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Aliases for CNTNAP3 Gene

Aliases for CNTNAP3 Gene

  • Contactin Associated Protein Like 3 2 3 5
  • Cell Recognition Molecule CASPR3 2 4
  • CASPR3 3 4
  • Contactin-Associated Protein-Like 3 3
  • Cell Recognition Molecule Caspr3 3
  • CNTNAP3A 3
  • KIAA1714 4

External Ids for CNTNAP3 Gene

Previous GeneCards Identifiers for CNTNAP3 Gene

  • GC09M039063
  • GC09M038813

Summaries for CNTNAP3 Gene

Entrez Gene Summary for CNTNAP3 Gene

  • The protein encoded by this gene belongs to the NCP family of cell-recognition molecules. This family represents a distinct subgroup of the neurexins. NCP proteins mediate neuron-glial interactions in vertebrates and glial-glial contact in invertebrates. The protein encoded by this gene may play a role in cell recognition within the nervous system. Alternatively spliced transcript variants encoding different isoforms have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for CNTNAP3 Gene

CNTNAP3 (Contactin Associated Protein Like 3) is a Protein Coding gene. Diseases associated with CNTNAP3 include Cyclothymic Disorder and Bladder Exstrophy-Epispadias-Cloacal Exstrophy Complex. An important paralog of this gene is CNTNAP3B.

Additional gene information for CNTNAP3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNTNAP3 Gene

Genomics for CNTNAP3 Gene

Regulatory Elements for CNTNAP3 Gene

Enhancers for CNTNAP3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09H038680 1.5 FANTOM5 Ensembl ENCODE 16.9 +606.4 606421 3 PKNOX1 ARNT SIN3A FEZF1 FOS JUNB TSHZ1 SMARCA4 GLIS1 WT1 CNTNAP3 ENSG00000273036 RNU6-765P FAM240B
GH09H038685 0.4 ENCODE 14.2 +602.6 602573 0 POU5F1 BATF CNTNAP3 FAM201A RNU6-765P FAM240B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CNTNAP3 on UCSC Golden Path with GeneCards custom track

Promoters for CNTNAP3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000235029 615 2600 GLIS2 ZNF610 ZNF341 GLIS1 ZNF600 ZBTB26 ZBTB20

Genomic Location for CNTNAP3 Gene

39,070,195 bp from pter
39,288,315 bp from pter
218,121 bases
Minus strand

Genomic View for CNTNAP3 Gene

Genes around CNTNAP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNTNAP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNTNAP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNTNAP3 Gene

Proteins for CNTNAP3 Gene

  • Protein details for CNTNAP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Contactin-associated protein-like 3
    Protein Accession:
    Secondary Accessions:
    • B1AMA0
    • Q9C0E9

    Protein attributes for CNTNAP3 Gene

    1288 amino acids
    Molecular mass:
    140690 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB21805.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CNTNAP3 Gene


neXtProt entry for CNTNAP3 Gene

Post-translational modifications for CNTNAP3 Gene

  • Glycosylation at Asn285, posLast=359359, posLast=441441, Asn497, Asn623, posLast=706706, Asn1023, posLast=10731073, and Asn1120
  • Modification sites at PhosphoSitePlus

Other Protein References for CNTNAP3 Gene

No data available for DME Specific Peptides for CNTNAP3 Gene

Domains & Families for CNTNAP3 Gene

Gene Families for CNTNAP3 Gene

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

Suggested Antigen Peptide Sequences for CNTNAP3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the neurexin family.
  • Belongs to the neurexin family.
genes like me logo Genes that share domains with CNTNAP3: view

Function for CNTNAP3 Gene

Phenotypes for CNTNAP3 Gene

GenomeRNAi human phenotypes for CNTNAP3:
genes like me logo Genes that share phenotypes with CNTNAP3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CNTNAP3

CRISPR Products

miRNA for CNTNAP3 Gene

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CNTNAP3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CNTNAP3 Gene

Localization for CNTNAP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNTNAP3 Gene

Isoform 1: Cell membrane; Single-pass type I membrane protein.
Isoform 2: 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 CNTNAP3 gene
Compartment Confidence
plasma membrane 5
extracellular 4
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CNTNAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS,IEA 12093160
genes like me logo Genes that share ontologies with CNTNAP3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNTNAP3 Gene

Pathways & Interactions for CNTNAP3 Gene

SuperPathways for CNTNAP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CNTNAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0008037 cell recognition NAS 12093160
genes like me logo Genes that share ontologies with CNTNAP3: view

No data available for Pathways by source and SIGNOR curated interactions for CNTNAP3 Gene

Drugs & Compounds for CNTNAP3 Gene

No Compound Related Data Available

Transcripts for CNTNAP3 Gene

mRNA/cDNA for CNTNAP3 Gene

Unigene Clusters for CNTNAP3 Gene

Contactin associated protein-like 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CNTNAP3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for CNTNAP3 Gene

No ASD Table

Relevant External Links for CNTNAP3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNTNAP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CNTNAP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNTNAP3 Gene

This gene is overexpressed in Whole Blood (x8.0) and Esophagus - Muscularis (x5.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CNTNAP3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CNTNAP3 Gene:


SOURCE GeneReport for Unigene cluster for CNTNAP3 Gene:


Evidence on tissue expression from TISSUES for CNTNAP3 Gene

  • Nervous system(4.6)
  • Lung(4)
  • Kidney(2.9)
genes like me logo Genes that share expression patterns with CNTNAP3: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CNTNAP3 Gene

Orthologs for CNTNAP3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CNTNAP3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNTNAP3 33 34
  • 99.09 (n)
(Mus musculus)
Mammalia Cntnap3 33 16 34
  • 78.49 (n)
(Bos Taurus)
Mammalia -- 34
  • 72 (a)
(Canis familiaris)
Mammalia -- 34
  • 71 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 67 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 47 (a)
(Gallus gallus)
Aves -- 34
  • 61 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 62 (a)
(Danio rerio)
Actinopterygii cntnap2a 34
  • 47 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 25 (a)
Species where no ortholog for CNTNAP3 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)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CNTNAP3 Gene

Gene Tree for CNTNAP3 (if available)
Gene Tree for CNTNAP3 (if available)

Paralogs for CNTNAP3 Gene

Variants for CNTNAP3 Gene

Sequence variations from dbSNP and Humsavar for CNTNAP3 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000013950 -- 39,119,721(+) CAAGT(A/C)TAATG intron-variant
rs1000024135 -- 39,094,696(+) TTCCA(C/T)TGATT intron-variant
rs1000103813 -- 39,160,634(+) CCAAC(A/G)TAGTA intron-variant
rs1000154317 -- 39,160,942(+) AGCTA(A/G)CCAGG intron-variant
rs1000197776 -- 39,135,147(+) TAGTA(A/G)AACAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CNTNAP3 Gene

Variant ID Type Subtype PubMed ID
dgv1217n67 CNV gain 20364138
dgv7524n100 CNV gain 25217958
dgv7525n100 CNV loss 25217958
dgv7530n100 CNV loss 25217958
dgv7532n100 CNV gain 25217958
esv24325 CNV gain+loss 19812545
esv29529 CNV gain+loss 19812545
esv3620449 CNV loss 21293372
esv3620450 CNV gain 21293372
esv3620451 CNV loss 21293372
esv3620452 CNV gain 21293372
nsv1015872 CNV gain 25217958
nsv1018148 CNV gain 25217958
nsv1019326 CNV gain+loss 25217958
nsv1075230 CNV deletion 25765185
nsv1076168 CNV deletion 25765185
nsv1124417 CNV deletion 24896259
nsv1126874 CNV deletion 24896259
nsv1126903 CNV deletion 24896259
nsv1129026 CNV duplication 24896259
nsv1132711 CNV duplication 24896259
nsv1137631 CNV deletion 24896259
nsv1137651 CNV deletion 24896259
nsv1137652 CNV deletion 24896259
nsv1145237 CNV deletion 24896259
nsv1146810 CNV duplication 26484159
nsv1149553 CNV duplication 26484159
nsv415608 CNV deletion 16902084
nsv428215 CNV gain+loss 18775914
nsv469512 CNV gain 16826518
nsv469632 CNV gain+loss 16826518
nsv469801 CNV gain 16826518
nsv471466 CNV gain 19718026
nsv519835 CNV gain 19592680
nsv520007 CNV gain+loss 19592680
nsv614282 CNV gain 21841781
nsv614283 CNV loss 21841781
nsv614284 CNV loss 21841781
nsv818702 CNV gain 17921354
nsv820048 CNV loss 19587683
nsv831553 CNV gain+loss 17160897
nsv831554 CNV gain 17160897
nsv831555 CNV gain 17160897
nsv8450 CNV gain+loss 18304495
nsv951179 CNV deletion 24416366
nsv972317 CNV duplication 23825009
nsv972318 CNV duplication 23825009
nsv972676 CNV duplication 23825009
nsv973668 CNV duplication 23825009
nsv982220 CNV duplication 23825009
nsv982221 CNV duplication 23825009
nsv982366 CNV duplication 23825009
nsv982464 CNV duplication 23825009

Variation tolerance for CNTNAP3 Gene

Gene Damage Index Score: 8.07; 84.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CNTNAP3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNTNAP3 Gene

Disorders for CNTNAP3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CNTNAP3 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
cyclothymic disorder
  • affective personality disorder
bladder exstrophy-epispadias-cloacal exstrophy complex
  • exstrophy-epispadias complex
exstrophy of bladder
  • bladder exstrophy
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for CNTNAP3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CNTNAP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNTNAP3 Gene

Publications for CNTNAP3 Gene

  1. Caspr3 and caspr4, two novel members of the caspr family are expressed in the nervous system and interact with PDZ domains. (PMID: 12093160) Spiegel I … Peles E (Molecular and cellular neurosciences 2002) 2 3 4 60
  2. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 60
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  4. Elevated mRNA expression of CASPR3 in patients with schizophrenia. (PMID: 28413940) Okita M … Ueno SI (Nordic journal of psychiatry 2017) 3 60
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 60

Products for CNTNAP3 Gene

Sources for CNTNAP3 Gene

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