) Fung S. … Hartenstein V. (J. Comp. Neurol. 2008) 23 67
  5. Neuroblastoma tumors with favorable and unfavorable outcomes: Significant differences in mRNA expression of genes mapped at 1p36.2. (PMID: 17044048) Fransson S. … EjeskAor K. (Genes Chromosomes Cancer 2007) 23 67

Products for CLSTN1 Gene

Sources for CLSTN1 Gene

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