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]
Transcription factors with Perturb-seq knockdown data for CNTNAP2. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = CNTNAP2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CNTNAP2, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr7:148,079,210–148,080,034 | 260.0 kb | Distal (>10kb) Multiome | 57 | |
| chr7:148,304,433–148,305,165 | 34.8 kb | Distal (>10kb) Multiome | 166 | |
| chr7:148,316,984–148,319,215 | 21.3 kb | Distal (>10kb) Multiome | 362 | |
| chr7:148,334,522–148,335,777 | 4.2 kb | Proximal (<10kb) Multiome | 360 | |
| chr7:148,336,864–148,337,869 | 1.6 kb | Proximal (<10kb) | 47 | |
| chr7:148,338,845–148,340,078 | 27 bp | At TSS Multiome | 612 | |
| chr7:148,340,176–148,341,211 | 716 bp | At TSS | 113 | |
| chr7:148,342,704–148,343,322 | 3.2 kb | Proximal (<10kb) | 20 | |
| chr7:148,344,506–148,344,751 | 5.0 kb | Proximal (<10kb) | 17 | |
| chr7:148,344,881–148,345,250 | 5.4 kb | Proximal (<10kb) | 23 | |
| chr7:148,367,810–148,368,682 | 28.8 kb | Distal (>10kb) Multiome | 103 | |
| chr7:148,501,343–148,502,380 | 162.5 kb | Distal (>10kb) Multiome | 188 |
Genomic view of the CNTNAP2 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.