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 m... See more...

Aliases for CNTN4 Gene

Aliases for CNTN4 Gene

  • Contactin 4 2 3 5
  • BIG-2 2 3 4
  • Brain-Derived Immunoglobulin Superfamily Protein 2 3 4
  • Contactin-4 3 4
  • Axonal-Associated Cell Adhesion Molecule 3
  • Neural Cell Adhesion Protein BIG-2 3
  • AXCAM 3
  • CNTN4 5

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 Chromosome 3Pter-P25 Deletion Syndrome and Spinocerebellar Ataxia 15. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. An important paralog of this gene is CNTN3.

UniProtKB/Swiss-Prot Summary 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 CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CNTN4 Gene

Genomics for CNTN4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CNTN4 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
GH03J002097 Promoter/Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas 600.7 +0.2 189 2.2 EZH2 ZNF561 CTCF ZBTB20 RAD21 ZBTB26 ZNF335 ZNF660 NRF1 SP1 CNTN4 lnc-CNTN6-4 lnc-IL5RA-3 piR-32539-025
GH03J002892 Promoter 0.3 EPDnew 600 +793.4 793415 0.1 CNTN4 piR-57460-465 HSALNG0023828 IL5RA
GH03J002421 Enhancer 0.7 Ensembl ENCODE 18.1 +321.8 321798 1.2 TEAD4 YY1 NANOG HLF SP1 USF2 CHD2 CNTN4 piR-39341-223 HSALNG0023823 IL5RA
GH03J003028 Enhancer 0.5 Ensembl 6.3 +929.5 929498 0.6 RUNX3 ELF1 ATF2 ATF7 TCF7 CNTN4 HSALNG0023832 piR-48553-182 IL5RA
GH03J002510 Enhancer 0.6 Ensembl CraniofacialAtlas 5 +412.5 412498 1.4 POLR2A SMARCA4 GATA2 CNTN4 piR-61101-462 piR-38426-014 IL5RA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNTN4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CNTN4

Top Transcription factor binding sites by QIAGEN in the CNTN4 gene promoter:
  • AREB6
  • C/EBPbeta
  • GR
  • GR-alpha
  • GR-beta
  • NRSF form 1
  • NRSF form 2
  • POU2F1
  • S8
  • Sox9

Genomic Locations for CNTN4 Gene

Genomic Locations for CNTN4 Gene
960,278 bases
Plus strand
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

Post-translational modifications for CNTN4 Gene

  • Glycosylation at Asn764, Asn370, Asn375, Asn65, Asn90, Asn858, Asn466, Asn893, Asn911, Asn929, Asn191, Asn954, Asn1006, and Asn705
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CNTN4_HUMAN (1156)

No data available for DME Specific Peptides for CNTN4 Gene

Domains & Families for CNTN4 Gene

Gene Families for CNTN4 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CNTN4 Gene

  • Immunoglobulin I-set

Suggested Antigen Peptide Sequences for CNTN4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ95172, Homo sapiens contactin 4 (CNTN4), transcript variant 3, mRNA (B2RAX3_HUMAN)
  • Brain-derived immunoglobulin superfamily protein 2 (CNTN4_HUMAN)

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 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.

Phenotypes From GWAS Catalog for CNTN4 Gene

Gene Ontology (GO) - Molecular Function for CNTN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0098632 cell-cell adhesion mediator activity IBA 21873635
genes like me logo Genes that share ontologies with CNTN4: view
genes like me logo Genes that share phenotypes with CNTN4: view

Animal Models for CNTN4 Gene

MGI Knock Outs for CNTN4:

Animal Model Products

  • Taconic Biosciences Mouse Models for CNTN4

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNTN4

Clone Products

  • Addgene plasmids for CNTN4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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

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 CNTN4 gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
lysosome 0

Gene Ontology (GO) - Cellular Components for CNTN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0030424 axon IBA,NAS 14571131
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with CNTN4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNTN4 Gene

Pathways & Interactions for CNTN4 Gene

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

Gene Ontology (GO) - Biological Process for CNTN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IBA 21873635
GO:0007158 neuron cell-cell adhesion TAS 14571131
GO:0007399 nervous system development IMP 15106122
GO:0007409 axonogenesis TAS 14571131
genes like me logo Genes that share ontologies with CNTN4: view

No data available for SIGNOR curated interactions for CNTN4 Gene

Drugs & Compounds for CNTN4 Gene

No Compound Related Data Available

Transcripts for CNTN4 Gene

mRNA/cDNA for CNTN4 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNTN4

Clone Products

  • Addgene plasmids for CNTN4

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

No ASD Table

Relevant External Links for CNTN4 Gene

GeneLoc Exon Structure for

Expression for CNTN4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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 and MOPED for CNTN4 Gene

Protein tissue co-expression partners for CNTN4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CNTN4

SOURCE GeneReport for Unigene cluster for CNTN4 Gene:


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.

Evidence on tissue expression from TISSUES for CNTN4 Gene

  • Bone marrow(4.1)
  • Nervous system(2.8)
  • Skin(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CNTN4 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • skull
  • heart
  • heart valve
  • pelvis
  • testicle
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • hair
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with CNTN4: view

Orthologs for CNTN4 Gene

This gene was present in the common ancestor of animals.

Orthologs for CNTN4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNTN4 30 31
  • 99.12 (n)
(Canis familiaris)
Mammalia CNTN4 30 31
  • 93.31 (n)
(Bos Taurus)
Mammalia CNTN4 30 31
  • 92.37 (n)
(Monodelphis domestica)
Mammalia CNTN4 31
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 91 (a)
-- 31
  • 89 (a)
(Mus musculus)
Mammalia Cntn4 30 17 31
  • 90.64 (n)
(Rattus norvegicus)
Mammalia Cntn4 30
  • 90.06 (n)
(Gallus gallus)
Aves FAR-1 31
  • 86 (a)
CNTN4 30
  • 78.47 (n)
(Anolis carolinensis)
Reptilia -- 31
  • 85 (a)
-- 31
  • 83 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cntn4 30
  • 70.57 (n)
(Danio rerio)
Actinopterygii cntn4 30 31
  • 63.99 (n)
cntn3a.1 31
  • 60 (a)
(Caenorhabditis elegans)
Secernentea rig-6 30
  • 42.41 (n)
Species where no ortholog for CNTN4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Evolutionary constrained regions (ECRs) for CNTN4: view image

Paralogs for CNTN4 Gene

(19) SIMAP similar genes for CNTN4 Gene using alignment to 7 proteins:

  • F8WD58_HUMAN
  • H0Y8U1_HUMAN
genes like me logo Genes that share paralogs with CNTN4: view

Variants for CNTN4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CNTN4 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
708711 Likely Benign: not provided 2,900,803(+) C/A SYNONYMOUS_VARIANT
709648 Benign: not provided 2,988,444(+) T/C SYNONYMOUS_VARIANT
716098 Benign: not provided 2,883,154(+) G/A MISSENSE_VARIANT
720244 Likely Benign: not provided 2,866,894(+) C/T SYNONYMOUS_VARIANT
729306 Likely Benign: not provided 3,026,111(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CNTN4 Gene

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

Variant ID Type Subtype PubMed ID
dgv1349e212 CNV loss 25503493
dgv1350e212 CNV loss 25503493
dgv1351e212 CNV loss 25503493
dgv1352e212 CNV loss 25503493
dgv4629n100 CNV gain 25217958
dgv4634n100 CNV gain 25217958
dgv4635n100 CNV gain 25217958
dgv4636n100 CNV gain 25217958
dgv587n27 CNV gain 19166990
dgv8157n54 CNV gain 21841781
dgv8164n54 CNV gain 21841781
dgv8165n54 CNV gain 21841781
dgv8166n54 CNV gain 21841781
dgv8167n54 CNV loss 21841781
dgv8168n54 CNV loss 21841781
dgv8169n54 CNV loss 21841781
dgv8170n54 CNV gain 21841781
dgv859e214 CNV gain 21293372
dgv860e214 CNV loss 21293372
dgv861e214 CNV loss 21293372
dgv862e214 CNV loss 21293372
esv1208689 CNV deletion 17803354
esv1396412 CNV deletion 17803354
esv1468650 CNV deletion 17803354
esv1537664 CNV insertion 17803354
esv1541174 CNV insertion 17803354
esv2183952 CNV deletion 18987734
esv2202540 CNV deletion 18987734
esv2297311 CNV deletion 18987734
esv2360836 CNV deletion 18987734
esv23648 CNV loss 19812545
esv2409980 CNV deletion 18987734
esv2422274 CNV duplication 17116639
esv2422325 CNV duplication 17116639
esv2422409 CNV deletion 17116639
esv2450966 CNV deletion 19546169
esv2607149 CNV deletion 19546169
esv2615600 CNV deletion 19546169
esv2660501 CNV deletion 23128226
esv2660849 CNV deletion 23128226
esv2663898 CNV deletion 23128226
esv2665144 CNV deletion 23128226
esv2669901 CNV deletion 23128226
esv2670015 CNV deletion 23128226
esv2672397 CNV deletion 23128226
esv2677526 CNV deletion 23128226
esv2724792 CNV deletion 23290073
esv2724793 CNV deletion 23290073
esv2724795 CNV deletion 23290073
esv2724796 CNV deletion 23290073
esv2724797 CNV deletion 23290073
esv2724798 CNV deletion 23290073
esv2724799 CNV deletion 23290073
esv2724800 CNV deletion 23290073
esv2724801 CNV deletion 23290073
esv2724802 CNV deletion 23290073
esv2724803 CNV deletion 23290073
esv2724804 CNV deletion 23290073
esv2724807 CNV deletion 23290073
esv2724808 CNV deletion 23290073
esv2724809 CNV deletion 23290073
esv2751990 CNV gain 17911159
esv2751993 CNV loss 17911159
esv2751994 CNV gain 17911159
esv2751996 CNV loss 17911159
esv2751998 CNV gain 17911159
esv2759124 CNV gain 17122850
esv2760757 CNV loss 21179565
esv2763774 CNV gain+loss 21179565
esv2838236 CNV deletion 24192839
esv29042 CNV loss 19812545
esv29782 CNV loss 19812545
esv3303799 CNV mobile element insertion 20981092
esv3306241 CNV mobile element insertion 20981092
esv3307471 CNV mobile element insertion 20981092
esv3342780 CNV insertion 20981092
esv3355356 CNV insertion 20981092
esv3355385 CNV insertion 20981092
esv3368 CNV loss 18987735
esv3424647 CNV insertion 20981092
esv34352 CNV gain 17911159
esv3439940 CNV insertion 20981092
esv3517 CNV loss 18987735
esv3561352 CNV deletion 23714750
esv3561353 CNV deletion 23714750
esv3561355 CNV deletion 23714750
esv3561357 CNV deletion 23714750
esv3561362 CNV deletion 23714750
esv3568548 CNV loss 25503493
esv3568551 CNV loss 25503493
esv3568552 CNV loss 25503493
esv3568562 CNV loss 25503493
esv3568566 CNV loss 25503493
esv3568567 CNV loss 25503493
esv3568568 CNV loss 25503493
esv3568569 CNV loss 25503493
esv3575531 CNV gain 25503493
esv3575534 CNV gain 25503493
esv3595011 CNV loss 21293372
esv3595012 CNV loss 21293372
esv3595013 CNV gain 21293372
esv3595015 CNV loss 21293372
esv3595016 CNV gain 21293372
esv3595022 CNV loss 21293372
esv3595023 CNV loss 21293372
esv3595024 CNV loss 21293372
esv3595027 CNV gain 21293372
esv3595028 CNV loss 21293372
esv3595030 CNV loss 21293372
esv3595031 CNV loss 21293372
esv3595032 CNV gain 21293372
esv3595033 CNV loss 21293372
esv3595034 CNV gain 21293372
esv3595035 CNV loss 21293372
esv3595036 CNV loss 21293372
esv3595037 CNV loss 21293372
esv3595041 CNV loss 21293372
esv3595045 CNV loss 21293372
esv3595046 CNV loss 21293372
esv3595048 CNV loss 21293372
esv3893608 CNV gain 25118596
esv3893620 CNV gain 25118596
esv3893621 CNV loss 25118596
esv3893622 CNV loss 25118596
esv3893624 CNV loss 25118596
esv3893625 CNV gain 25118596
esv3893626 CNV loss 25118596
esv7459 CNV loss 19470904
esv999364 CNV deletion 20482838
esv999388 CNV insertion 20482838
nsv1001545 CNV gain 25217958
nsv1002427 CNV gain 25217958
nsv1003271 CNV loss 25217958
nsv1005807 CNV gain 25217958
nsv1006039 CNV gain 25217958
nsv1006501 CNV loss 25217958
nsv1007298 CNV loss 25217958
nsv1007537 CNV loss 25217958
nsv1007848 CNV loss 25217958
nsv1008276 CNV loss 25217958
nsv1009279 CNV gain 25217958
nsv1009942 CNV gain 25217958
nsv1011386 CNV loss 25217958
nsv1011485 CNV gain 25217958
nsv1011872 CNV gain 25217958
nsv1012867 CNV loss 25217958
nsv1013960 CNV loss 25217958
nsv10245 CNV loss 18304495
nsv1071854 CNV deletion 25765185
nsv1072230 CNV deletion 25765185
nsv1072805 CNV deletion 25765185
nsv1078895 OTHER inversion 25765185
nsv1110943 OTHER inversion 24896259
nsv1117324 CNV tandem duplication 24896259
nsv1121602 CNV deletion 24896259
nsv1123616 CNV deletion 24896259
nsv1123617 CNV deletion 24896259
nsv1130794 CNV deletion 24896259
nsv1136701 CNV deletion 24896259
nsv1142351 CNV tandem duplication 24896259
nsv236276 CNV deletion 16902084
nsv237257 CNV deletion 16902084
nsv3675 CNV deletion 18451855
nsv460312 CNV gain 19166990
nsv460321 CNV gain 19166990
nsv460323 CNV gain 19166990
nsv460324 CNV loss 19166990
nsv460325 CNV gain 19166990
nsv460329 CNV gain 19166990
nsv470993 CNV gain 18288195
nsv478205 CNV novel sequence insertion 20440878
nsv515751 CNV loss 19592680
nsv520139 CNV loss 19592680
nsv521796 CNV loss 19592680
nsv524378 CNV gain 19592680
nsv525486 CNV loss 19592680
nsv526340 CNV loss 19592680
nsv589322 CNV loss 21841781
nsv589345 CNV gain 21841781
nsv589362 CNV gain 21841781
nsv589363 CNV gain 21841781
nsv589368 CNV loss 21841781
nsv589370 CNV gain 21841781
nsv589371 CNV loss 21841781
nsv589374 CNV gain 21841781
nsv589376 CNV loss 21841781
nsv589377 CNV loss 21841781
nsv589378 CNV loss 21841781
nsv589381 CNV loss 21841781
nsv589388 CNV gain 21841781
nsv589391 CNV gain 21841781
nsv589392 CNV loss 21841781
nsv589393 CNV gain 21841781
nsv818122 CNV loss 17921354
nsv820649 CNV deletion 20802225
nsv821951 CNV gain 20364138
nsv821952 CNV loss 20364138
nsv821953 CNV gain 20364138
nsv821955 CNV gain 20364138
nsv834600 CNV loss 17160897
nsv834601 CNV loss 17160897
nsv834603 CNV loss 17160897
nsv955311 CNV duplication 24416366
nsv956814 CNV deletion 24416366
nsv956822 CNV deletion 24416366
nsv998345 CNV gain 25217958
nsv998614 CNV gain 25217958

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)

Additional Variant Information for CNTN4 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 CNTN4 Gene

Disorders for CNTN4 Gene

MalaCards: The human disease database

(12) MalaCards diseases for CNTN4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
chromosome 3pter-p25 deletion syndrome
  • 3p- syndrome
spinocerebellar ataxia 15
  • sca15
coffin-siris syndrome 6
  • css6
  • autistic disorder
chromosome 14q11-q22 deletion syndrome
  • 14q11.2 microdeletion syndrome
- 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}.

Additional Disease Information for CNTN4

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 (Journal of human genetics 2002) 2 3 4 23
  2. Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome. (PMID: 15106122) Fernandez T … State MW (American journal of human genetics 2004) 3 4 23
  3. Cloning and characterization of the human neural cell adhesion molecule, CNTN4 (alias BIG-2). (PMID: 14571131) Hansford LM … Marshall GM (Cytogenetic and genome research 2003) 3 4 23
  4. Genome-wide association study of intelligence: additive effects of novel brain expressed genes. (PMID: 22449649) Loo SK … Nelson SF (Journal of the American Academy of Child and Adolescent Psychiatry 2012) 3 41
  5. A genome-wide association study identifies SNP in DCC is associated with gallbladder cancer in the Japanese population. (PMID: 22318345) Cha PC … Nakamura Y (Journal of human genetics 2012) 3 41

Products for CNTN4 Gene

Sources for CNTN4 Gene