The M channel is a slowly activating and deactivating potassium channel that plays a critical role in the regulation of neuronal excitability. The M channel is formed by the association of the protein encoded by this gene and a related protein encoded by the KCNQ3 gene, both integral membrane proteins. M channel currents are inhibited by M1 muscarinic acetylcholine receptors and activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 1 (BFNC), also known as epilepsy, benign neonatal type 1 (EBN1). At least five transcript variants encoding five different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for KCNQ2. 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 = KCNQ2 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 KCNQ2, 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 |
|---|---|---|---|---|
| chr20:63,178,716–63,179,743 | 293.4 kb | Distal (>10kb) Multiome | 386 | |
| chr20:63,215,706–63,216,790 | 256.3 kb | Distal (>10kb) Multiome | 965 | |
| chr20:63,272,274–63,273,137 | 199.8 kb | Distal (>10kb) Multiome | 736 | |
| chr20:63,409,631–63,410,124 | 62.7 kb | Distal (>10kb) Multiome | 60 | |
| chr20:63,471,533–63,472,788 | 61 bp | At TSS Multiome | 219 | |
| chr20:63,488,166–63,488,632 | 15.9 kb | Distal (>10kb) Multiome | 127 | |
| chr20:63,498,850–63,499,391 | 26.7 kb | Distal (>10kb) Multiome | 232 | |
| chr20:63,519,657–63,521,677 | 48.0 kb | Distal (>10kb) Multiome | 712 | |
| chr20:63,537,759–63,538,455 | 65.5 kb | Distal (>10kb) Multiome | 823 | |
| chr20:63,552,551–63,554,733 | 81.0 kb | Distal (>10kb) Multiome | 544 | |
| chr20:63,573,969–63,574,596 | 101.7 kb | Distal (>10kb) Multiome | 551 | |
| chr20:63,626,480–63,627,647 | 154.4 kb | Distal (>10kb) Multiome | 982 | |
| chr20:63,641,266–63,642,913 | 169.5 kb | Distal (>10kb) Multiome | 691 | |
| chr20:63,652,233–63,654,166 | 181.0 kb | Distal (>10kb) Multiome | 1011 | |
| chr20:63,657,813–63,658,939 | 185.9 kb | Distal (>10kb) Multiome | 1055 | |
| chr20:63,696,254–63,697,070 | 224.0 kb | Distal (>10kb) Multiome | 458 | |
| chr20:63,707,489–63,708,488 | 235.4 kb | Distal (>10kb) Multiome | 1008 | |
| chr20:63,737,573–63,741,470 | 267.1 kb | Distal (>10kb) Multiome | 1098 |
Genomic view of the KCNQ2 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.