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CNTNAP3 contactin associated protein family member 3 [ Homo sapiens (human) ]

Gene ID: 79937, updated on 5-Mar-2024

Summary

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Official Symbol
CNTNAP3provided by HGNC
Official Full Name
contactin associated protein family member 3provided by HGNC
Primary source
HGNC:HGNC:13834
See related
Ensembl:ENSG00000106714 MIM:610517; AllianceGenome:HGNC:13834
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CASPR3; CNTNAP3A
Summary
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]
Annotation information
Annotation category: suggests misassembly
Expression
Broad expression in esophagus (RPKM 5.9), skin (RPKM 4.1) and 22 other tissues See more
Orthologs
all
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Genomic context

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Location:
9p12
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (39064710..39288167, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (39078097..39301583, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (39064707..39288164, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902157 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:40134136-40134683 Neighboring gene MPRA-validated peak7240 silencer Neighboring gene MPRA-validated peak7241 silencer Neighboring gene vomeronasal 2 receptor 3, pseudogene Neighboring gene RNA binding motif protein 17 pseudogene 1 Neighboring gene RNA, 7SL, cytoplasmic 640, pseudogene Neighboring gene ubiquitin specific peptidase 12 pseudogene Neighboring gene uncharacterized LOC105376045 Neighboring gene NANOG hESC enhancer GRCh37_chr9:39328452-39328996 Neighboring gene SPATA31 subfamily A member 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Elevated mRNA expression of CASPR3 in patients with schizophrenia. Okita M, et al. Nord J Psychiatry, 2017 May. PMID 28413940
  2. Genomic screening of testicular germ cell tumors from monozygotic twins. Silveira SM, et al. Orphanet J Rare Dis, 2014 Nov 26. PMID 25424124, Free PMC Article
  3. CircCNTNAP3-TP53-positive feedback loop suppresses malignant progression of esophageal squamous cell carcinoma. Wang H, et al. Cell Death Dis, 2020 Nov 25. PMID 33239613, Free PMC Article
  4. The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice. Tong DL, et al. Neurobiol Dis, 2019 Oct. PMID 31150793
  5. CNTNAP3 associated ATG16L1 expression and Crohn's disease. Qiao YQ, et al. Mediators Inflamm, 2015. PMID 25883416, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircCNTNAP3-TP53-positive feedback loop suppresses malignant progression of esophageal squamous cell carcinoma.
    Title: CircCNTNAP3-TP53-positive feedback loop suppresses malignant progression of esophageal squamous cell carcinoma.
  2. there are 5 mutations of CNTNAP3 (G410S, P614A, R786C/H, R1219X) which were reported to be found in autism spectrum disorders patients yet, which caused 4 amino acid changed and one stop-gain de novo mutation
    Title: The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice.
  3. Considering that CASPR3 is involved in building the brain neural network and autophagy in circulating leukocytes, abnormal CASPR3 expression in SCZ subjects may be associated with the pathogenesis of SCZ.
    Title: Elevated mRNA expression of CASPR3 in patients with schizophrenia.
  4. CNTNAP3 could upregulate the expression of ATG16L1 and increase autophagy vacuoles
    Title: CNTNAP3 associated ATG16L1 expression and Crohn's disease.
  5. Loss of 9p13.1-p12 was the novel copy number variant shared by twins with testicular germ cell tumors, confirming the involvement of CNTNAP3.
    Title: Genomic screening of testicular germ cell tumors from monozygotic twins.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in cell recognition NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
contactin-associated protein-like 3
Names
cell recognition molecule Caspr3
contactin associated protein like 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001393379.1 → NP_001380308.1  contactin-associated protein-like 3 isoform 2 precursor

    Status: REVIEWED

    Source sequence(s)
    AL162501, AL353729
    Consensus CDS
    CCDS94411.1
    UniProtKB/TrEMBL
    A2RU34, A6NC89
    Related
    ENSP00000366884.2, ENST00000377656.6
    Conserved Domains (5) summary
    cd00057
    Location:54 → 176
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
    cd00110
    Location:371 → 519
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam00008
    Location:551 → 582
    EGF; EGF-like domain
    pfam02210
    Location:212 → 341
    Laminin_G_2; Laminin G domain
    cl00085
    Location:590 → 634
    FReD; Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular ...

  2. NM_033655.5 → NP_387504.2  contactin-associated protein-like 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_387504.2

    Status: REVIEWED

    Source sequence(s)
    AL162501, AL353729
    Consensus CDS
    CCDS6616.1
    UniProtKB/Swiss-Prot
    B1AMA0, Q9BZ76, Q9C0E9
    UniProtKB/TrEMBL
    A2RU34
    Related
    ENSP00000297668.6, ENST00000297668.11
    Conserved Domains (6) summary
    smart00231
    Location:55 → 177
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain
    cd00057
    Location:54 → 176
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
    cd00110
    Location:794 → 938
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam00008
    Location:551 → 582
    EGF; EGF-like domain
    pfam02210
    Location:212 → 341
    Laminin_G_2; Laminin G domain
    cl00085
    Location:590 → 635
    FReD; Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    39064710..39288167 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791789.1 Reference GRCh38.p14 PATCHES

    Range
    48900..272351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    39078097..39301583 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_024879.3: Suppressed sequence

    Description
    NM_024879.3: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZ76.3 GenPept UniProtKB/Swiss-Prot:Q9BZ76

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