HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CNTNAP2
contactin associated protein 2
Chromosome 7 Β· 7q35-q36.1
NCBI Gene: 26047Ensembl: ENSG00000174469.23HGNC: HGNC:13830UniProt: A0A090N7T7
149PubMed Papers
22Diseases
0Drugs
111Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
Golgi apparatusthalamus developmentcerebral cortex developmentadult behaviorcortical dysplasia-focal epilepsy syndromeCortical dysplasia - focal epilepsy syndromePitt-Hopkins-like syndromeautism
✦AI Summary

CNTNAP2 (contactin associated protein-like 2) is a scaffolding protein essential for organizing myelinated axons and forming functional neuronal domains critical for saltatory conduction 1. The protein demarcates the juxtaparanodal region of axo-glial junctions and likely participates in gap junction formation. CNTNAP2 plays a central role in early brain development, particularly in neuronal migration and interneuron specification 1. At the circuit level, CNTNAP2 maintains proper thalamocortical connectivity and social brain network organization 2, partly through oxytocin system regulation; Cntnap2 knockout mice exhibit reduced oxytocin-producing neurons in the paraventricular hypothalamus 3. Mechanistically, CNTNAP2 loss leads to reticular thalamic hyperexcitability, enhanced T-type calcium currents, and aberrant intrathalamic oscillations that drive autism-related behaviors 4. Mutations in CNTNAP2 cause cortical dysplasia and focal epilepsy (CDFE) syndrome with high autism spectrum disorder (ASD) penetrance 3. In humans, CNTNAP2 variants confer ASD susceptibility, though associations with specific polymorphisms (rs2710102, rs7794745) show weak to suggestive evidence 5. Notably, CNTNAP2-related neuromyotonia involves autoimmune targeting of CASPR2, a functionally related juxtaparanodal protein 6. Therapeutic interventions including oxytocin, reticular thalamic calcium channel blockers, and antipsychotics ameliorate behavioral deficits in animal models 134.

Sources cited
1
CNTNAP2 is essential for brain development, neuronal migration, and interneuron specification; mutations cause epilepsy and core autism behaviors in mice
PMID: 21962519
2
CNTNAP2 SNPs rs2710102 and rs7794745 show weak evidence for association with ASD risk in meta-analysis
PMID: 35705542
3
CASPR2, a juxtaparanodal protein functionally related to CNTNAP2, is a target of autoimmune antibodies causing neuromyotonia
PMID: 39174249
4
Cntnap2 knockout mice have reduced oxytocin neurons in the paraventricular nucleus; oxytocin administration rescues social deficits
PMID: 25609168
5
Reticular thalamic hyperexcitability and elevated T-type calcium currents drive ASD behaviors in Cntnap2 knockout mice; these can be reversed by T-type calcium channel blockers
PMID: 40834072
6
Cntnap2 knockout mice show reduced functional coupling across social brain regions; oxytocin normalizes connectivity patterns and stimulates the nucleus accumbens
PMID: 34932941
7
Meta-analysis found no significant association between CNTNAP2 SNPs and high-functioning autism, suggesting the gene may be more relevant in intellectual disability and neurodevelopmental disorders
PMID: 26559825
Disease Associationsβ“˜22
cortical dysplasia-focal epilepsy syndromeOpen Targets
0.78Strong
Cortical dysplasia - focal epilepsy syndromeOpen Targets
0.72Strong
Pitt-Hopkins-like syndromeOpen Targets
0.57Moderate
autismOpen Targets
0.57Moderate
genetic disorderOpen Targets
0.54Moderate
Rolandic epilepsyOpen Targets
0.51Moderate
self-limited epilepsy with centrotemporal spikesOpen Targets
0.50Moderate
mathematical abilityOpen Targets
0.42Moderate
ulcerative colitisOpen Targets
0.41Moderate
dislocationOpen Targets
0.38Weak
Alzheimer diseaseOpen Targets
0.38Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
benign neoplasm of eyeOpen Targets
0.34Weak
crush injuryOpen Targets
0.34Weak
Intellectual disabilityOpen Targets
0.33Weak
peripheral vascular diseaseOpen Targets
0.32Weak
ovarian dysfunctionOpen Targets
0.31Weak
autism spectrum disorderOpen Targets
0.30Weak
colon carcinomaOpen Targets
0.30Weak
stomach diseaseOpen Targets
0.30Weak
Autism 15UniProt
Pitt-Hopkins-like syndrome 1UniProt
Pathogenic Variants111
NM_014141.6(CNTNAP2):c.3382-2A>CLikely pathogenic
not provided|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2026
NM_014141.6(CNTNAP2):c.2646G>A (p.Trp882Ter)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 882
NM_014141.6(CNTNAP2):c.2497del (p.Trp833fs)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|not provided|Inborn genetic diseases|Cortical dysplasia-focal epilepsy syndrome;Autism, susceptibility to, 15
β˜…β˜…β˜†β˜†2025β†’ Residue 833
NM_014141.6(CNTNAP2):c.3283C>T (p.Arg1095Ter)Pathogenic
not provided|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1095
NM_014141.6(CNTNAP2):c.1447C>T (p.Arg483Ter)Pathogenic
not provided|Cortical dysplasia-focal epilepsy syndrome|See cases|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 483
NM_014141.6(CNTNAP2):c.97+1G>APathogenic
Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2025
NM_014141.6(CNTNAP2):c.1843dup (p.Asp615fs)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 615
NM_014141.6(CNTNAP2):c.3709del (p.Asp1237fs)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1237
NM_014141.6(CNTNAP2):c.551G>A (p.Trp184Ter)Pathogenic
Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 184
NM_014141.6(CNTNAP2):c.3262C>T (p.Arg1088Ter)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1088
NM_014141.6(CNTNAP2):c.3331C>T (p.Gln1111Ter)Pathogenic
not provided|Inborn genetic diseases|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1111
NM_014141.6(CNTNAP2):c.2153G>A (p.Trp718Ter)Pathogenic
not provided|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 718
NM_014141.6(CNTNAP2):c.682G>T (p.Gly228Ter)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|not provided|Cortical dysplasia-focal epilepsy syndrome;Autism, susceptibility to, 15
β˜…β˜…β˜†β˜†2024β†’ Residue 228
NM_014141.6(CNTNAP2):c.3480_3481del (p.Gly1161fs)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|Autism, susceptibility to, 15|Cortical dysplasia-focal epilepsy syndrome;Autism, susceptibility to, 15
β˜…β˜…β˜†β˜†2024β†’ Residue 1161
NM_014141.6(CNTNAP2):c.3556dup (p.Gln1186fs)Pathogenic
Inborn genetic diseases|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 1186
NM_014141.6(CNTNAP2):c.1689_1690del (p.Cys563_Glu564delinsTer)Pathogenic
Cortical dysplasia-focal epilepsy syndrome|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 563
NM_014141.6(CNTNAP2):c.1348+1G>ALikely pathogenic
Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2023
NM_014141.6(CNTNAP2):c.1361_1362del (p.Asn454fs)Pathogenic
Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 454
NM_014141.6(CNTNAP2):c.252G>A (p.Trp84Ter)Pathogenic
not provided|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 84
NM_014141.6(CNTNAP2):c.2101G>T (p.Gly701Ter)Pathogenic
Inborn genetic diseases|Cortical dysplasia-focal epilepsy syndrome
β˜…β˜…β˜†β˜†2022β†’ Residue 701
View on ClinVar β†—
Related Genes
KCNA2Protein interaction100%NFASCProtein interaction100%FOXP2Protein interaction98%NLGN4XProtein interaction96%NLGN3Protein interaction96%DPP10Protein interaction89%
Tissue Expression6 tissues
Brain
100%
Liver
4%
Ovary
2%
Bone Marrow
1%
Heart
0%
Lung
0%
Gene Interaction Network
Click a node to explore
CNTNAP2KCNA2NFASCFOXP2NLGN4XNLGN3DPP10
PROTEIN STRUCTURE
Preparing viewer…
PDB5Y4M Β· 1.31 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.72LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.61 [0.52–0.72]
RankingsWhere CNTNAP2 stands among ~20K protein-coding genes
  • #3,035of 20,598
    Most Researched149 Β· top quartile
  • #708of 5,498
    Most Pathogenic Variants111 Β· top quartile
  • #5,567of 17,882
    Most Constrained (LOEUF)0.72
Genes detectedCNTNAP2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Neuromyotonia.
PMID: 39174249
Handb Clin Neurol Β· 2024
1.00
2
Absence of CNTNAP2 leads to epilepsy, neuronal migration abnormalities, and core autism-related deficits.
PMID: 21962519
Cell Β· 2011
0.90
3
Genetics of autism spectrum disorder: an umbrella review of systematic reviews and meta-analyses.
PMID: 35705542
Transl Psychiatry Β· 2022
0.80
4
Magnetic Resonance Imaging Characteristics of LGI1-Antibody and CASPR2-Antibody Encephalitis.
PMID: 38497971
JAMA Neurol Β· 2024
0.70
5
CNTNAP2 gene in high functioning autism: no association according to family and meta-analysis approaches.
PMID: 26559825
J Neural Transm (Vienna) Β· 2016
0.60