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CNTN3 contactin 3 [ Homo sapiens (human) ]

Gene ID: 5067, updated on 5-Mar-2024

Summary

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Official Symbol
CNTN3provided by HGNC
Official Full Name
contactin 3provided by HGNC
Primary source
HGNC:HGNC:2173
See related
Ensembl:ENSG00000113805 MIM:601325; AllianceGenome:HGNC:2173
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCS; PANG; BIG-1
Summary
Predicted to be involved in cell adhesion and nervous system development. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in neuron projection. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 2.7), prostate (RPKM 1.8) and 18 other tissues See more
Orthologs
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Genomic context

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Location:
3p12.3
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (74262568..74614659, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (74304615..74656673, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (74311719..74663810, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene heat shock protein 90 alpha family class B member 5, pseudogene Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:74648227-74649426 Neighboring gene uncharacterized LOC105377166 Neighboring gene uncharacterized LOC105377167 Neighboring gene uncharacterized LOC105377168

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. Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period. Korotkov A, et al. J Neurodev Disord, 2022 Jan 15. PMID 35030990, Free PMC Article
  2. Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association. Elmore JR, et al. J Vasc Surg, 2009 Jun. PMID 19497516
  3. PANG, a gene encoding a neuronal glycoprotein, is ectopically activated by intracisternal A-type particle long terminal repeats in murine plasmacytomas. Connelly MA, et al. Proc Natl Acad Sci U S A, 1994 Feb 15. PMID 8108413, Free PMC Article
  4. SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer. Zhou J, et al. Biomed Res Int, 2020. PMID 32566650, Free PMC Article
  5. Human NB-2 of the contactin subgroup molecules: chromosomal localization of the gene (CNTN5) and distinct expression pattern from other subgroup members. Kamei Y, et al. Genomics, 2000 Oct 1. PMID 11013081

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period.
    Title: Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period.
  2. SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer.
    Title: SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer.
  3. BIG1 and BIG2 have roles in endomembrane organization
    Title: Specific functions of BIG1 and BIG2 in endomembrane organization.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: 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.
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

EBI GWAS Catalog

Description
Genome-wide association study of smoking behaviours among Bangladeshi adults.
EBI GWAS Catalog
The genetic architecture of economic and political preferences.
EBI GWAS Catalog

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

General gene information

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Markers

Homology

Clone Names

  • KIAA1496

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in side of membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
contactin-3
Names
brain-derived immunoglobulin superfamily protein 1
contactin 3 (plasmacytoma associated)
plasmacytoma-associated neuronal glycoprotein

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_001393376.1 → NP_001380305.1  contactin-3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC016945, AC016950, AC024222, AC128653, AC128656
    Consensus CDS
    CCDS33790.1
    UniProtKB/Swiss-Prot
    B9EK50, Q9H039, Q9P232
    Conserved Domains (3) summary
    cd00063
    Location:598 → 695
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd00096
    Location:498 → 504
    Ig; Ig strand A [structural motif]
    cl11960
    Location:498 → 598
    Ig; Immunoglobulin domain

  2. NM_020872.3 → NP_065923.1  contactin-3 precursor

    See identical proteins and their annotated locations for NP_065923.1

    Status: VALIDATED

    Source sequence(s)
    AC016945, AC016950, AC024222, AC128653, AC128656
    Consensus CDS
    CCDS33790.1
    UniProtKB/Swiss-Prot
    B9EK50, Q9H039, Q9P232
    Related
    ENSP00000263665.6, ENST00000263665.7
    Conserved Domains (3) summary
    cd00063
    Location:598 → 695
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd00096
    Location:498 → 504
    Ig; Ig strand A [structural motif]
    cl11960
    Location:498 → 598
    Ig; Immunoglobulin domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    74262568..74614659 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533768.3 → XP_011532070.1  contactin-3 isoform X1

    Conserved Domains (4) summary
    smart00410
    Location:419 → 496
    IG_like; Immunoglobulin like
    cd00063
    Location:598 → 695
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:318 → 403
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:227 → 315
    Ig; Immunoglobulin domain

  2. XM_017006508.2 → XP_016861997.1  contactin-3 isoform X2

  3. XM_017006509.1 → XP_016861998.1  contactin-3 isoform X3

    Conserved Domains (3) summary
    smart00410
    Location:64 → 152
    IG_like; Immunoglobulin like
    cd00063
    Location:156 → 253
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cl11960
    Location:73 → 156
    Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    74304615..74656673 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346680.1 → XP_054202655.1  contactin-3 isoform X1

  2. XM_054346681.1 → XP_054202656.1  contactin-3 isoform X2

  3. XM_054346682.1 → XP_054202657.1  contactin-3 isoform X3

  4. XM_054346683.1 → XP_054202658.1  contactin-3 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P232.3 GenPept UniProtKB/Swiss-Prot:Q9P232

Gene LinkOut

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