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Aliases for CNTN4 Gene

Aliases for CNTN4 Gene

  • Contactin 4 2 3 5
  • Brain-Derived Immunoglobulin Superfamily Protein 2 3 4
  • BIG-2 3 4
  • Axonal-Associated Cell Adhesion Molecule 3
  • Neural Cell Adhesion Protein BIG-2 3
  • AXCAM 3

External Ids for CNTN4 Gene

Previous GeneCards Identifiers for CNTN4 Gene

  • GC00U990741
  • GC03P002492
  • GC03P002134

Summaries for CNTN4 Gene

Entrez Gene Summary for CNTN4 Gene

  • This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

GeneCards Summary for CNTN4 Gene

CNTN4 (Contactin 4) is a Protein Coding gene. Diseases associated with CNTN4 include 3P- Syndrome and Spinocerebellar Ataxia Type 16. An important paralog of this gene is DSCAML1.

UniProtKB/Swiss-Prot for CNTN4 Gene

  • Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity. May be involved in synaptogenesis.

Gene Wiki entry for CNTN4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNTN4 Gene

Genomics for CNTN4 Gene

Regulatory Elements for CNTN4 Gene

Enhancers for CNTN4 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 CNTN4 on UCSC Golden Path with GeneCards custom track

Genomic Location for CNTN4 Gene

2,098,813 bp from pter
3,057,961 bp from pter
959,149 bases
Plus strand

Genomic View for CNTN4 Gene

Genes around CNTN4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNTN4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNTN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNTN4 Gene

Proteins for CNTN4 Gene

  • Protein details for CNTN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2RAX3
    • Q8IX14
    • Q8TC35

    Protein attributes for CNTN4 Gene

    1026 amino acids
    Molecular mass:
    113454 Da
    Quaternary structure:
    • Interacts with PTPRG.

    Alternative splice isoforms for CNTN4 Gene


neXtProt entry for CNTN4 Gene

Proteomics data for CNTN4 Gene at MOPED

Post-translational modifications for CNTN4 Gene

  • Glycosylation at Asn 65, Asn 90, Asn 191, Asn 370, Asn 375, Asn 466, Asn 705, Asn 764, Asn 858, Asn 893, Asn 911, Asn 929, and Asn 954
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for CNTN4 Gene

Domains & Families for CNTN4 Gene

Protein Domains for CNTN4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 4 fibronectin type-III domains.
  • Belongs to the immunoglobulin superfamily. Contactin family.
  • Contains 4 fibronectin type-III domains.
  • Contains 6 Ig-like C2-type (immunoglobulin-like) domains.
  • Belongs to the immunoglobulin superfamily. Contactin family.
genes like me logo Genes that share domains with CNTN4: view

Function for CNTN4 Gene

Molecular function for CNTN4 Gene

UniProtKB/Swiss-Prot Function:
Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity. May be involved in synaptogenesis.
UniProtKB/Swiss-Prot Induction:
By retinoic acid, suggesting that it may act in response to differentiating agents.
genes like me logo Genes that share phenotypes with CNTN4: view

Human Phenotype Ontology for CNTN4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CNTN4 Gene

MGI Knock Outs for CNTN4:

Animal Model Products

  • Taconic Biosciences Mouse Models for CNTN4

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for CNTN4 Gene

Localization for CNTN4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNTN4 Gene

Cell membrane; Lipid-anchor, GPI-anchor. Secreted.

Subcellular locations from

Jensen Localization Image for CNTN4 Gene COMPARTMENTS Subcellular localization image for CNTN4 gene
Compartment Confidence
plasma membrane 5
extracellular 4
lysosome 1
mitochondrion 1
nucleus 1
vacuole 1

Gene Ontology (GO) - Cellular Components for CNTN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
genes like me logo Genes that share ontologies with CNTN4: view

Pathways & Interactions for CNTN4 Gene

SuperPathways for CNTN4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CNTN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007158 neuron cell-cell adhesion TAS 14571131
GO:0007409 axonogenesis TAS 14571131
GO:0007413 axonal fasciculation TAS 15106122
GO:0007420 brain development ISS --
GO:0045665 negative regulation of neuron differentiation IMP 14571131
genes like me logo Genes that share ontologies with CNTN4: view

No data available for Pathways by source and SIGNOR curated interactions for CNTN4 Gene

Drugs & Compounds for CNTN4 Gene

No Compound Related Data Available

Transcripts for CNTN4 Gene

Unigene Clusters for CNTN4 Gene

Contactin 4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CNTN4 Gene

No ASD Table

Relevant External Links for CNTN4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNTN4 Gene

mRNA expression in normal human tissues for CNTN4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNTN4 Gene

This gene is overexpressed in Artery - Aorta (x5.7) and Artery - Tibial (x5.0).

Protein differential expression in normal tissues from HIPED for CNTN4 Gene

This gene is overexpressed in Cerebrospinal fluid (37.7), Vitreous humor (13.4), Plasma (7.4), and Fetal Brain (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CNTN4 Gene

SOURCE GeneReport for Unigene cluster for CNTN4 Gene Hs.298705

mRNA Expression by UniProt/SwissProt for CNTN4 Gene

Tissue specificity: Mainly expressed in brain. Highly expressed in cerebellum and weakly expressed in corpus callosum, caudate nucleus, amygdala and spinal cord. Also expressed in testis, pancreas, thyroid, uterus, small intestine and kidney. Not expressed in skeletal muscle. Isoform 2 is weakly expressed in cerebral cortex.
genes like me logo Genes that share expression patterns with CNTN4: view

Protein tissue co-expression partners for CNTN4 Gene

Primer Products

Orthologs for CNTN4 Gene

This gene was present in the common ancestor of animals.

Orthologs for CNTN4 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CNTN4 35
  • 92.37 (n)
  • 96.3 (a)
CNTN4 36
  • 97 (a)
(Canis familiaris)
Mammalia CNTN4 35
  • 93.31 (n)
  • 96.69 (a)
CNTN4 36
  • 97 (a)
(Mus musculus)
Mammalia Cntn4 35
  • 90.64 (n)
  • 95.13 (a)
Cntn4 16
Cntn4 36
  • 95 (a)
(Pan troglodytes)
Mammalia CNTN4 35
  • 99.12 (n)
  • 99.32 (a)
CNTN4 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Cntn4 35
  • 90.06 (n)
  • 94.54 (a)
(Monodelphis domestica)
Mammalia CNTN4 36
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 91 (a)
-- 36
  • 89 (a)
(Gallus gallus)
Aves CNTN4 35
  • 78.47 (n)
  • 86.34 (a)
FAR-1 36
  • 86 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 83 (a)
-- 36
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cntn4 35
  • 70.57 (n)
  • 75.61 (a)
(Danio rerio)
Actinopterygii cntn4 35
  • 63.99 (n)
  • 64.77 (a)
cntn3a.1 36
  • 60 (a)
cntn4 36
  • 64 (a)
(Caenorhabditis elegans)
Secernentea rig-6 35
  • 42.41 (n)
  • 27.98 (a)
Species with no ortholog for CNTN4:
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • wheat (Triticum aestivum)

Evolution for CNTN4 Gene

Gene Tree for CNTN4 (if available)
Gene Tree for CNTN4 (if available)

Paralogs for CNTN4 Gene

genes like me logo Genes that share paralogs with CNTN4: view

Variants for CNTN4 Gene

Sequence variations from dbSNP and Humsavar for CNTN4 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
VAR_035507 A colorectal cancer sample
VAR_035508 A colorectal cancer sample
rs2218 -- 2,917,764(+) TAACT(C/T)ATAAG intron-variant
rs340804 -- 2,972,376(-) TCGGG(A/G)ATTTA intron-variant
rs340816 -- 2,986,038(+) GCCCC(C/G)CAAGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CNTN4 Gene

Variant ID Type Subtype PubMed ID
nsv526340 CNV Loss 19592680
nsv460312 CNV Gain 19166990
nsv876343 CNV Gain 21882294
nsv876359 CNV Gain 21882294
nsv460321 CNV Gain 19166990
esv2422325 CNV Duplication 17116639
esv2422409 CNV Deletion 17116639
nsv834600 CNV Loss 17160897
nsv876384 CNV Loss 21882294
esv2751990 CNV Gain 17911159
nsv460323 CNV Gain 19166990
nsv460324 CNV Loss 19166990
nsv876385 CNV Gain 21882294
esv2422274 CNV Duplication 17116639
nsv460325 CNV Gain 19166990
esv271745 CNV Insertion 20981092
nsv524378 CNV Gain 19592680
dgv1428e1 CNV Complex 17122850
dgv5088n71 CNV Loss 21882294
nsv834601 CNV Loss 17160897
nsv876389 CNV Gain 21882294
esv2751993 CNV Loss 17911159
nsv876391 CNV Loss 21882294
esv2751994 CNV Gain 17911159
nsv821951 CNV Gain 20364138
esv34352 CNV Gain 17911159
esv2724792 CNV Deletion 23290073
esv2672397 CNV Deletion 23128226
nsv470993 CNV Gain 18288195
dgv587n27 CNV Gain 19166990
esv2615600 CNV Deletion 19546169
esv2409980 CNV Deletion 18987734
esv3517 CNV Deletion 18987735
esv2724793 CNV Deletion 23290073
esv999364 CNV Deletion 20482838
esv1468650 CNV Deletion 17803354
esv2660501 CNV Deletion 23128226
esv2297311 CNV Deletion 18987734
esv2724795 CNV Deletion 23290073
nsv460329 CNV Gain 19166990
esv2724796 CNV Deletion 23290073
esv2751996 CNV Loss 17911159
esv2724797 CNV Deletion 23290073
nsv834603 CNV Loss 17160897
nsv10245 CNV Loss 18304495
dgv5089n71 CNV Loss 21882294
esv2677526 CNV Deletion 23128226
esv2724798 CNV Deletion 23290073
nsv821952 CNV Loss 20364138
esv2724799 CNV Deletion 23290073
esv2183952 CNV Deletion 18987734
esv2724800 CNV Deletion 23290073
esv2724802 CNV Deletion 23290073
esv2724801 CNV Deletion 23290073
nsv237257 CNV Loss 16902084
esv1396412 CNV Deletion 17803354
esv2724803 CNV Deletion 23290073
nsv876394 CNV Gain 21882294
esv2670015 CNV Deletion 23128226
nsv876395 CNV Gain 21882294
esv2607149 CNV Deletion 19546169
esv1208689 CNV Deletion 17803354
esv23648 CNV Loss 19812545
nsv820649 CNV Deletion 20802225
esv2724804 CNV Deletion 23290073
nsv821953 CNV Gain 20364138
nsv876396 CNV Loss 21882294
nsv876397 CNV Gain 21882294
nsv876398 CNV Gain 21882294
esv2724807 CNV Deletion 23290073
nsv818122 CNV Loss 17921354
esv2663898 CNV Deletion 23128226
nsv876399 CNV Loss 21882294
esv2450966 CNV Deletion 19546169
esv2202540 CNV Deletion 18987734
esv3368 CNV Deletion 18987735
nsv236276 CNV Loss 16902084
esv2724808 CNV Deletion 23290073
esv7459 CNV Loss 19470904
nsv525486 CNV Loss 19592680
nsv876400 CNV Loss 21882294
nsv821955 CNV Gain 20364138
esv1537664 CNV Insertion 17803354
esv2751998 CNV Gain 17911159
esv1541174 CNV Insertion 17803354
esv999388 CNV Insertion 20482838
esv270518 CNV Insertion 20981092
nsv876401 CNV Loss 21882294
esv268078 CNV Insertion 20981092
esv2669901 CNV Deletion 23128226
nsv876402 CNV Loss 21882294
nsv876403 CNV Gain 21882294
esv2724809 CNV Deletion 23290073
nsv520139 CNV Loss 19592680
esv29042 CNV Loss 19812545
esv270209 CNV Insertion 20981092
esv272298 CNV Insertion 20981092
esv29782 CNV Loss 19812545
esv2665144 CNV Deletion 23128226
esv2360836 CNV Deletion 18987734
nsv3675 CNV Loss 18451855
nsv876404 CNV Gain 21882294
esv2660849 CNV Deletion 23128226
nsv515751 CNV Loss 19592680
nsv521796 CNV Loss 19592680

Variation tolerance for CNTN4 Gene

Residual Variation Intolerance Score: 21% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.94; 59.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CNTN4 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNTN4 Gene

Disorders for CNTN4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CNTN4 Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
3p- syndrome
  • chromosome 3pter-p25 deletion syndrome
spinocerebellar ataxia type 16
autism spectrum disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards
Search CNTN4 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving CNTN4 has been found in a boy with characteristic physical features of 3p deletion syndrome (3PDS). Translocation t(3;10)(p26;q26). 3PDS is a rare contiguous gene disorder involving the loss of the telomeric portion of the short arm of chromosome 3 and characterized by developmental delay, growth retardation, and dysmorphic features. {ECO:0000269 PubMed:15106122}.

Relevant External Links for CNTN4

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 CNTN4: view

No data available for Genatlas for CNTN4 Gene

Publications for CNTN4 Gene

  1. A novel splice variant of the cell adhesion molecule contactin 4 (CNTN4) is mainly expressed in human brain. (PMID: 12202991) Zeng L. … Mao Y. (J. Hum. Genet. 2002) 2 3 4 23 67
  2. Disruption of contactin 4 in three subjects with autism spectrum disorder. (PMID: 18349135) Roohi J. … Hatchwell E. (J. Med. Genet. 2009) 3 23
  3. Contactins: emerging key roles in the development and function of the nervous system. (PMID: 19262165) Shimoda Y. … Watanabe K. (Cell Adh Migr 2009) 3 23
  4. Molecular genetic analysis of a cell adhesion molecule with homology to L1CAM, contactin 6, and contactin 4 candidate chromosome 3p26pter tumor suppressor genes in ovarian cancer. (PMID: 19509545) Manderson E.N. … Tonin P.N. (Int. J. Gynecol. Cancer 2009) 3 23
  5. Interaction of amyloid precursor protein with contactins and NgCAM in the retinotectal system. (PMID: 18272596) Osterfield M. … Flanagan J.G. (Development 2008) 3 23

Products for CNTN4 Gene

Sources for CNTN4 Gene