This gene encodes a transmembrane receptor of the patched gene family. The encoded protein may function as a tumor suppressor in the hedgehog signaling pathway. Alterations in this gene have been associated with nevoid basal cell carcinoma syndrome, basal cell carcinoma, medulloblastoma, and susceptibility to congenital macrostomia. Alternatively spliced transcript variants have been described.[provided by RefSeq, Oct 2009]
Transcription factors with Perturb-seq knockdown data for PTCH2. 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 = PTCH2 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 PTCH2, 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 |
|---|---|---|---|---|
| chr1:44,542,481–44,544,064 | 300.0 kb | Distal (>10kb) Multiome | 277 | |
| chr1:44,631,466–44,632,956 | 211.2 kb | Distal (>10kb) Multiome | 928 | |
| chr1:44,673,636–44,675,002 | 168.8 kb | Distal (>10kb) Multiome | 750 | |
| chr1:44,720,791–44,722,329 | 121.5 kb | Distal (>10kb) Multiome | 1059 | |
| chr1:44,730,465–44,731,848 | 112.2 kb | Distal (>10kb) Multiome | 1164 | |
| chr1:44,739,368–44,740,265 | 103.5 kb | Distal (>10kb) Multiome | 828 | |
| chr1:44,775,008–44,776,007 | 67.7 kb | Distal (>10kb) Multiome | 1041 | |
| chr1:44,783,907–44,784,940 | 58.8 kb | Distal (>10kb) Multiome | 497 | |
| chr1:44,786,163–44,786,815 | 56.9 kb | Distal (>10kb) Multiome | 616 | |
| chr1:44,799,477–44,801,039 | 43.2 kb | Distal (>10kb) Multiome | 1017 | |
| chr1:44,807,115–44,808,920 | 34.7 kb | Distal (>10kb) Multiome | 987 | |
| chr1:44,812,965–44,814,105 | 29.5 kb | Distal (>10kb) Multiome | 349 | |
| chr1:44,818,937–44,820,693 | 23.3 kb | Distal (>10kb) Multiome | 1101 | |
| chr1:44,835,944–44,836,184 | 7.1 kb | Proximal (<10kb) | 329 | |
| chr1:44,842,822–44,843,695 | 75 bp | At TSS Multiome | 539 | |
| chr1:44,986,311–44,986,894 | 143.4 kb | Distal (>10kb) Multiome | 979 | |
| chr1:45,010,856–45,013,180 | 169.0 kb | Distal (>10kb) Multiome HiCAR | 909 | |
| chr1:45,303,203–45,304,881 | 460.6 kb | Distal (>10kb) Multiome HiCAR | 1034 |
Genomic view of the PTCH2 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.