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

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: mouse all
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Genomic context

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_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel and known minor alleles of CNTNAP2 gene variants are associated with comorbidity of intellectual disability and epilepsy phenotypes: a case-control association study reveals potential biomarkers.
Title: Novel and known minor alleles of CNTNAP2 gene variants are associated with comorbidity of intellectual disability and epilepsy phenotypes: a case-control association study reveals potential biomarkers.
Bilateral temporal lobe dysplasia and seizure onset associated with biallelic CNTNAP2 variants.
Title: Bilateral temporal lobe dysplasia and seizure onset associated with biallelic CNTNAP2 variants.
Loss of CNTNAP2 Alters Human Cortical Excitatory Neuron Differentiation and Neural Network Development.
Title: Loss of CNTNAP2 Alters Human Cortical Excitatory Neuron Differentiation and Neural Network Development.
Genotype-phenotype correlation in contactin-associated protein-like 2 (CNTNAP-2) developmental disorder.
Title: Genotype-phenotype correlation in contactin-associated protein-like 2 (CNTNAP-2) developmental disorder.
Effect of CNTNAP2 polymorphism on receptive language in children with autism spectrum disorder without language developmental delay.
Title: Effect of CNTNAP2 polymorphism on receptive language in children with autism spectrum disorder without language developmental delay.
PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas.
Title: PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas.
Human CASPR2 Antibodies Reversibly Alter Memory and the CASPR2 Protein Complex.
Title: Human CASPR2 Antibodies Reversibly Alter Memory and the CASPR2 Protein Complex.
Shed CNTNAP2 ectodomain is detectable in CSF and regulates Ca(2+) homeostasis and network synchrony via PMCA2/ATP2B2.
Title: Shed CNTNAP2 ectodomain is detectable in CSF and regulates Ca(2+) homeostasis and network synchrony via PMCA2/ATP2B2.
Two new cases of interstitial 7q35q36.1 deletion including CNTNAP2 and KMT2C.
Title: Two new cases of interstitial 7q35q36.1 deletion including CNTNAP2 and KMT2C.
Common variants of the autism-associated CNTNAP2 gene contribute to the modulatory effect of social function mediated by temporal cortex.
Title: Common variants of the autism-associated CNTNAP2 gene contribute to the modulatory effect of social function mediated by temporal cortex.

Submit: New GeneRIF Correction See all GeneRIFs (106)

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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-68650 (e-PCR)
- UniSTS:95496

GDB:1234254 (e-PCR)
- UniSTS:51466

GDB:3755031 (e-PCR)
- UniSTS:60171

SHGC-144982 (e-PCR)
- UniSTS:174352

RH121890 (e-PCR)
- UniSTS:137745

SHGC-24343 (e-PCR)
- UniSTS:84241

GDB:1318092 (e-PCR)
- UniSTS:66328

SHGC-149313 (e-PCR)
- UniSTS:176925

AFMa082xc9 (e-PCR)
- UniSTS:64286

GDB:1317490 (e-PCR)
- UniSTS:40224

G17196 (e-PCR)
- UniSTS:70946

RH119047 (e-PCR)
- UniSTS:138275

GDB:1318130 (e-PCR)
- UniSTS:35370

SHGC-172105 (e-PCR)
- UniSTS:184620

G20646 (e-PCR)
- UniSTS:42545

A006A14 (e-PCR)
- UniSTS:42546

GDB:1318136 (e-PCR)
- UniSTS:3123

G48196 (e-PCR)
- UniSTS:95293

GDB:1317468 (e-PCR)
- UniSTS:31553

RH120447 (e-PCR)
- UniSTS:133442

GDB:3754357 (e-PCR)
- UniSTS:21571

SHGC-80946 (e-PCR)
- UniSTS:184645

RH93425 (e-PCR)
- UniSTS:84044

SHGC-146796 (e-PCR)
- UniSTS:175436

GDB:1318708 (e-PCR)
- UniSTS:333

RH78475 (e-PCR)
- UniSTS:64077

D7S2511 (e-PCR), detects polymorphism
- UniSTS:25679

D7S2086E (e-PCR)
- UniSTS:151122

G66883 (e-PCR)
- UniSTS:166740

D7S2511 (e-PCR), detects polymorphism
- UniSTS:1365

SHGC-31280 (e-PCR)
- UniSTS:20823

WI-15593 (e-PCR)
- UniSTS:82777

GDB:1317500 (e-PCR)
- UniSTS:10586

RH64839 (e-PCR)
- UniSTS:72542

WI-21561 (e-PCR)
- UniSTS:81759

GDB:1317592 (e-PCR)
- UniSTS:61793

D7S1443 (e-PCR)
- UniSTS:48483

SHGC-81498 (e-PCR)
- UniSTS:103526

D7S2247 (e-PCR)
- UniSTS:70761

G63015 (e-PCR)
- UniSTS:140140

SHGC-82952 (e-PCR)
- UniSTS:96111

GDB:1318162 (e-PCR)
- UniSTS:33652

D1S1425 (e-PCR)
- UniSTS:149621

SHGC-153501 (e-PCR)
- UniSTS:177788

RH18454 (e-PCR)
- UniSTS:16517

GDB:1317638 (e-PCR)
- UniSTS:41605

RH11687 (e-PCR)
- UniSTS:72332

D7S615 (e-PCR)
- UniSTS:20876

RH18453 (e-PCR)
- UniSTS:72087

GDB:1318218 (e-PCR)
- UniSTS:72359

D7S739 (e-PCR)
- UniSTS:22439

GDB:3755029 (e-PCR)
- UniSTS:59562

GDB:1317522 (e-PCR)
- UniSTS:78508

SHGC-156000 (e-PCR)
- UniSTS:185260

D7S2692 (e-PCR)
- UniSTS:58287

SHGC-146544 (e-PCR)
- UniSTS:175283

D7S1883 (e-PCR)
- UniSTS:20669

G10405 (e-PCR)
- UniSTS:447

WI-10718 (e-PCR)
- UniSTS:15552

SHGC-132899 (e-PCR)
- UniSTS:184514

RH46536 (e-PCR)
- UniSTS:57796

SHGC-106566 (e-PCR)
- UniSTS:169926

WI-13838 (e-PCR)
- UniSTS:62666

GDB:1318058 (e-PCR)
- UniSTS:4558

SHGC-5619 (e-PCR)
- UniSTS:53722

SHGC-84652 (e-PCR)
- UniSTS:103139

fc79b09.x1 (e-PCR)
- UniSTS:194539

D7S2352 (e-PCR)
- UniSTS:82156

RH93051 (e-PCR)
- UniSTS:90609

GDB:1318716 (e-PCR)
- UniSTS:61169

GDB:1318643 (e-PCR)
- UniSTS:75250

GDB:1318378 (e-PCR)
- UniSTS:36087

AFM177xd6 (e-PCR)
- UniSTS:49657

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

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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)

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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.

Genomic

NG_007092.3 RefSeqGene

Range

5801..2309998

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_014141.6 → NP_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:1282 → 1300

4.1m; putative band 4.1 homologues' binding motif

smart00231
Location:34 → 181

FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain

smart00282
Location:1050 → 1185

LamG; Laminin G domain

cd00054
Location:555 → 590

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:70 → 180

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:800 → 943

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:216 → 345

Laminin_G_2; Laminin G domain

cl02436
Location:609 → 632

COLFI; Fibrillar collagen C-terminal domain