CNTNAP2

Chr 7AR

contactin associated protein 2

Also known as: AUTS15, CASPR2, CDFE, NRXN4, PTHSL1

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]

OMIMResearchGenerating clinical summary…
LOFmechanismARLOEUF 0.552 OMIM phenotypes
Clinical SummaryCNTNAP2
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Gene-Disease Validity (ClinGen)
complex neurodevelopmental disorder · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

2 total gene-disease associations curated

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?
0.55LOEUF
pLI 0.000
Z-score 4.61
OE 0.40 (0.290.55)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
-0.29Z-score
OE missense 1.03 (0.971.09)
772 obs / 749.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.40 (0.290.55)
00.351.4
Missense OE?1.03 (0.971.09)
00.61.4
Synonymous OE?1.12
01.21.6
LoF obs/exp: 27 / 68.0Missense obs/exp: 772 / 749.5Syn Z: -1.60
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCNTNAP2-related cortical dysplasia-focal epilepsy syndromeLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6936th %ile
GOF
0.5953th %ile
LOF
0.2874th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CNTNAP2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.