Aliases for CLSTN2 Gene

Aliases for CLSTN2 Gene

  • Calsyntenin 2 2 3 5
  • CS2 2 3 4
  • Cadherin-Related Family Member 13 2 3
  • Calsyntenin-2 3 4
  • CDHR13 2 3
  • CSTN2 2 3
  • Alcadein Gamma 3
  • Alcadein-Gamma 4
  • Alcagamma 3
  • Alc-Gamma 4
  • FLJ39113 2
  • CLSTN2 5

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 Astigmatism and Achondroplasia, Severe, With Developmental Delay And Acanthosis Nigricans. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CLSTN1.

UniProtKB/Swiss-Prot Summary for CLSTN2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLSTN2 Gene

Genomics for CLSTN2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLSTN2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J139934 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 262.2 +0.5 495 2.6 ZNF654 ZIC2 ZBTB10 ZNF341 CTCF ZBTB7B ZNF217 SIN3A CTBP1 ZNF610 CLSTN2 HSALNG0029343 TRIM42
GH03J140205 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 15.6 +269.8 269816 4.4 REST FEZF1 CTCF SIN3A ZNF513 SMC3 YY1 ZNF843 EHMT2 MIER2 CLSTN2 HSALNG0029348 HSALNG0029347 TRIM42
GH03J139771 Enhancer 0.9 ENCODE CraniofacialAtlas dbSUPER 8.5 -161.4 -161362 4.3 NFE2 MAFG NR2F6 PKNOX1 KDM1A EGR2 NFE2L2 POLR2A CTCF USF1 CLSTN2 LOC100507291 HSALNG0029335 piR-31292-129 NMNAT3
GH03J139763 Enhancer 0.7 Ensembl ENCODE dbSUPER 4.7 -170.6 -170583 2.4 HLF FOS NMNAT3 CLSTN2 HSALNG0029335 piR-31292-129 LOC100507291
GH03J140051 Enhancer 0.6 Ensembl 5.5 +116.2 116215 0.8 ZNF654 REST CTCF RAD21 MAFG ZNF143 SMC3 PRDM10 TRIM22 USF1 CLSTN2 lnc-NMNAT3-7 HSALNG0029346 TRIM42
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLSTN2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLSTN2

Top Transcription factor binding sites by QIAGEN in the CLSTN2 gene promoter:
  • C/EBPalpha
  • FOXD1
  • FOXL1
  • HOXA3
  • IRF-7A
  • Nkx2-5
  • p53
  • Sp1

Genomic Locations for CLSTN2 Gene

Latest Assembly
642,213 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
642,213 bases
Plus strand

(GRCh37/hg19 by Ensembl)
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

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 Asn56, Asn98, Asn342, Asn374, Asn716, and Asn729
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CSTN2_HUMAN (1061)

Other Protein References for CLSTN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLSTN2 Gene

Domains & Families for CLSTN2 Gene

Gene Families for CLSTN2 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for CLSTN2 Gene

Suggested Antigen Peptide Sequences for CLSTN2 Gene

GenScript: Design optimal peptide antigens:
  • Alcadein-gamma (CSTN2_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Binds synaptic Ca(2+) with its cytoplasmic domain.
  • Binds synaptic Ca(2+) with its cytoplasmic domain.
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.

Phenotypes From GWAS Catalog for CLSTN2 Gene

Gene Ontology (GO) - Molecular Function for CLSTN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with CLSTN2: view
genes like me logo Genes that share phenotypes with CLSTN2: view

Animal Models for CLSTN2 Gene

MGI Knock Outs for CLSTN2:

Animal Models for research

  • Taconic Biosciences Mouse Models for CLSTN2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLSTN2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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. Cell junction, synapse, postsynapse. Cell projection, dendrite. Note=Most prominent in the postsynaptic specializations of asymmetric (type I) synapses with both axodendritic and axospinous localization. {ECO:0000250 UniProtKB:Q9ER65}.

Subcellular locations from

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 CLSTN2 gene
Compartment Confidence
plasma membrane 4
golgi apparatus 3
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLSTN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with CLSTN2: view

Pathways & Interactions for CLSTN2 Gene

PathCards logo

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:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0050806 positive regulation of synaptic transmission IEA,IBA 21873635
GO:0051965 positive regulation of synapse assembly IEA,IBA 21873635
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 6959
genes like me logo Genes that share compounds with CLSTN2: view

Transcripts for CLSTN2 Gene

mRNA/cDNA for CLSTN2 Gene

11 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLSTN2

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

No ASD Table

Relevant External Links for CLSTN2 Gene

GeneLoc Exon Structure for

Expression for CLSTN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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 and MOPED for CLSTN2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLSTN2

SOURCE GeneReport for Unigene cluster for CLSTN2 Gene:


mRNA Expression by UniProt/SwissProt for CLSTN2 Gene:

Tissue specificity: Restricted to the brain.

Evidence on tissue expression from TISSUES for CLSTN2 Gene

  • Nervous system(4.5)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with CLSTN2: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia CLSTN2 29 30
  • 99.13 (n)
(Canis familiaris)
Mammalia CLSTN2 29 30
  • 90.12 (n)
(Bos Taurus)
Mammalia CLSTN2 29 30
  • 89.83 (n)
(Mus musculus)
Mammalia Clstn2 29 16 30
  • 89.73 (n)
(Rattus norvegicus)
Mammalia Clstn2 29
  • 88.21 (n)
(Monodelphis domestica)
Mammalia CLSTN2 30
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia CLSTN2 30
  • 74 (a)
(Gallus gallus)
Aves CLSTN2 29 30
  • 73.6 (n)
(Anolis carolinensis)
Reptilia CLSTN2 30
  • 78 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clstn2 29
  • 71.24 (n)
(Danio rerio)
Actinopterygii clstn2 29 30
  • 69.67 (n)
CLSTN2 (2 of 2) 30
  • 58 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007103 29
  • 50.95 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Cals 29
  • 45.76 (n)
cals 30
  • 30 (a)
calsyntenin-1 31
  • 30 (a)
(Caenorhabditis elegans)
Secernentea casy-1 30
  • 27 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 31 (a)
-- 30
  • 27 (a)
Species where no ortholog for CLSTN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Evolutionary constrained regions (ECRs) for CLSTN2: view image
Alliance of Genome Resources:
Additional Orthologs for CLSTN2

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLSTN2 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs10573488 Benign: not provided 140,566,154(+) AGAGGAG/A
NM_022131.3(CLSTN2):c.2772_2774GGA[3] (p.Glu928_Glu929del)
rs140202819 Likely Benign: not provided 140,566,113(+) G/A
NM_022131.3(CLSTN2):c.2728G>A (p.Glu910Lys)
rs144701273 Benign: not provided 140,558,844(+) C/T
NM_022131.3(CLSTN2):c.2028C>T (p.Asp676=)
rs147446326 Likely Benign: not provided 140,562,862(+) G/A
NM_022131.3(CLSTN2):c.2264G>A (p.Arg755His)
rs1576621338 Likely Benign: not provided 140,546,648(+) T/C
NM_022131.3(CLSTN2):c.1641T>C (p.Ile547=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLSTN2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv4909n100 CNV loss 25217958
dgv4910n100 CNV gain 25217958
esv1009174 CNV loss 20482838
esv1072371 CNV insertion 17803354
esv1479020 CNV deletion 17803354
esv21980 CNV gain 19812545
esv22085 CNV gain 19812545
esv2284794 CNV deletion 18987734
esv2455650 CNV deletion 19546169
esv2498948 CNV insertion 19546169
esv2668734 CNV deletion 23128226
esv2675504 CNV deletion 23128226
esv2676006 CNV deletion 23128226
esv2725978 CNV deletion 23290073
esv2725979 CNV deletion 23290073
esv2725980 CNV deletion 23290073
esv2725981 CNV deletion 23290073
esv2725982 CNV deletion 23290073
esv2725983 CNV deletion 23290073
esv2725985 CNV deletion 23290073
esv2759181 CNV gain+loss 17122850
esv29420 CNV loss 19812545
esv29912 CNV loss 19812545
esv3310518 CNV novel sequence insertion 20981092
esv3382266 CNV insertion 20981092
esv3394534 CNV insertion 20981092
esv3397906 CNV insertion 20981092
esv3417054 CNV insertion 20981092
esv3428644 CNV insertion 20981092
esv34489 CNV gain 17911159
esv3451180 CNV duplication 20981092
esv3562625 CNV deletion 23714750
esv3562628 CNV deletion 23714750
esv3569024 CNV loss 25503493
esv3597943 CNV loss 21293372
esv3597944 CNV loss 21293372
esv3597946 CNV loss 21293372
esv3597948 CNV loss 21293372
esv3597950 CNV loss 21293372
esv3597952 CNV loss 21293372
esv3597953 CNV gain 21293372
esv3597954 CNV gain 21293372
esv3597955 CNV loss 21293372
esv3597956 CNV gain 21293372
esv3597958 CNV gain 21293372
esv3597959 CNV loss 21293372
esv3597960 CNV gain 21293372
nsv10331 CNV loss 18304495
nsv1073684 CNV deletion 25765185
nsv1121614 CNV deletion 24896259
nsv1129700 CNV tandem duplication 24896259
nsv1142587 CNV deletion 24896259
nsv1152083 CNV deletion 26484159
nsv236382 CNV insertion 16902084
nsv236797 CNV deletion 16902084
nsv236799 CNV insertion 16902084
nsv4036 CNV insertion 18451855
nsv4037 CNV deletion 18451855
nsv460867 CNV gain 19166990
nsv476015 CNV novel sequence insertion 20440878
nsv483106 CNV gain 15286789
nsv509854 OTHER sequence alteration 20534489
nsv513078 CNV loss 21212237
nsv520404 CNV loss 19592680
nsv527831 CNV gain 19592680
nsv591858 CNV loss 21841781
nsv591859 CNV loss 21841781
nsv591860 CNV gain 21841781
nsv591861 CNV gain 21841781
nsv591862 CNV loss 21841781
nsv591863 CNV gain 21841781
nsv818169 CNV gain 17921354
nsv829738 CNV gain 17160897
nsv829739 CNV gain 17160897
nsv829740 CNV gain+loss 17160897
nsv829741 CNV loss 17160897
nsv955356 CNV duplication 24416366
nsv998423 CNV gain 25217958

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)

Additional Variant Information for CLSTN2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

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

Disorders for CLSTN2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CLSTN2 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLSTN2

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 (Molecular and cellular neurosciences 2002) 2 3 4 22
  2. KIBRA and CLSTN2 polymorphisms exert interactive effects on human episodic memory. (PMID: 19804789) Preuschhof C … Bäckman L (Neuropsychologia 2010) 3 22 40
  3. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. (PMID: 21658281) Aouizerat BE … Tseng ZH (BMC cardiovascular disorders 2011) 3 40
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  5. Genetic associations of brain structural networks in schizophrenia: a preliminary study. (PMID: 20691427) Jagannathan K … Pearlson GD (Biological psychiatry 2010) 3 40

Products for CLSTN2 Gene

Sources for CLSTN2 Gene