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Aliases for CNTN3 Gene

Aliases for CNTN3 Gene

  • Contactin 3 2 3 5
  • Brain-Derived Immunoglobulin Superfamily Protein 1 3 4
  • Plasmacytoma-Associated Neuronal Glycoprotein 3 4
  • Contactin 3 (Plasmacytoma Associated) 2 3
  • BIG-1 3 4
  • PANG 3 4
  • Contactin-3 3
  • KIAA1496 4
  • PCS 3

External Ids for CNTN3 Gene

Previous HGNC Symbols for CNTN3 Gene

  • PANG

Previous GeneCards Identifiers for CNTN3 Gene

  • GC03M072881
  • GC03M073925
  • GC03M074117
  • GC03M074394

Summaries for CNTN3 Gene

GeneCards Summary for CNTN3 Gene

CNTN3 (Contactin 3) is a Protein Coding gene. Diseases associated with CNTN3 include Plasmacytoma and Taylor's Syndrome. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. An important paralog of this gene is CNTN4.

UniProtKB/Swiss-Prot for CNTN3 Gene

  • Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity (By similarity).

Gene Wiki entry for CNTN3 Gene

Additional gene information for CNTN3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNTN3 Gene

Genomics for CNTN3 Gene

GeneHancer (GH) Regulatory Elements for CNTN3 Gene

Promoters and enhancers for CNTN3 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
GH03J074613 Enhancer 0.8 Ensembl ENCODE dbSUPER 657 0.0 -28 1.6 SUZ12 ZFX YY1 CNTN3 LOC105377166
GH03J074633 Enhancer 0.6 dbSUPER 8.6 -20.5 -20540 2 ATF1 ZBTB21 CEBPG ZEB2 ATF2 ZNF366 ZNF629 CREB1 ATF7 ZNF600 CNTN3 FAM86DP LOC105377166 GC03P074677
GH03J074638 Enhancer 0.3 dbSUPER 8.6 -25.6 -25637 2.3 CREB1 CNTN3 HNRNPA3P6 FAM86DP LOC105377166 GC03P074677
GH03J074620 Enhancer 0.4 dbSUPER 5.1 -8.6 -8649 5.2 USF1 MAFK CNTN3 LINC02018 LOC105377166 GC03P074677
GH03J074598 Enhancer 0.5 dbSUPER 0.4 +14.7 14708 2 SP1 ATF4 JUND ATF3 RXRA HNF4A YY1 CNTN3 PIR33009
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNTN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CNTN3 gene promoter:
  • POU2F1
  • POU2F1a
  • STAT5B
  • NF-E2
  • AML1a
  • NF-E2 p45
  • GR-alpha
  • GR-beta
  • En-1
  • GR

Genomic Locations for CNTN3 Gene

Genomic Locations for CNTN3 Gene
351,878 bases
Minus strand
258,625 bases
Minus strand

Genomic View for CNTN3 Gene

Genes around CNTN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNTN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNTN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNTN3 Gene

Proteins for CNTN3 Gene

  • Protein details for CNTN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B9EK50
    • Q9H039

    Protein attributes for CNTN3 Gene

    1028 amino acids
    Molecular mass:
    112883 Da
    Quaternary structure:
    • Interacts with PTPRG.

    Three dimensional structures from OCA and Proteopedia for CNTN3 Gene

neXtProt entry for CNTN3 Gene

Post-translational modifications for CNTN3 Gene

  • Glycosylation at posLast=956956, posLast=931931, Asn913, posLast=895895, posLast=860860, Asn765, posLast=489489, Asn468, posLast=375375, posLast=193193, and posLast=6565
  • Modification sites at PhosphoSitePlus

Other Protein References for CNTN3 Gene

No data available for DME Specific Peptides for CNTN3 Gene

Domains & Families for CNTN3 Gene

Protein Domains for CNTN3 Gene

Suggested Antigen Peptide Sequences for CNTN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the immunoglobulin superfamily. Contactin family.
  • Belongs to the immunoglobulin superfamily. Contactin family.
genes like me logo Genes that share domains with CNTN3: view

Function for CNTN3 Gene

Molecular function for CNTN3 Gene

UniProtKB/Swiss-Prot Function:
Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity (By similarity).

Phenotypes From GWAS Catalog for CNTN3 Gene

genes like me logo Genes that share phenotypes with CNTN3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CNTN3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CNTN3 Gene

Localization for CNTN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNTN3 Gene

Cell membrane; Lipid-anchor, GPI-anchor.

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 CNTN3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CNTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with CNTN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNTN3 Gene

Pathways & Interactions for CNTN3 Gene

genes like me logo Genes that share pathways with CNTN3: view

Gene Ontology (GO) - Biological Process for CNTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006501 C-terminal protein lipidation TAS --
GO:0007155 cell adhesion IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with CNTN3: view

No data available for SIGNOR curated interactions for CNTN3 Gene

Drugs & Compounds for CNTN3 Gene

No Compound Related Data Available

Transcripts for CNTN3 Gene

mRNA/cDNA for CNTN3 Gene

Unigene Clusters for CNTN3 Gene

Contactin 3 (plasmacytoma associated):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CNTN3 Gene

No ASD Table

Relevant External Links for CNTN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNTN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CNTN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNTN3 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.1).

Protein differential expression in normal tissues from HIPED for CNTN3 Gene

This gene is overexpressed in Serum (32.2), Pancreas (14.6), Plasma (9.3), and Bone (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CNTN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CNTN3 Gene:


SOURCE GeneReport for Unigene cluster for CNTN3 Gene:


mRNA Expression by UniProt/SwissProt for CNTN3 Gene:

Tissue specificity: In brain, it is expressed in frontal lobe, occipital lobe, cerebellum and amygdala.

Evidence on tissue expression from TISSUES for CNTN3 Gene

  • Nervous system(4.4)
  • Bone marrow(4.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with CNTN3: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CNTN3 Gene

Orthologs for CNTN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CNTN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNTN3 34 33
  • 99.29 (n)
(Canis familiaris)
Mammalia CNTN3 34 33
  • 90.88 (n)
(Bos Taurus)
Mammalia CNTN3 34 33
  • 90.4 (n)
(Mus musculus)
Mammalia Cntn3 16 34 33
  • 88.23 (n)
(Rattus norvegicus)
Mammalia Cntn3 33
  • 87.19 (n)
(Monodelphis domestica)
Mammalia CNTN3 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia CNTN3 34
  • 76 (a)
(Gallus gallus)
Aves CNTN3 34 33
  • 76.53 (n)
(Anolis carolinensis)
Reptilia CNTN3 34
  • 80 (a)
(Danio rerio)
Actinopterygii LOC556251 33
  • 61.73 (n)
CABZ01012080.1 34
  • 58 (a)
cntn3a.2 34
  • 57 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cont 33
  • 43.46 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta IGL1 33
  • 24.77 (n)
Species where no ortholog for CNTN3 was found in the sources mined by GeneCards:
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CNTN3 Gene

Gene Tree for CNTN3 (if available)
Gene Tree for CNTN3 (if available)
Evolutionary constrained regions (ECRs) for CNTN3: view image

Paralogs for CNTN3 Gene

Paralogs for CNTN3 Gene

(7) SIMAP similar genes for CNTN3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CNTN3: view

Variants for CNTN3 Gene

Sequence variations from dbSNP and Humsavar for CNTN3 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs199931035 uncertain-significance, not provided 74,285,487(-) C/T coding_sequence_variant, missense_variant
rs369703868 uncertain-significance, not provided 74,302,811(-) T/C intron_variant
rs1000011596 -- 74,399,501(-) C/G genic_upstream_transcript_variant, intron_variant
rs1000024734 -- 74,319,860(-) G/C intron_variant
rs1000040259 -- 74,279,574(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CNTN3 Gene

Variant ID Type Subtype PubMed ID
esv2678039 CNV deletion 23128226
esv2725408 CNV deletion 23290073
esv2762337 CNV loss 21179565
esv3304215 CNV mobile element insertion 20981092
esv3309045 CNV mobile element insertion 20981092
esv3309665 CNV mobile element insertion 20981092
esv3399031 CNV insertion 20981092
esv3422306 CNV insertion 20981092
esv3427386 CNV insertion 20981092
esv3596573 CNV loss 21293372
esv3596575 CNV loss 21293372
nsv1136366 CNV deletion 24896259
nsv1152489 CNV deletion 26484159
nsv1160946 CNV duplication 26073780
nsv477714 CNV novel sequence insertion 20440878
nsv477972 CNV novel sequence insertion 20440878
nsv526012 CNV loss 19592680
nsv526832 CNV gain 19592680
nsv834733 CNV loss 17160897
nsv834734 CNV loss 17160897

Variation tolerance for CNTN3 Gene

Residual Variation Intolerance Score: 71.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.20; 80.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNTN3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNTN3 Gene

Disorders for CNTN3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CNTN3 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
  • myeloma - solitary
taylor's syndrome
  • congestion-fibrosis syndrome
pneumonic tularemia
  • bronchopneumonic tularemia
inhalation anthrax
  • pulmonary anthrax
- elite association - COSMIC cancer census association via MalaCards
Search CNTN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CNTN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CNTN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNTN3 Gene

Publications for CNTN3 Gene

  1. Human NB-2 of the contactin subgroup molecules: chromosomal localization of the gene (CNTN5) and distinct expression pattern from other subgroup members. (PMID: 11013081) Kamei Y … Watanabe K (Genomics 2000) 3 4 22 58
  2. Plasmacytoma-associated neuronal glycoprotein, Pang, maps to mouse chromosome 6 and human chromosome 3. (PMID: 8661054) Mock BA … Marcu KB (Genomics 1996) 2 3 22 58
  3. 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 44 58
  4. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 44 58
  5. Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association. (PMID: 19497516) Elmore JR … Carey DJ (Journal of vascular surgery 2009) 3 44 58

Products for CNTN3 Gene

Sources for CNTN3 Gene

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