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Aliases for CLSTN2 Gene

Aliases for CLSTN2 Gene

  • Calsyntenin 2 2 3 5
  • Cadherin-Related Family Member 13 2 3
  • Alcadein-Gamma 3 4
  • ALC-GAMMA 3 4
  • CS2 3 4
  • Alcadein Gamma 3
  • Alcagamma 3
  • CDHR13 3
  • CSTN2 3

External Ids for CLSTN2 Gene

Previous GeneCards Identifiers for CLSTN2 Gene

  • GC03P136552
  • GC03P140483
  • GC03P140935
  • GC03P140975
  • GC03P141136
  • GC03P139654
  • GC03P137029

Summaries for CLSTN2 Gene

GeneCards Summary for CLSTN2 Gene

CLSTN2 (Calsyntenin 2) is a Protein Coding gene. Diseases associated with CLSTN2 include Keratinizing Squamous Cell Carcinoma and Connective Tissue Cancer. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is CLSTN3.

UniProtKB/Swiss-Prot for CLSTN2 Gene

  • May modulate calcium-mediated postsynaptic signals.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLSTN2 Gene

Genomics for CLSTN2 Gene

Regulatory Elements for CLSTN2 Gene

Enhancers for CLSTN2 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CLSTN2 on UCSC Golden Path with GeneCards custom track

Promoters for CLSTN2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around CLSTN2 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLSTN2 Gene

139,935,185 bp from pter
140,577,397 bp from pter
642,213 bases
Plus strand

Genomic View for CLSTN2 Gene

Genes around CLSTN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLSTN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLSTN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLSTN2 Gene

Proteins for CLSTN2 Gene

  • Protein details for CLSTN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2RCW5
    • D3DNF4
    • Q3SX54
    • Q3ZB76
    • Q5UE56
    • Q96HZ2
    • Q9BSS0

    Protein attributes for CLSTN2 Gene

    955 amino acids
    Molecular mass:
    107006 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLSTN2 Gene

Proteomics data for CLSTN2 Gene at MOPED

Post-translational modifications for CLSTN2 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 gamma-secretase within the transmembrane domain releases the beta-Alc-gamma 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 (By similarity).
  • Glycosylation at Asn 56, Asn 98, Asn 342, Asn 374, Asn 716, and Asn 729
  • Modification sites at PhosphoSitePlus

Other Protein References for CLSTN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for CLSTN2 (Calsyntenin-2)

No data available for DME Specific Peptides for CLSTN2 Gene

Domains & Families for CLSTN2 Gene

Gene Families for CLSTN2 Gene

Protein Domains for CLSTN2 Gene

Suggested Antigen Peptide Sequences for CLSTN2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Binds synaptic Ca(2+) with its cytoplasmic domain.
  • Binds synaptic Ca(2+) with its cytoplasmic domain.
  • Contains 2 cadherin domains.
genes like me logo Genes that share domains with CLSTN2: view

Function for CLSTN2 Gene

Molecular function for CLSTN2 Gene

UniProtKB/Swiss-Prot Function:
May modulate calcium-mediated postsynaptic signals.
genes like me logo Genes that share phenotypes with CLSTN2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CLSTN2

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLSTN2 Gene

Localization for CLSTN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLSTN2 Gene

Cell membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane. Golgi apparatus membrane. Note=Most prominent in the postsynaptic specializations of asymmetric (type I) synapses with both axodendritic and axospinous localization. {ECO:0000250}.

Subcellular locations from

Jensen Localization Image for CLSTN2 Gene COMPARTMENTS Subcellular localization image for CLSTN2 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 4
extracellular 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CLSTN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0009986 cell surface IEA --
GO:0016021 integral component of membrane IEA --
GO:0045211 postsynaptic membrane IEA --
genes like me logo Genes that share ontologies with CLSTN2: view

Pathways & Interactions for CLSTN2 Gene

SuperPathways for CLSTN2 Gene

No Data Available

Interacting Proteins for CLSTN2 Gene

Gene Ontology (GO) - Biological Process for CLSTN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050806 positive regulation of synaptic transmission IEA --
genes like me logo Genes that share ontologies with CLSTN2: view

No data available for Pathways by source and SIGNOR curated interactions for CLSTN2 Gene

Drugs & Compounds for CLSTN2 Gene

(1) Drugs for CLSTN2 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 CLSTN2: view

Transcripts for CLSTN2 Gene

mRNA/cDNA for CLSTN2 Gene

Unigene Clusters for CLSTN2 Gene

Calsyntenin 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLSTN2 Gene

No ASD Table

Relevant External Links for CLSTN2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLSTN2 Gene

mRNA expression in normal human tissues for CLSTN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLSTN2 Gene

This gene is overexpressed in Ovary (x10.1).

Protein differential expression in normal tissues from HIPED for CLSTN2 Gene

This gene is overexpressed in Amniocyte (66.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CLSTN2 Gene

SOURCE GeneReport for Unigene cluster for CLSTN2 Gene Hs.158529

mRNA Expression by UniProt/SwissProt for CLSTN2 Gene

Tissue specificity: Restricted to the brain.
genes like me logo Genes that share expression patterns with CLSTN2: view

Primer Products

No data available for Protein tissue co-expression partners for CLSTN2 Gene

Orthologs for CLSTN2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLSTN2 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLSTN2 35
  • 89.83 (n)
  • 93.08 (a)
  • 91 (a)
(Canis familiaris)
Mammalia CLSTN2 35
  • 90.12 (n)
  • 94.24 (a)
  • 91 (a)
(Mus musculus)
Mammalia Clstn2 35
  • 89.73 (n)
  • 95.09 (a)
Clstn2 16
Clstn2 36
  • 93 (a)
(Pan troglodytes)
Mammalia CLSTN2 35
  • 99.13 (n)
  • 98.85 (a)
  • 99 (a)
(Rattus norvegicus)
Mammalia Clstn2 35
  • 88.21 (n)
  • 93.24 (a)
(Monodelphis domestica)
Mammalia CLSTN2 36
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia CLSTN2 36
  • 74 (a)
(Gallus gallus)
Aves CLSTN2 35
  • 73.6 (n)
  • 80.83 (a)
  • 74 (a)
(Anolis carolinensis)
Reptilia CLSTN2 36
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clstn2 35
  • 71.24 (n)
  • 76.05 (a)
(Danio rerio)
Actinopterygii clstn2 35
  • 69.67 (n)
  • 70.5 (a)
clstn2 36
  • 67 (a)
CLSTN2 (2 of 2) 36
  • 58 (a)
fruit fly
(Drosophila melanogaster)
Insecta calsyntenin-1 37
  • 30 (a)
Cals 35
  • 45.76 (n)
  • 36.65 (a)
cals 36
  • 30 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007103 35
  • 50.95 (n)
  • 37.65 (a)
(Caenorhabditis elegans)
Secernentea casy-1 36
  • 27 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 31 (a)
-- 36
  • 27 (a)
Species with no ortholog for CLSTN2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 CLSTN2 Gene

Gene Tree for CLSTN2 (if available)
Gene Tree for CLSTN2 (if available)

Paralogs for CLSTN2 Gene

Paralogs for CLSTN2 Gene

(2) SIMAP similar genes for CLSTN2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CLSTN2: view

Variants for CLSTN2 Gene

Sequence variations from dbSNP and Humsavar for CLSTN2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
VAR_036112 A colorectal cancer sample
VAR_036113 A colorectal cancer sample
VAR_039557 -
VAR_055615 -
rs1691 -- 140,444,490(-) ATGAT(A/T)AAACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLSTN2 Gene

Variant ID Type Subtype PubMed ID
nsv877544 CNV Loss 21882294
esv29420 CNV Loss 19812545
esv2725978 CNV Deletion 23290073
nsv829738 CNV Gain 17160897
esv2498948 CNV Insertion 19546169
nsv236799 CNV Insertion 16902084
esv1072371 CNV Insertion 17803354
nsv236382 CNV Insertion 16902084
esv2675504 CNV Deletion 23128226
esv1009174 CNV Loss 20482838
esv21980 CNV Gain 19812545
nsv520404 CNV Loss 19592680
esv270693 CNV Insertion 20981092
nsv4036 CNV Insertion 18451855
nsv877545 CNV Gain 21882294
nsv483106 CNV Gain 15286789
nsv829739 CNV Gain 17160897
esv2725979 CNV Deletion 23290073
esv2676006 CNV Deletion 23128226
nsv509854 CNV Loss 20534489
esv22085 CNV Gain 19812545
dgv1513e1 CNV Complex 17122850
nsv829740 CNV Gain+Loss 17160897
nsv527831 CNV Gain 19592680
nsv460867 CNV Gain 19166990
esv34489 CNV Gain 17911159
nsv818169 CNV Gain 17921354
nsv4037 CNV Loss 18451855
nsv829741 CNV Loss 17160897
esv2725980 CNV Deletion 23290073
esv2668734 CNV Deletion 23128226
esv2725981 CNV Deletion 23290073
esv2284794 CNV Deletion 18987734
esv2725982 CNV Deletion 23290073
nsv236797 CNV Loss 16902084
esv2725983 CNV Deletion 23290073
esv2725985 CNV Deletion 23290073
essv19147 CNV CNV 17122850
nsv10331 CNV Loss 18304495
esv2455650 CNV Deletion 19546169
esv29912 CNV Loss 19812545
nsv513078 CNV Loss 21212237
esv1479020 CNV Deletion 17803354

Variation tolerance for CLSTN2 Gene

Residual Variation Intolerance Score: 52.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.45; 64.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLSTN2 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLSTN2 Gene

Disorders for CLSTN2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLSTN2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
keratinizing squamous cell carcinoma
  • keratinizing epidermoid carcinoma
connective tissue cancer
  • connective tissue neoplasm
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for CLSTN2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLSTN2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLSTN2 Gene

Publications for CLSTN2 Gene

  1. The calsyntenins - a family of postsynaptic membrane proteins with distinct neuronal expression patterns. (PMID: 12498782) Hintsch G. … Sonderegger P. (Mol. Cell. Neurosci. 2002) 2 3 4 23 67
  2. KIBRA and CLSTN2 polymorphisms exert interactive effects on human episodic memory. (PMID: 19804789) Preuschhof C. … BAockman L. (Neuropsychologia 2010) 3 23
  3. A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. (PMID: 24920014) Cozen W. … McKay J.D. (Nat Commun 2014) 3
  4. Interactive effects of KIBRA and CLSTN2 polymorphisms on episodic memory in old-age unipolar depression. (PMID: 25080189) Pantzar A. … BAockman L. (Neuropsychologia 2014) 3
  5. Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. (PMID: 25367360) Li Q. … Guggenheim J.A. (Hum. Genet. 2014) 3

Products for CLSTN2 Gene

Sources for CLSTN2 Gene