This gene encodes a phospholipase that deacetylates intracellular phosphatidylcholine to produce glycerophosphocholine. It is thought to function in neurite outgrowth and process elongation during neuronal differentiation. The protein is anchored to the cytoplasmic face of the endoplasmic reticulum in both neurons and non-neuronal cells. Mutations in this gene result in autosomal recessive spastic paraplegia, and the protein is the target for neurodegeneration induced by organophosphorus compounds and chemical warfare agents. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
Transcription factors with Perturb-seq knockdown data for PNPLA6. 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 = PNPLA6 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 PNPLA6, 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 |
|---|---|---|---|---|
| chr19:7,293,755–7,294,636 | 239.7 kb | Distal (>10kb) Multiome | 668 | |
| chr19:7,394,774–7,395,629 | 139.1 kb | Distal (>10kb) Multiome | 601 | |
| chr19:7,482,657–7,483,489 | 51.0 kb | Distal (>10kb) Multiome | 201 | |
| chr19:7,488,712–7,489,463 | 45.1 kb | Distal (>10kb) Multiome | 542 | |
| chr19:7,500,843–7,501,401 | 33.0 kb | Distal (>10kb) Multiome | 556 | |
| chr19:7,505,850–7,507,270 | 27.7 kb | Distal (>10kb) Multiome | 516 | |
| chr19:7,507,812–7,508,356 | 26.1 kb | Distal (>10kb) Multiome | 168 | |
| chr19:7,522,263–7,523,208 | 11.6 kb | Distal (>10kb) Multiome | 917 | |
| chr19:7,533,457–7,533,679 | 510 bp | At TSS | 131 | |
| chr19:7,533,976–7,536,472 | 167 bp | At TSS Multiome | 882 | |
| chr19:7,541,199–7,541,410 | 7.0 kb | Proximal (<10kb) | 91 | |
| chr19:7,550,673–7,551,762 | 17.2 kb | Distal (>10kb) Multiome | 377 | |
| chr19:7,554,651–7,555,821 | 21.1 kb | Distal (>10kb) Multiome | 224 | |
| chr19:7,595,485–7,596,417 | 61.6 kb | Distal (>10kb) Multiome | 405 | |
| chr19:7,629,285–7,629,891 | 95.5 kb | Distal (>10kb) Multiome | 650 | |
| chr19:7,636,753–7,637,571 | 102.9 kb | Distal (>10kb) Multiome | 689 | |
| chr19:7,680,480–7,681,546 | 146.6 kb | Distal (>10kb) Multiome | 679 | |
| chr19:7,829,238–7,830,666 | 295.7 kb | Distal (>10kb) Multiome | 621 |
Genomic view of the PNPLA6 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.