This gene encodes a glycosylphosphatidylinositol (GPI)-specific phospholipase that primarily localizes to the Golgi apparatus. This ubiquitously expressed gene is predicted to encode a seven-transmembrane protein that removes unsaturated fatty acids from the sn-2 position of GPI. The remodeling of the constituent fatty acids on GPI is thought to be important for the proper association between GPI-anchored proteins and lipid rafts. The tethering of proteins to plasma membranes via posttranslational GPI-anchoring is thought to play a role in protein sorting and trafficking. Mutations in this gene cause an autosomal recessive form of neurologic hyperphosphatasia with cognitive disability (HPMRS4). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]
Transcription factors with Perturb-seq knockdown data for PGAP3. 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 = PGAP3 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 PGAP3, 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 |
|---|---|---|---|---|
| chr17:39,400,997–39,402,766 | 285.4 kb | Distal (>10kb) Multiome | 898 | |
| chr17:39,450,919–39,451,504 | 236.7 kb | Distal (>10kb) Multiome | 722 | |
| chr17:39,461,043–39,462,217 | 226.5 kb | Distal (>10kb) Multiome | 1026 | |
| chr17:39,573,453–39,574,243 | 114.2 kb | Distal (>10kb) Multiome | 520 | |
| chr17:39,636,769–39,637,600 | 50.9 kb | Distal (>10kb) Multiome | 853 | |
| chr17:39,652,588–39,653,348 | 35.0 kb | Distal (>10kb) Multiome | 263 | |
| chr17:39,668,234–39,668,690 | 19.5 kb | Distal (>10kb) Multiome | 706 | |
| chr17:39,687,710–39,688,437 | 8 bp | At TSS Multiome | 800 | |
| chr17:39,695,905–39,696,636 | 8.3 kb | Proximal (<10kb) Multiome | 499 | |
| chr17:39,699,516–39,700,527 | 11.9 kb | Distal (>10kb) Multiome | 528 | |
| chr17:39,730,039–39,730,906 | 42.5 kb | Distal (>10kb) Multiome | 886 | |
| chr17:39,739,067–39,739,915 | 51.5 kb | Distal (>10kb) Multiome | 648 | |
| chr17:39,740,384–39,740,910 | 52.7 kb | Distal (>10kb) Multiome | 513 | |
| chr17:39,753,811–39,754,996 | 66.4 kb | Distal (>10kb) Multiome | 1000 | |
| chr17:39,926,716–39,928,343 | 239.7 kb | Distal (>10kb) Multiome | 942 | |
| chr17:39,952,356–39,953,923 | 265.1 kb | Distal (>10kb) Multiome | 598 | |
| chr17:39,979,964–39,981,234 | 292.6 kb | Distal (>10kb) Multiome | 1148 |
Genomic view of the PGAP3 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.