This gene encodes a type I transmembrane glycoprotein that is an integral component of the multimeric gamma-secretase complex. The encoded protein cleaves integral membrane proteins, including Notch receptors and beta-amyloid precursor protein, and may be a stabilizing cofactor required for gamma-secretase complex assembly. The cleavage of beta-amyloid precursor protein yields amyloid beta peptide, the main component of the neuritic plaque and the hallmark lesion in the brains of patients with Alzheimer's disease; however, the nature of the encoded protein's role in Alzheimer's disease is not known for certain. Mutations in this gene are associated with familial acne inversa. A pseudogene of this gene is present on chromosome 21. Alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Feb 2014]
Transcription factors with Perturb-seq knockdown data for NCSTN. 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 = NCSTN 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 NCSTN, 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 |
|---|---|---|---|---|
| chr1:160,046,290–160,047,082 | 296.7 kb | Distal (>10kb) Multiome | 540 | |
| chr1:160,069,829–160,071,049 | 272.9 kb | Distal (>10kb) Multiome | 419 | |
| chr1:160,083,809–160,084,575 | 259.2 kb | Distal (>10kb) Multiome | 327 | |
| chr1:160,095,707–160,096,231 | 247.4 kb | Distal (>10kb) Multiome | 79 | |
| chr1:160,097,214–160,099,572 | 244.5 kb | Distal (>10kb) Multiome | 659 | |
| chr1:160,100,845–160,101,543 | 242.2 kb | Distal (>10kb) Multiome | 530 | |
| chr1:160,169,049–160,170,141 | 173.7 kb | Distal (>10kb) Multiome | 330 | |
| chr1:160,192,913–160,193,769 | 150.1 kb | Distal (>10kb) Multiome | 551 | |
| chr1:160,204,860–160,206,035 | 137.9 kb | Distal (>10kb) Multiome | 637 | |
| chr1:160,261,515–160,263,143 | 80.9 kb | Distal (>10kb) Multiome | 992 | |
| chr1:160,284,609–160,285,332 | 58.2 kb | Distal (>10kb) Multiome | 638 | |
| chr1:160,342,945–160,343,700 | 70 bp | At TSS Multiome | 868 | |
| chr1:160,399,764–160,401,441 | 57.0 kb | Distal (>10kb) Multiome | 590 | |
| chr1:160,539,925–160,540,644 | 196.9 kb | Distal (>10kb) Multiome | 479 | |
| chr1:160,619,659–160,620,443 | 276.7 kb | Distal (>10kb) Multiome | 187 |
Genomic view of the NCSTN 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.