This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]
Transcription factors with Perturb-seq knockdown data for PHGDH. 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 = PHGDH 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 PHGDH, 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 |
|---|---|---|---|---|
| chr1:119,431,427–119,432,339 | 280.0 kb | Distal (>10kb) Multiome | 65 | |
| chr1:119,608,622–119,609,421 | 102.9 kb | Distal (>10kb) Multiome | 123 | |
| chr1:119,611,469–119,612,104 | 100.1 kb | Distal (>10kb) Multiome | 217 | |
| chr1:119,631,383–119,631,939 | 80.3 kb | Distal (>10kb) Multiome | 532 | |
| chr1:119,647,047–119,648,868 | 63.7 kb | Distal (>10kb) Multiome | 849 | |
| chr1:119,651,267–119,651,393 | 2.9 kb | Proximal (<10kb) | 14 | |
| chr1:119,675,324–119,675,863 | 36.4 kb | Distal (>10kb) Multiome | 314 | |
| chr1:119,711,713–119,714,041 | 810 bp | At TSS Multiome | 763 | |
| chr1:119,920,154–119,920,860 | 208.6 kb | Distal (>10kb) Multiome | 105 |
Genomic view of the PHGDH 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.