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Aliases for CLSTN1 Gene

Aliases for CLSTN1 Gene

  • Calsyntenin 1 2 3 5
  • 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
  • Calsyntenin-1 3
  • 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 Schnyder Corneal Dystrophy and Alzheimer Disease. Gene Ontology (GO) annotations related to this gene include calcium ion binding and amyloid-beta binding. An important paralog of this gene is CLSTN2.

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

Additional gene information for CLSTN1 Gene

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

Genomics for CLSTN1 Gene

GeneHancer (GH) Regulatory Elements for CLSTN1 Gene

Promoters and enhancers for CLSTN1 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
GH01I009821 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 561.6 +0.4 360 5.5 PKNOX1 CLOCK ZFP64 ARID4B SIN3A ZNF2 YY1 ZNF766 ZNF213 ZNF143 CLSTN1 ENSG00000223989 ENSG00000280113 MZT1P1
GH01I010790 Promoter/Enhancer 3.3 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 14.2 -969.3 -969287 6.4 PKNOX1 ARID4B NEUROD1 SIN3A ZNF2 YY1 ZNF213 ZNF548 KLF13 SP3 CASZ1 TARDBP ANGPTL7 ENSG00000226849 CLSTN1 UBIAD1 FBXO44 EXOSC10 GC01P010673
GH01I008869 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.1 +948.7 948736 11.8 CLOCK DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 NFYC ENO1 LOC102724552 MIR34AHG RERE GPR157 CLSTN1 PIK3CD-AS2 SLC45A1 H6PD ENO1-IT1
GH01I009291 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 14.2 +530.5 530537 5.1 HDGF PKNOX1 ARID4B SIN3A FEZF1 YBX1 ZNF2 ZNF213 ZNF207 ZNF143 SPSB1 SLC45A1 CLSTN1 LOC102724552 ENSG00000284652
GH01I009786 Enhancer 0.9 Ensembl ENCODE 22.5 +37.1 37052 1.7 PKNOX1 EBF1 BATF IRF4 POLR2A ATF7 ETV6 IKZF2 RUNX3 SMARCA5 CLSTN1 ENSG00000223989 CTNNBIP1 ENSG00000228150 RN7SKP269 NMNAT1 LZIC MZT1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLSTN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLSTN1 gene promoter:

Genomic Locations for CLSTN1 Gene

Genomic Locations for CLSTN1 Gene
chr1:9,729,021-9,824,526
(GRCh38/hg38)
Size:
95,506 bases
Orientation:
Minus strand
chr1:9,789,079-9,884,584
(GRCh37/hg19)

Genomic View for CLSTN1 Gene

Genes around CLSTN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLSTN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

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 Asn346, posLast=366366, and Asn515
  • Modification sites at PhosphoSitePlus

Other Protein References for CLSTN1 Gene

No data available for DME Specific Peptides for CLSTN1 Gene

Domains & Families for CLSTN1 Gene

Gene Families for CLSTN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted membrane proteins

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+).
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).

Phenotypes From GWAS Catalog for CLSTN1 Gene

Gene Ontology (GO) - Molecular Function for CLSTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 amyloid-beta 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

Animal Models for CLSTN1 Gene

MGI Knock Outs for CLSTN1:

Animal Model Products

CRISPR Products

miRNA for CLSTN1 Gene

miRTarBase miRNAs that target CLSTN1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
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 CLSTN1 gene
Compartment Confidence
extracellular 5
plasma membrane 4
endoplasmic reticulum 4
golgi apparatus 4
nucleus 3
cytoskeleton 1
mitochondrion 1
peroxisome 1
cytosol 1
lysosome 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 IEA --
GO:0005615 extracellular space IEA --
GO:0005634 nucleus IEA --
GO:0005783 endoplasmic reticulum IEA --
genes like me logo Genes that share ontologies with CLSTN1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLSTN1 Gene

Pathways & Interactions for CLSTN1 Gene

SuperPathways for CLSTN1 Gene

No Data Available

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 Pathways by source and 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 Approved 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:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for CLSTN1 Gene



NURSA nuclear receptor signaling pathways regulating expression of CLSTN1 Gene:

CLSTN1

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).

Evidence on tissue expression from TISSUES for CLSTN1 Gene

  • Nervous system(5)
  • Eye(3.8)
  • Intestine(3.7)
  • Lung(3.4)
  • Pancreas(2.7)
  • Kidney(2.5)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with CLSTN1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia CLSTN1 33 34
  • 99.29 (n)
dog
(Canis familiaris)
Mammalia CLSTN1 33 34
  • 87.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLSTN1 34
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLSTN1 33 34
  • 86.04 (n)
mouse
(Mus musculus)
Mammalia Clstn1 33 16 34
  • 85.78 (n)
rat
(Rattus norvegicus)
Mammalia Clstn1 33
  • 85.62 (n)
oppossum
(Monodelphis domestica)
Mammalia CLSTN1 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves CALSYNTENIN-1 34
  • 85 (a)
OneToOne
CLSTN1 33
  • 77.37 (n)
lizard
(Anolis carolinensis)
Reptilia CLSTN1 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clstn3 33
  • 68.23 (n)
zebrafish
(Danio rerio)
Actinopterygii clstn1 33 34
  • 74.41 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta cals 34
  • 30 (a)
OneToMany
calsyntenin-1 35
  • 29 (a)
worm
(Caenorhabditis elegans)
Secernentea casy-1 33 34
  • 45.71 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
ManyToMany
-- 34
  • 26 (a)
ManyToMany
Species where no ortholog for CLSTN1 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)
  • 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 Variation AA Info Type
rs1000007155 -- 9,808,003(-) G/A intron_variant
rs1000011742 -- 9,804,712(-) G/T intron_variant
rs1000028076 -- 9,730,273(-) G/A 3_prime_UTR_variant
rs1000039691 -- 9,807,722(-) C/T intron_variant
rs1000070610 -- 9,771,499(-) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
dgv102n54 CNV loss 21841781
dgv11n67 CNV loss 20364138
dgv14e212 CNV loss 25503493
esv2656500 CNV deletion 23128226
esv2662594 CNV deletion 23128226
esv2669918 CNV deletion 23128226
esv2669984 CNV deletion 23128226
esv2743630 CNV deletion 23290073
esv3543788 CNV deletion 23714750
esv3543899 CNV deletion 23714750
esv3577725 CNV loss 25503493
esv3585187 CNV loss 21293372
esv3585188 CNV loss 21293372
nsv1076086 CNV deletion 25765185
nsv1126976 CNV deletion 24896259
nsv1137727 CNV deletion 24896259
nsv2298 CNV deletion 18451855
nsv498662 CNV loss 21111241
nsv827364 CNV loss 20364138
nsv832203 CNV loss 17160897

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)

Additional Variant Information for CLSTN1 Gene

Human Gene Mutation Database (HGMD)
CLSTN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
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: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
schnyder corneal dystrophy
  • sccd
alzheimer disease
  • ad
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for 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. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  2. The novel cargo Alcadein induces vesicle association of kinesin-1 motor components and activates axonal transport. (PMID: 17332754) Araki Y … Suzuki T (The EMBO journal 2007) 3 4 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Coordinated metabolism of Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation. (PMID: 15037614) Araki Y … Suzuki T (The Journal of biological chemistry 2004) 3 4 58

Products for CLSTN1 Gene

Sources for CLSTN1 Gene

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