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Aliases for CNTN6 Gene

Aliases for CNTN6 Gene

  • Contactin 6 2 3 5
  • Neural Recognition Molecule NB-3 3 4
  • Neural Adhesion Molecule 2 3
  • Contactin-6 3
  • HNB-3 4
  • NB3 3

External Ids for CNTN6 Gene

Previous GeneCards Identifiers for CNTN6 Gene

  • GC03P001109

Summaries for CNTN6 Gene

Entrez Gene Summary for CNTN6 Gene

  • The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

GeneCards Summary for CNTN6 Gene

CNTN6 (Contactin 6) is a Protein Coding gene. Diseases associated with CNTN6 include Autonomic Nervous System Neoplasm and Peripheral Nervous System Neoplasm. Among its related pathways are Canonical and Non-canonical Notch signaling and Developmental Biology. An important paralog of this gene is CNTN4.

UniProtKB/Swiss-Prot for CNTN6 Gene

  • Contactins mediate cell surface interactions during nervous system development. Participates in oligodendrocytes generation by acting as a ligand of NOTCH1. Its association with NOTCH1 promotes NOTCH1 activation through the released notch intracellular domain (NICD) and subsequent translocation to the nucleus. Involved in motor coordination (By similarity).

Additional gene information for CNTN6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNTN6 Gene

Genomics for CNTN6 Gene

GeneHancer (GH) Regulatory Elements for CNTN6 Gene

Promoters and enhancers for CNTN6 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
GH03J000535 Promoter 1.3 EPDnew Ensembl 650 -471.7 -471734 1.2 SP1 CTCF POLR2A SETDB1 LINC01266 CNTN6 RPSAP32
GH03J001092 Promoter/Enhancer 1 EPDnew Ensembl ENCODE 680.5 +84.8 84846 1 POLR2A CNTN6 GC03P001114 RN7SL120P
GH03J001117 Enhancer 0.5 ENCODE 17.5 +110.1 110114 0.9 FOSL1 JUND JUN ZFP37 USF2 FOS CNTN6 GC03P001114 LOC105376924
GH03J001086 Enhancer 0.8 Ensembl ENCODE 10.5 +79.3 79339 1 CTCF MAX CEBPB CEBPG EP300 RAD21 ATF4 JUND CNTN6 RN7SL120P GC03P001114
GH03J001183 Enhancer 0.5 ENCODE 10.1 +175.7 175677 0.2 JUN CEBPB CEBPG TCF7L2 CNTN6 LOC105376923 LOC105376924 GC03P001114
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNTN6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CNTN6 gene promoter:
  • CHOP-10
  • C/EBPalpha
  • Sox5
  • TBP
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • POU2F1

Genomic Locations for CNTN6 Gene

Genomic Locations for CNTN6 Gene
396,083 bases
Plus strand
311,642 bases
Plus strand

Genomic View for CNTN6 Gene

Genes around CNTN6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNTN6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNTN6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNTN6 Gene

Proteins for CNTN6 Gene

  • Protein details for CNTN6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q2KHM2

    Protein attributes for CNTN6 Gene

    1028 amino acids
    Molecular mass:
    113956 Da
    Quaternary structure:
    • Interacts with PTPRG.

neXtProt entry for CNTN6 Gene

Post-translational modifications for CNTN6 Gene

  • Glycosylation at posLast=957957, Asn956, Asn931, Asn895, Asn865, posLast=860860, Asn765, Asn659, Asn468, posLast=377377, posLast=368368, posLast=193193, and Asn65
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CNTN6 Gene

Domains & Families for CNTN6 Gene

Suggested Antigen Peptide Sequences for CNTN6 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 CNTN6: view

Function for CNTN6 Gene

Molecular function for CNTN6 Gene

UniProtKB/Swiss-Prot Function:
Contactins mediate cell surface interactions during nervous system development. Participates in oligodendrocytes generation by acting as a ligand of NOTCH1. Its association with NOTCH1 promotes NOTCH1 activation through the released notch intracellular domain (NICD) and subsequent translocation to the nucleus. Involved in motor coordination (By similarity).

Phenotypes From GWAS Catalog for CNTN6 Gene

Gene Ontology (GO) - Molecular Function for CNTN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005112 Notch binding IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with CNTN6: view
genes like me logo Genes that share phenotypes with CNTN6: view

Animal Models for CNTN6 Gene

MGI Knock Outs for CNTN6:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CNTN6 Gene

Localization for CNTN6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNTN6 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 CNTN6 gene
Compartment Confidence
plasma membrane 4
extracellular 2
peroxisome 2
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CNTN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with CNTN6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNTN6 Gene

Pathways & Interactions for CNTN6 Gene

genes like me logo Genes that share pathways with CNTN6: view

Pathways by source for CNTN6 Gene

SIGNOR curated interactions for CNTN6 Gene


Gene Ontology (GO) - Biological Process for CNTN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS,IEA --
GO:0007219 Notch signaling pathway IEA --
GO:0007399 nervous system development IEA --
GO:0007417 central nervous system development TAS 9486763
GO:0022008 neurogenesis IEA --
genes like me logo Genes that share ontologies with CNTN6: view

Drugs & Compounds for CNTN6 Gene

No Compound Related Data Available

Transcripts for CNTN6 Gene

Unigene Clusters for CNTN6 Gene

Contactin 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CNTN6 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6
SP1: -
SP2: - - - - -
SP3: - -
SP4: -

Relevant External Links for CNTN6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNTN6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CNTN6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNTN6 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x12.0), Brain - Cerebellum (x9.3), and Brain - Anterior cingulate cortex (BA24) (x4.6).

Protein differential expression in normal tissues from HIPED for CNTN6 Gene

This gene is overexpressed in Heart (27.2), Fetal Brain (23.3), and Fetal ovary (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CNTN6 Gene

Protein tissue co-expression partners for CNTN6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CNTN6 Gene:


SOURCE GeneReport for Unigene cluster for CNTN6 Gene:


mRNA Expression by UniProt/SwissProt for CNTN6 Gene:

Tissue specificity: Expressed in nervous system. Highly expressed in cerebellum. Expressed at intermediate level in thalamus, subthalamic nucleus. Weakly expressed in corpus callosum, caudate nucleus and spinal cord.

Evidence on tissue expression from TISSUES for CNTN6 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with CNTN6: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CNTN6 Gene

Orthologs for CNTN6 Gene

This gene was present in the common ancestor of animals.

Orthologs for CNTN6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNTN6 34 33
  • 99.42 (n)
(Canis familiaris)
Mammalia CNTN6 34 33
  • 91.78 (n)
(Bos Taurus)
Mammalia CNTN6 34 33
  • 90.22 (n)
(Mus musculus)
Mammalia Cntn6 16 34 33
  • 86.78 (n)
(Rattus norvegicus)
Mammalia Cntn6 33
  • 86.61 (n)
(Monodelphis domestica)
Mammalia CNTN6 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 59 (a)
-- 34
  • 46 (a)
(Gallus gallus)
Aves CNTN6 34 33
  • 73.99 (n)
(Anolis carolinensis)
Reptilia CNTN6 34
  • 74 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cont 35
  • 30 (a)
(Caenorhabditis elegans)
Secernentea C33F10.5b 35
  • 25 (a)
C33F10.5a 35
  • 24 (a)
Species where no ortholog for CNTN6 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 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)
  • zebrafish (Danio rerio)

Evolution for CNTN6 Gene

Gene Tree for CNTN6 (if available)
Gene Tree for CNTN6 (if available)
Evolutionary constrained regions (ECRs) for CNTN6: view image

Paralogs for CNTN6 Gene

Paralogs for CNTN6 Gene

(8) SIMAP similar genes for CNTN6 Gene using alignment to 5 proteins:

  • F5H752_HUMAN
  • L0R839_HUMAN
genes like me logo Genes that share paralogs with CNTN6: view

Variants for CNTN6 Gene

Sequence variations from dbSNP and Humsavar for CNTN6 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
VAR_035509 A breast cancer sample p.Thr108Ala
VAR_035510 A breast cancer sample p.Ser585Cys
rs140337334 uncertain-significance, not specified 1,385,797(+) C/G/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs772031522 uncertain-significance, not specified 1,385,610(+) G/A genic_downstream_transcript_variant, splice_acceptor_variant
rs2291101 benign, not specified 1,383,034(+) G/A/T coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for CNTN6 Gene

Variant ID Type Subtype PubMed ID
dgv268n21 CNV gain 19592680
dgv4613n100 CNV loss 25217958
dgv4616n100 CNV gain 25217958
dgv4617n100 CNV gain 25217958
dgv4618n100 CNV gain 25217958
dgv4619n100 CNV gain 25217958
dgv4620n100 CNV gain 25217958
dgv4621n100 CNV gain 25217958
dgv4622n100 CNV gain 25217958
dgv4623n100 CNV gain 25217958
dgv4624n100 CNV gain 25217958
dgv8153n54 CNV gain 21841781
dgv8154n54 CNV gain 21841781
dgv8157n54 CNV gain 21841781
dgv8158n54 CNV gain 21841781
dgv854e214 CNV loss 21293372
esv1669273 CNV deletion 17803354
esv2179526 CNV deletion 18987734
esv2422404 CNV duplication 17116639
esv2422485 CNV duplication 17116639
esv2484315 CNV deletion 19546169
esv2614118 CNV loss 19546169
esv2656847 CNV deletion 23128226
esv2662624 CNV deletion 23128226
esv2664438 CNV deletion 23128226
esv2670366 CNV deletion 23128226
esv2724770 CNV deletion 23290073
esv2759123 CNV gain+loss 17122850
esv2763731 CNV gain+loss 21179565
esv27779 CNV loss 19812545
esv33501 CNV gain 17666407
esv34599 CNV gain 17911159
esv3561337 CNV deletion 23714750
esv3561339 CNV deletion 23714750
esv3568543 CNV loss 25503493
esv3568544 CNV loss 25503493
esv3575529 CNV gain 25503493
esv3575530 CNV gain 25503493
esv3575531 CNV gain 25503493
esv3575532 CNV gain 25503493
esv3594941 CNV loss 21293372
esv3594942 CNV gain 21293372
esv3594943 CNV gain 21293372
esv3594946 CNV gain 21293372
esv3594947 CNV loss 21293372
esv3594948 CNV loss 21293372
esv3594950 CNV gain 21293372
esv3594951 CNV loss 21293372
esv3594952 CNV gain 21293372
esv3594953 CNV loss 21293372
esv3594954 CNV loss 21293372
esv3594955 CNV gain 21293372
esv3893597 CNV gain 25118596
esv3893598 CNV loss 25118596
esv3893599 CNV gain 25118596
esv3893600 CNV loss 25118596
nsv1000168 CNV loss 25217958
nsv1001956 CNV loss 25217958
nsv1004878 CNV loss 25217958
nsv1004897 CNV loss 25217958
nsv1007343 CNV loss 25217958
nsv1007613 CNV gain 25217958
nsv1009085 CNV loss 25217958
nsv1009942 CNV gain 25217958
nsv1010848 CNV loss 25217958
nsv1010970 CNV gain 25217958
nsv1012451 CNV loss 25217958
nsv1014397 CNV gain 25217958
nsv10242 CNV loss 18304495
nsv10243 CNV loss 18304495
nsv1072655 CNV deletion 25765185
nsv1073180 CNV deletion 25765185
nsv1109486 CNV deletion 24896259
nsv1136700 CNV deletion 24896259
nsv1141428 CNV duplication 24896259
nsv1148831 CNV deletion 26484159
nsv1160912 CNV deletion 26073780
nsv237313 CNV deletion 16902084
nsv460311 CNV gain 19166990
nsv460312 CNV gain 19166990
nsv460313 CNV gain 19166990
nsv460315 CNV gain 19166990
nsv470660 CNV loss 18288195
nsv517343 CNV gain+loss 19592680
nsv526340 CNV loss 19592680
nsv527266 CNV gain 19592680
nsv527267 CNV gain 19592680
nsv589313 CNV loss 21841781
nsv589314 CNV gain 21841781
nsv589316 CNV gain 21841781
nsv589317 CNV gain 21841781
nsv589319 CNV gain 21841781
nsv589320 CNV loss 21841781
nsv589322 CNV loss 21841781
nsv589325 CNV loss 21841781
nsv589326 CNV gain 21841781
nsv589327 CNV gain 21841781
nsv589328 CNV loss 21841781
nsv589329 CNV loss 21841781
nsv834593 CNV loss 17160897
nsv834594 CNV loss 17160897
nsv834595 CNV loss 17160897
nsv999732 CNV loss 25217958

Variation tolerance for CNTN6 Gene

Residual Variation Intolerance Score: 12.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.93; 59.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNTN6 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 CNTN6 Gene

Disorders for CNTN6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CNTN6 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
autonomic nervous system neoplasm
  • tumor of autonomic nervous system
peripheral nervous system neoplasm
  • neoplasm of peripheral nerve
- elite association - COSMIC cancer census association via MalaCards
Search CNTN6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CNTN6

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 CNTN6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNTN6 Gene

Publications for CNTN6 Gene

  1. cDNA cloning and chromosomal localization of neural adhesion molecule NB-3 in human. (PMID: 9486763) Kamei Y … Watanabe K (Journal of neuroscience research 1998) 2 3 4 22 58
  2. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. (PMID: 22219177) Tao S … Sun J (Carcinogenesis 2012) 3 44 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. Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients. (PMID: 20398908) Saus E … Estivill X (Journal of psychiatric research 2010) 3 44 58
  5. 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

Products for CNTN6 Gene

Sources for CNTN6 Gene

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