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Aliases for CLSTN3 Gene

Aliases for CLSTN3 Gene

  • Calsyntenin 3 2 3 5
  • Cadherin-Related Family Member 14 2 3
  • Alc-Beta 3 4
  • Alcadein Beta 3
  • Calsyntenin-3 3
  • Alcadein-Beta 4
  • KIAA0726 4
  • Alcbeta 3
  • CDHR14 3
  • CSTN3 3
  • CS3 4

External Ids for CLSTN3 Gene

Previous GeneCards Identifiers for CLSTN3 Gene

  • GC12P007242
  • GC12P007418
  • GC12P007174
  • GC12P007282
  • GC12P007095
  • GC12P007130
  • GC12P007210
  • GC12P007267
  • GC12P007313
  • GC12P007362
  • GC12P007407
  • GC12P007450
  • GC12P007495

Summaries for CLSTN3 Gene

GeneCards Summary for CLSTN3 Gene

CLSTN3 (Calsyntenin 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CLSTN1.

UniProtKB/Swiss-Prot for CLSTN3 Gene

  • May modulate calcium-mediated postsynaptic signals. 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.

Additional gene information for CLSTN3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLSTN3 Gene

Genomics for CLSTN3 Gene

GeneHancer (GH) Regulatory Elements for CLSTN3 Gene

Promoters and enhancers for CLSTN3 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
GH12J007127 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 668.1 +0.4 407 5 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YBX1 YY1 POLR2B FOS SP3 CLSTN3 ENSG00000256967 RBP5 ENSG00000219410 PEX5 ZNF384 NCAPD2 SPSB2 ENSG00000247853 CHD4
GH12J007155 Promoter 0.9 EPDnew 662.1 +26.2 26158 0.1 PKNOX1 FOXA2 RXRA NFIB MAX MNT REST RFX5 GABPA SP1 CLSTN3 PEX5 ENSG00000256967 RBP5 ENSG00000126749 SCARNA12 PHB2 EMG1
GH12J007121 Enhancer 1.2 Ensembl ENCODE 19.4 -5.9 -5870 3.9 HDGF PKNOX1 FOXA2 ARID4B ZNF48 YY1 TCF12 GATA2 ATF7 RXRA ENSG00000256967 CLSTN3 PEX5 RNU6-485P RBP5 C1RL-AS1
GH12J007107 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 6.5 -21.1 -21131 2.9 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B C1RL-AS1 C1RL ENSG00000256967 ZNF384 NCAPD2 SPSB2 ENSG00000219410 ENSG00000247853 PEX5 CLSTN3
GH12J007111 Enhancer 0.6 ENCODE 21.6 -16.8 -16808 2.2 CTCF ZNF654 TRIM22 REST RAD21 SP1 ZNF335 ZNF629 ZSCAN5C ZNF143 CLSTN3 C1RL-AS1 CD27 ENSG00000256967 C1RL ENSG00000276144
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLSTN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLSTN3 gene promoter:
  • RORalpha2
  • MZF-1
  • ISGF-3
  • PPAR-gamma2
  • PPAR-gamma1
  • HNF-4alpha2
  • HNF-4alpha1
  • AML1a
  • ARP-1
  • RREB-1

Genomic Locations for CLSTN3 Gene

Genomic Locations for CLSTN3 Gene
chr12:7,129,698-7,158,945
(GRCh38/hg38)
Size:
29,248 bases
Orientation:
Plus strand
chr12:7,282,294-7,311,541
(GRCh37/hg19)
Size:
29,248 bases
Orientation:
Plus strand

Genomic View for CLSTN3 Gene

Genes around CLSTN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLSTN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLSTN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLSTN3 Gene

Proteins for CLSTN3 Gene

  • Protein details for CLSTN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQT9-CSTN3_HUMAN
    Recommended name:
    Calsyntenin-3
    Protein Accession:
    Q9BQT9
    Secondary Accessions:
    • D3DUT6
    • O94831
    • Q2T9J5
    • Q5UE57

    Protein attributes for CLSTN3 Gene

    Size:
    956 amino acids
    Molecular mass:
    106098 Da
    Quaternary structure:
    • Directly interacts with APBA2. Forms a tripartite complex with APBA2 and APP. Interacts with low affinity with KLC1 (By similarity).
    SequenceCaution:
    • Sequence=BAA34446.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for CLSTN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLSTN3 Gene

Post-translational modifications for CLSTN3 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-beta 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 gamma-secretase (By similarity).
  • Glycosylation at posLast=740740, posLast=693693, posLast=691691, Asn507, posLast=347347, Asn327, and posLast=299299
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for CLSTN3
  • Boster Bio Antibodies for CLSTN3

No data available for DME Specific Peptides for CLSTN3 Gene

Domains & Families for CLSTN3 Gene

Gene Families for CLSTN3 Gene

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

Protein Domains for CLSTN3 Gene

Suggested Antigen Peptide Sequences for CLSTN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BQT9

UniProtKB/Swiss-Prot:

CSTN3_HUMAN :
  • Binds synaptic Ca(2+) with its cytoplasmic domain.
Domain:
  • Binds synaptic Ca(2+) with its cytoplasmic domain.
genes like me logo Genes that share domains with CLSTN3: view

Function for CLSTN3 Gene

Molecular function for CLSTN3 Gene

UniProtKB/Swiss-Prot Function:
May modulate calcium-mediated postsynaptic signals. 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.

Phenotypes From GWAS Catalog for CLSTN3 Gene

Gene Ontology (GO) - Molecular Function for CLSTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with CLSTN3: view
genes like me logo Genes that share phenotypes with CLSTN3: view

Animal Models for CLSTN3 Gene

MGI Knock Outs for CLSTN3:

Animal Model Products

  • Taconic Biosciences Mouse Models for CLSTN3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLSTN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLSTN3 Gene

Localization for CLSTN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLSTN3 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

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 CLSTN3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 4
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLSTN3 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 CLSTN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLSTN3 Gene

Pathways & Interactions for CLSTN3 Gene

SuperPathways for CLSTN3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLSTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001558 regulation of cell growth IEA --
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007416 synapse assembly IEA --
GO:0035249 synaptic transmission, glutamatergic IEA --
genes like me logo Genes that share ontologies with CLSTN3: view

No data available for Pathways by source and SIGNOR curated interactions for CLSTN3 Gene

Drugs & Compounds for CLSTN3 Gene

(1) Drugs for CLSTN3 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 CLSTN3: view

Transcripts for CLSTN3 Gene

mRNA/cDNA for CLSTN3 Gene

Unigene Clusters for CLSTN3 Gene

Calsyntenin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLSTN3

Alternative Splicing Database (ASD) splice patterns (SP) for CLSTN3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c · 9d ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^
SP1: - - - - - - - - -
SP2: - - -
SP3:
SP4: - - - - - - - - - - -
SP5: - - - - - -
SP6: - - - - -
SP7: - - - -
SP8: - - -
SP9:
SP10:
SP11: - - - - - - -
SP12:
SP13:
SP14:

ExUns: 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b · 25c · 25d
SP1: - - - -
SP2: - - - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -
SP11:
SP12:
SP13:
SP14:

Relevant External Links for CLSTN3 Gene

GeneLoc Exon Structure for
CLSTN3
ECgene alternative splicing isoforms for
CLSTN3

Expression for CLSTN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLSTN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLSTN3 Gene

This gene is overexpressed in Amniocyte (29.0), Urine (15.2), Vitreous humor (10.3), and Fetal Brain (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLSTN3 Gene



Protein tissue co-expression partners for CLSTN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLSTN3 Gene:

CLSTN3

SOURCE GeneReport for Unigene cluster for CLSTN3 Gene:

Hs.535378

mRNA Expression by UniProt/SwissProt for CLSTN3 Gene:

Q9BQT9-CSTN3_HUMAN
Tissue specificity: According to PubMed:12498782, expressed predominantly in the brain and in kidney. Low levels in heart, skeletal muscle, liver, placenta, pancreas and lung. According to PubMed:12972431, predominant expression in brain, and only marginal in kidney. In brain, present throughout all cortical layers, highest levels in GABAergic neurons (based on morphology and distribution pattern).

Evidence on tissue expression from TISSUES for CLSTN3 Gene

  • Nervous system(5)
  • Blood(4)
genes like me logo Genes that share expression patterns with CLSTN3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLSTN3 Gene

Orthologs for CLSTN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLSTN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLSTN3 34 33
  • 98.14 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLSTN3 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLSTN3 34 33
  • 92.45 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CLSTN3 34 33
  • 92.08 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clstn3 33
  • 90.24 (n)
mouse
(Mus musculus)
Mammalia Clstn3 16 34 33
  • 89.99 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLSTN3 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLSTN3 34 33
  • 77.28 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLSTN3 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100036725 33
  • 65.36 (n)
Str.13295 33
zebrafish
(Danio rerio)
Actinopterygii clstn3 34 33
  • 65.46 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta calsyntenin-1 35
  • 27 (a)
cals 34
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea casy-1 34
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
ManyToMany
-- 34
  • 23 (a)
ManyToMany
Species where no ortholog for CLSTN3 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 CLSTN3 Gene

ENSEMBL:
Gene Tree for CLSTN3 (if available)
TreeFam:
Gene Tree for CLSTN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLSTN3: view image

Paralogs for CLSTN3 Gene

Paralogs for CLSTN3 Gene

(2) SIMAP similar genes for CLSTN3 Gene using alignment to 7 proteins:

  • CSTN3_HUMAN
  • F5H172_HUMAN
  • F5H5C6_HUMAN
  • F5H5D7_HUMAN
  • F5H746_HUMAN
  • F5H7C7_HUMAN
  • Q8IUW6_HUMAN
genes like me logo Genes that share paralogs with CLSTN3: view

Variants for CLSTN3 Gene

Sequence variations from dbSNP and Humsavar for CLSTN3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
VAR_036114 A colorectal cancer sample p.His874Tyr
rs1000052341 -- 7,155,076(+) C/A/T intron_variant
rs1000096304 -- 7,154,707(+) A/G intron_variant
rs1000159541 -- 7,144,880(+) G/A intron_variant
rs1000670307 -- 7,133,265(+) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLSTN3 Gene

Variant ID Type Subtype PubMed ID
esv3428840 CNV duplication 20981092
nsv1069638 CNV deletion 25765185
nsv818882 CNV gain 17921354
nsv832325 CNV gain+loss 17160897

Variation tolerance for CLSTN3 Gene

Residual Variation Intolerance Score: 23.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.70; 57.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLSTN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLSTN3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLSTN3 Gene

Disorders for CLSTN3 Gene

Additional Disease Information for CLSTN3

No disorders were found for CLSTN3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLSTN3 Gene

Publications for CLSTN3 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 58
  2. 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
  3. 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 58
  4. Novel cadherin-related membrane proteins, Alcadeins, enhance the X11-like protein-mediated stabilization of amyloid beta-protein precursor metabolism. (PMID: 12972431) Araki Y … Suzuki T (The Journal of biological chemistry 2003) 3 4 58
  5. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 58

Products for CLSTN3 Gene

Sources for CLSTN3 Gene

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