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]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

{Autism susceptibility 15}MIM #612100
Pitt-Hopkins like syndrome 1MIM #610042
AR
UniProtAutism 15
UniProtPitt-Hopkins-like syndrome 1

Clinical highlights

Gene-disease validity (ClinGen)
complex neurodevelopmental disorder · ARDefinitivesufficient evidence for diagnostic panels2 gene-disease associations curated in total
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
85
Pubs (1 yr)
P/LP submissions
P/LP missense
0.55
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — CNTNAP2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

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

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.