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 transcr... See more...

Aliases for CNTNAP3 Gene

Aliases for CNTNAP3 Gene

  • Contactin Associated Protein Family Member 3 2 3 5
  • CASPR3 2 3 4
  • Contactin Associated Protein Like 3 2 3
  • Contactin-Associated Protein-Like 3 3 4
  • Cell Recognition Molecule Caspr3 3 4
  • CNTNAP3A 2 3
  • KIAA1714 2 4
  • Cell Recognition Molecule CASPR3 2
  • FLJ14195 2
  • CNTNAP3 5

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 Family Member 3) is a Protein Coding gene. Diseases associated with CNTNAP3 include Autosomal Dominant Non-Syndromic Intellectual Disability 2 and Cloacal Exstrophy. An important paralog of this gene is CNTNAP3B.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CNTNAP3 Gene

Genomics for CNTNAP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CNTNAP3 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
GH09J039285 Promoter 1 EPDnew Ensembl 250.7 +0.9 915 3.6 ZNF600 ZNF341 ZNF610 GLIS1 GLIS2 ZBTB6 ZBTB20 ZBTB26 CNTNAP3 HSALNG0071172 piR-33432-536 FAM240B
GH09J038680 Enhancer 1.2 FANTOM5 Ensembl ENCODE 16.9 +606.0 606005 4.2 IKZF1 ZNF10 BCL11A CEBPB ETS1 FEZF1 ZNF639 ZEB1 EP300 TAF9B CNTNAP3 ENSG00000273036 HSALNG0071151 RF00026-1069 RNU6-765P lnc-FAM240B-5 FAM240B ANKRD18A MN298114-286
GH09J038685 Enhancer 0.4 ENCODE 14.2 +602.6 602573 1 BATF POU5F1 NANOG HSALNG0071151 CNTNAP3 FAM201A lnc-FAM240B-5 RF00026-1069 RNU6-765P FAM240B ANKRD18A MN298114-286
GH09J039284 Enhancer 0.2 Ensembl 0.7 +4.2 4214 0.2 CNTNAP3 piR-33432-536 FAM240B
GH09J039268 Enhancer 0.2 Ensembl 0.4 +20.6 20614 0.2 LOC100420437 piR-33432-536 CNTNAP3 FAM240B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNTNAP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CNTNAP3

Top Transcription factor binding sites by QIAGEN in the CNTNAP3 gene promoter:
  • ATF-2
  • Cart-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXO1
  • FOXO1a
  • Lhx3a
  • LHX3b
  • RSRFC4
  • XBP-1

Genomic Locations for CNTNAP3 Gene

Latest Assembly
223,606 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
223,458 bases
Minus strand

(GRCh37/hg19 by Ensembl)
215,549 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, Asn359, Asn441, Asn497, Asn623, Asn706, Asn1023, Asn1073, 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

Protein Domains for CNTNAP3 Gene

  • Coagulation factor 5/8 type C domain (FA58C)
  • Type I EGF
  • Laminin G

Suggested Antigen Peptide Sequences for CNTNAP3 Gene

GenScript: Design optimal peptide antigens:
  • CNTNAP3 protein (A2RU34_HUMAN)
  • Cell recognition molecule Caspr3 (CNTP3_HUMAN)

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 From GWAS Catalog for CNTNAP3 Gene

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

Animal Models for CNTNAP3 Gene

MGI Knock Outs for CNTNAP3:

Animal Models for research

  • Taconic Biosciences Mouse Models for CNTNAP3

miRNA for CNTNAP3 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNTNAP3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , 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 4
extracellular 4
cytoskeleton 1
nucleus 1
cytosol 1
peroxisome 0
endoplasmic reticulum 0

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 IEA,NAS 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

PathCards logo

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

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNTNAP3

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

No ASD Table

Relevant External Links for CNTNAP3 Gene

GeneLoc Exon Structure for

Expression for CNTNAP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for CNTNAP3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CNTNAP3

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 for research

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 29 30
  • 99.09 (n)
(Mus musculus)
Mammalia Cntnap3 29 16 30
  • 78.49 (n)
(Bos Taurus)
Mammalia -- 30
  • 72 (a)
(Canis familiaris)
Mammalia -- 30
  • 71 (a)
(Monodelphis domestica)
Mammalia -- 30
  • 67 (a)
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 47 (a)
(Gallus gallus)
Aves -- 30
  • 61 (a)
(Anolis carolinensis)
Reptilia -- 30
  • 62 (a)
(Danio rerio)
Actinopterygii cntnap2a 30
  • 47 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 25 (a)
Species where no ortholog for CNTNAP3 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
Evolutionary constrained regions (ECRs) for CNTNAP3: view image
Alliance of Genome Resources:
Additional Orthologs for CNTNAP3

Paralogs for CNTNAP3 Gene

(7) SIMAP similar genes for CNTNAP3 Gene using alignment to 8 proteins:

  • A2RU34_HUMAN
  • A6NC89_HUMAN
  • B1AM99_HUMAN
  • F2Z2X6_HUMAN
genes like me logo Genes that share paralogs with CNTNAP3: view

Variants for CNTNAP3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CNTNAP3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs1758272 -- p.Ala628Ser
rs7852039 -- p.Arg845His

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CNTNAP3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for CNTNAP3 Gene

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for CNTNAP3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CNTNAP3 Gene - From: COP

Disorder Aliases PubMed IDs
autosomal dominant non-syndromic intellectual disability 2
  • mrd2
cloacal exstrophy
  • omphalocele, exstrophy of the cloaca, imperforate anus, and spinal defects complex
cyclothymic disorder
  • affective personality disorder
bladder exstrophy-epispadias-cloacal exstrophy complex
  • exstrophy-epispadias complex
ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 1
  • eec1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CNTNAP3

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
  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
  3. The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice. (PMID: 31150793) Tong DL … Qiu Z (Neurobiology of disease 2019) 3
  4. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for CNTNAP3 Gene

Sources for CNTNAP3 Gene