Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CNTNAP3B Gene

Aliases for CNTNAP3B Gene

  • Contactin Associated Protein Like 3B 2 3 5
  • Cell Recognition Molecule Caspr3b 4
  • CASPR3B 4

External Ids for CNTNAP3B Gene

Previous GeneCards Identifiers for CNTNAP3B Gene

  • GC09M040099
  • GC09P043624

Summaries for CNTNAP3B Gene

GeneCards Summary for CNTNAP3B Gene

CNTNAP3B (Contactin Associated Protein Like 3B) is a Protein Coding gene. Diseases associated with CNTNAP3B include Exstrophy Of Bladder. An important paralog of this gene is CNTNAP3.

Additional gene information for CNTNAP3B Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNTNAP3B Gene

Genomics for CNTNAP3B Gene

GeneHancer (GH) Regulatory Elements for CNTNAP3B Gene

Promoters and enhancers for CNTNAP3B 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
GH09I042127 Promoter 0.9 Ensembl 550.8 +0.8 810 2.6 CTCF ZNF654 SIN3A FEZF1 ZNF664 ZNF335 PRDM6 POLR2A ZSCAN5C PRDM10 CNTNAP3B LOC100420440
GH09I042852 Promoter 0.9 Ensembl 9 -723.0 -722991 1 ELF3 CTCF SAP130 L3MBTL2 ELF1 RAD21 ZNF48 POLR2A SMAD4 ZSCAN29 ANKRD20A7P CNTNAP3B LOC102724818
GH09I042183 Promoter 0.5 EPDnew 0.2 -54.1 -54130 0.1 SPATA31A6 CNTNAP3B
GH09I042070 Enhancer 0.2 Ensembl 0.2 +58.9 58909 0.4 LOC100420440 CNTNAP3B RN7SL343P
GH09I041898 Enhancer 0.3 Ensembl 0.1 +230.7 230658 0.7 EZH2 VN2R6P RBM17P3 CNTNAP3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CNTNAP3B on UCSC Golden Path with GeneCards custom track

Genomic Locations for CNTNAP3B Gene

Genomic Locations for CNTNAP3B Gene
239,197 bases
Minus strand

Genomic View for CNTNAP3B Gene

Genes around CNTNAP3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNTNAP3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNTNAP3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNTNAP3B Gene

Proteins for CNTNAP3B Gene

  • Protein details for CNTNAP3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Contactin-associated protein-like 3B
    Protein Accession:
    Secondary Accessions:
    • B1B0V7
    • B1B0V8
    • B1B0V9
    • B1B0W0
    • B1B0X8
    • B1B162
    • Q4VXF0
    • Q9H7W3

    Protein attributes for CNTNAP3B Gene

    1288 amino acids
    Molecular mass:
    140468 Da
    Quaternary structure:
    No Data Available
    • The gene encoding CNTNAP3B is the result of a pericentromeric duplication of the genomic region encoding CNTNAP3 on chromosome 9.
    • Sequence=CAI12626.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI16324.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI95046.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI95048.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI95321.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for CNTNAP3B Gene


neXtProt entry for CNTNAP3B Gene

Post-translational modifications for CNTNAP3B Gene

  • Glycosylation at posLast=359359 and Asn706
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CNTNAP3B Gene

Domains & Families for CNTNAP3B Gene

Gene Families for CNTNAP3B Gene

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

Suggested Antigen Peptide Sequences for CNTNAP3B Gene

GenScript: Design optimal peptide antigens:

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 CNTNAP3B: view

Function for CNTNAP3B Gene

Animal Model Products

miRNA for CNTNAP3B Gene

miRTarBase miRNAs that target CNTNAP3B

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CNTNAP3B Gene

Localization for CNTNAP3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNTNAP3B Gene

Membrane; Single-pass type I membrane protein.

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 CNTNAP3B gene
Compartment Confidence
plasma membrane 3
extracellular 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for CNTNAP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CNTNAP3B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNTNAP3B Gene

Pathways & Interactions for CNTNAP3B Gene

SuperPathways for CNTNAP3B Gene

No Data Available

Interacting Proteins for CNTNAP3B Gene

Gene Ontology (GO) - Biological Process for CNTNAP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
genes like me logo Genes that share ontologies with CNTNAP3B: view

No data available for Pathways by source and SIGNOR curated interactions for CNTNAP3B Gene

Drugs & Compounds for CNTNAP3B Gene

No Compound Related Data Available

Transcripts for CNTNAP3B Gene


(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CNTNAP3B Gene

Contactin associated protein-like 3B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CNTNAP3B Gene

No ASD Table

Relevant External Links for CNTNAP3B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNTNAP3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CNTNAP3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNTNAP3B Gene

This gene is overexpressed in Esophagus - Muscularis (x5.0).

Protein differential expression in normal tissues from HIPED for CNTNAP3B Gene

This gene is overexpressed in Breast (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CNTNAP3B Gene

Protein tissue co-expression partners for CNTNAP3B Gene

NURSA nuclear receptor signaling pathways regulating expression of CNTNAP3B Gene:


SOURCE GeneReport for Unigene cluster for CNTNAP3B Gene:

genes like me logo Genes that share expression patterns with CNTNAP3B: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CNTNAP3B Gene

Orthologs for CNTNAP3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for CNTNAP3B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNTNAP3B 33 34
  • 99.09 (n)
(Canis familiaris)
Mammalia CNTNAP3 33
  • 78.14 (n)
-- 34
  • 45 (a)
(Mus musculus)
Mammalia Cntnap3 34
  • 73 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 67 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 47 (a)
(Bos Taurus)
Mammalia -- 34
  • 40 (a)
(Gallus gallus)
Aves -- 34
  • 61 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 61 (a)
(Danio rerio)
Actinopterygii CR382299.1 34
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 25 (a)
Species where no ortholog for CNTNAP3B 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 CNTNAP3B Gene

Gene Tree for CNTNAP3B (if available)
Gene Tree for CNTNAP3B (if available)

Paralogs for CNTNAP3B Gene

(7) SIMAP similar genes for CNTNAP3B Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CNTNAP3B: view

Variants for CNTNAP3B Gene

Sequence variations from dbSNP and Humsavar for CNTNAP3B Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs375643696 benign, not specified 41,960,805(-) A/ coding_sequence_variant, frameshift
rs1000074699 -- 41,997,953(-) T/A intron_variant
rs1000076866 -- 42,075,696(-) C/T intron_variant
rs1000080391 -- 42,075,023(-) C/A intron_variant
rs1000123757 -- 41,984,059(-) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CNTNAP3B Gene

Variant ID Type Subtype PubMed ID
esv1507615 CNV insertion 17803354
esv28947 CNV gain+loss 19812545
nsv1075207 CNV deletion 25765185
nsv1119261 CNV duplication 24896259
nsv1132683 CNV duplication 24896259
nsv1133723 CNV deletion 24896259
nsv1146356 CNV duplication 26484159
nsv1152947 CNV duplication 26484159
nsv469519 CNV gain+loss 16826518
nsv831568 CNV gain+loss 17160897
nsv831591 CNV loss 17160897
nsv972372 CNV duplication 23825009
nsv972680 CNV duplication 23825009
nsv972681 CNV duplication 23825009
nsv972731 CNV duplication 23825009
nsv972732 CNV duplication 23825009
nsv972733 CNV duplication 23825009
nsv973219 CNV duplication 23825009
nsv982229 CNV duplication 23825009

Variation tolerance for CNTNAP3B Gene

Gene Damage Index Score: 19.92; 98.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNTNAP3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNTNAP3B Gene

Disorders for CNTNAP3B Gene

MalaCards: The human disease database

(1) MalaCards diseases for CNTNAP3B Gene - From: DISEASES

Disorder Aliases PubMed IDs
exstrophy of bladder
  • bladder exstrophy
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CNTNAP3B

genes like me logo Genes that share disorders with CNTNAP3B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNTNAP3B Gene

Publications for CNTNAP3B Gene

  1. A reciprocal translocation 46,XY,t(8;9)(p11.2;q13) in a bladder exstrophy patient disrupts CNTNAP3 and presents evidence of a pericentromeric duplication on chromosome 9. (PMID: 15820314) Boyadjiev SA … Stetten G (Genomics 2005) 2 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for CNTNAP3B Gene

Sources for CNTNAP3B Gene

Loading form....