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CNTNAP2 contactin associated protein 2 [ Homo sapiens (human) ]

Gene ID: 26047, updated on 17-Jun-2024

Summary

Official Symbol
CNTNAP2provided by HGNC
Official Full Name
contactin associated protein 2provided by HGNC
Primary source
HGNC:HGNC:13830
See related
Ensembl:ENSG00000174469 MIM:604569; AllianceGenome:HGNC:13830
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
CDFE; NRXN4; AUTS15; CASPR2; PTHSL1
Summary
This gene encodes a member of the neurexin family which functions in the vertebrate nervous system as cell adhesion molecules and receptors. This protein, like other neurexin proteins, contains epidermal growth factor repeats and laminin G domains. In addition, it includes an F5/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, thrombospondin N-terminal-like domains and a putative PDZ binding site. This protein is localized at the juxtaparanodes of myelinated axons, and mediates interactions between neurons and glia during nervous system development and is also involved in localization of potassium channels within differentiating axons. This gene encompasses almost 1.5% of chromosome 7 and is one of the largest genes in the human genome. It is directly bound and regulated by forkhead box protein P2, a transcription factor related to speech and language development. This gene has been implicated in multiple neurodevelopmental disorders, including Gilles de la Tourette syndrome, schizophrenia, epilepsy, autism, ADHD and intellectual disability. [provided by RefSeq, Jul 2017]
Expression
Biased expression in brain (RPKM 12.9), prostate (RPKM 4.1) and 7 other tissues See more
Orthologs
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Genomic context

See CNTNAP2 in Genome Data Viewer
Location:
7q35-q36.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (146116801..148420998)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (147296849..149602894)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (145813893..148118090)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375553 Neighboring gene MPRA-validated peak6819 silencer Neighboring gene MPRA-validated peak6820 silencer Neighboring gene uncharacterized LOC124901765 Neighboring gene MPRA-validated peak6822 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:145629475-145629976 Neighboring gene NANOG hESC enhancer GRCh37_chr7:145694161-145694662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:145715805-145716394 Neighboring gene MPRA-validated peak6823 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:145750296-145751495 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:145858210-145858754 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:145945721-145946492 Neighboring gene transmembrane protein 183A pseudogene Neighboring gene MPRA-validated peak6825 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:146485317-146485842 Neighboring gene Sharpr-MPRA regulatory region 553 Neighboring gene NANOG hESC enhancer GRCh37_chr7:146572321-146572837 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:146602536-146603152 Neighboring gene CNTNAP2 antisense RNA 1 Neighboring gene deoxyuridine triphosphatase pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:147120875-147121406 Neighboring gene RAN pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:147133565-147134311 Neighboring gene microRNA 548f-4 Neighboring gene uncharacterized LOC107986721 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:147304031-147304584 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:147304585-147305137 Neighboring gene uncharacterized LOC105375556 Neighboring gene NANOG hESC enhancer GRCh37_chr7:147500602-147501173 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_97821 Neighboring gene RNA, U6 small nuclear 1184, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:147605052-147605552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:147605553-147606053 Neighboring gene RNA, 5S ribosomal pseudogene 249 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:147696507-147697163 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:147697164-147697819 Neighboring gene NANOG hESC enhancer GRCh37_chr7:147708749-147709250 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:147717495-147718281 Neighboring gene RNA, 7SL, cytoplasmic 456, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26798 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:147868766-147869965 Neighboring gene Sharpr-MPRA regulatory region 9018 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:147977203-147977403 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:147987619-147988173 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:148012335-148012894 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148024709-148025285 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148032138-148033043 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:148036315-148036845 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:148037465-148038070 Neighboring gene uncharacterized LOC105375554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148080395-148080896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148080897-148081398 Neighboring gene small nucleolar RNA U3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148092562-148093198 Neighboring gene exosome component 6 pseudogene Neighboring gene RNA, 7SL, cytoplasmic 72, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Autism, susceptibility to, 15
MedGen: C2677504 OMIM: 612100 GeneReviews: Not available
Compare labs
Cortical dysplasia-focal epilepsy syndrome
MedGen: C2750246 OMIM: 610042 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-10-23)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2019-10-23)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A comprehensive genetic association study of Alzheimer disease in African Americans.
EBI GWAS Catalog
A genome wide association study (GWAS) providing evidence of an association between common genetic variants and late radiotherapy toxicity.
EBI GWAS Catalog
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval.
EBI GWAS Catalog
Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study.
EBI GWAS Catalog
Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment.
EBI GWAS Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog
Genome-wide association with bone mass and geometry in the Framingham Heart Study.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • DKFZp781D1846

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protease binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transmembrane transporter binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in adult behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in brain development TAS
Traceable Author Statement
more info
PubMed 
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in cell population proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cerebral cortex development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in clustering of voltage-gated potassium channels ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in learning IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in limbic system development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in neuron projection morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in neuron recognition NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of gap junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in prepulse inhibition IEA
Inferred from Electronic Annotation
more info
 
involved_in protein localization to juxtaparanode region of axon ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in social behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in striatum development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in superior temporal gyrus development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in thalamus development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in transmission of nerve impulse NAS
Non-traceable Author Statement
more info
PubMed 
involved_in vocal learning IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in vocalization behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in axolemma IDA
Inferred from Direct Assay
more info
PubMed 
located_in axon NAS
Non-traceable Author Statement
more info
PubMed 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in dendrite NAS
Non-traceable Author Statement
more info
PubMed 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in juxtaparanode region of axon ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in neuronal cell body NAS
Non-traceable Author Statement
more info
PubMed 
located_in paranodal junction IEA
Inferred from Electronic Annotation
more info
 
located_in paranode region of axon IEA
Inferred from Electronic Annotation
more info
 
located_in perikaryon NAS
Non-traceable Author Statement
more info
PubMed 
located_in synaptic membrane IEA
Inferred from Electronic Annotation
more info
 
part_of voltage-gated potassium channel complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of voltage-gated potassium channel complex NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
contactin-associated protein-like 2
Names
cell recognition molecule Caspr2
contactin associated protein like 2
homolog of Drosophila neurexin IV

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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.

Genomic

  1. NG_007092.3 RefSeqGene

    Range
    5801..2309998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014141.6NP_054860.1  contactin-associated protein-like 2 precursor

    See identical proteins and their annotated locations for NP_054860.1

    Status: REVIEWED

    Source sequence(s)
    AC073308, AC083849, AK315113, BC093780
    Consensus CDS
    CCDS5889.1
    UniProtKB/Swiss-Prot
    D3DWG2, Q14DG2, Q52LV1, Q5H9Q7, Q9UHC6, Q9UQ12
    UniProtKB/TrEMBL
    A0A090N7T7, B2RCH4
    Related
    ENSP00000354778.3, ENST00000361727.8
    Conserved Domains (8) summary
    smart00294
    Location:12821300
    4.1m; putative band 4.1 homologues' binding motif
    smart00231
    Location:34181
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain
    smart00282
    Location:10501185
    LamG; Laminin G domain
    cd00054
    Location:555590
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00057
    Location:70180
    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:800943
    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 ...
    pfam02210
    Location:216345
    Laminin_G_2; Laminin G domain
    cl02436
    Location:609632
    COLFI; Fibrillar collagen C-terminal 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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    146116801..148420998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011950.3XP_016867439.1  contactin-associated protein-like 2 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187564.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    2405..204593
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    147296849..149602894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357812.1XP_054213787.1  contactin-associated protein-like 2 isoform X1