The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene have been associated with long QT syndrome type 3 (LQT3), atrial fibrillation, cardiomyopathy, and Brugada syndrome 1, all autosomal dominant cardiac diseases. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2022]
Transcription factors with Perturb-seq knockdown data for SCN5A. 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 = SCN5A 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 SCN5A, 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 |
|---|---|---|---|---|
| chr3:38,028,710–38,030,184 | 620.0 kb | Distal (>10kb) Multiome HiCAR | 378 | |
| chr3:38,039,093–38,039,944 | 610.3 kb | Distal (>10kb) Multiome HiCAR | 357 | |
| chr3:38,452,852–38,456,220 | 196.0 kb | Distal (>10kb) Multiome | 971 | |
| chr3:38,495,771–38,496,881 | 153.3 kb | Distal (>10kb) Multiome HiCAR | 764 | |
| chr3:38,580,074–38,580,574 | 69.3 kb | Distal (>10kb) Multiome | 109 | |
| chr3:38,601,761–38,602,426 | 47.6 kb | Distal (>10kb) Multiome | 48 | |
| chr3:38,640,708–38,641,494 | 8.6 kb | Proximal (<10kb) Multiome | 182 | |
| chr3:38,649,012–38,650,212 | 5 bp | At TSS Multiome | 437 | |
| chr3:38,651,034–38,651,663 | 1.7 kb | Proximal (<10kb) Multiome | 351 | |
| chr3:38,655,779–38,656,034 | 6.1 kb | Proximal (<10kb) | 125 | |
| chr3:38,658,747–38,659,115 | 9.1 kb | Proximal (<10kb) | 28 | |
| chr3:38,669,439–38,670,183 | 20.1 kb | Distal (>10kb) Multiome | 85 |
Genomic view of the SCN5A 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.