This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
Transcription factors with Perturb-seq knockdown data for SPTLC1. 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 = SPTLC1 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 SPTLC1, 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 |
|---|---|---|---|---|
| chr9:91,886,525–91,887,118 | 228.6 kb | Distal (>10kb) Multiome | 127 | |
| chr9:91,899,016–91,900,833 | 215.1 kb | Distal (>10kb) Multiome | 545 | |
| chr9:91,907,557–91,908,633 | 207.3 kb | Distal (>10kb) Multiome | 400 | |
| chr9:91,939,791–91,941,167 | 175.2 kb | Distal (>10kb) Multiome | 168 | |
| chr9:91,948,140–91,949,358 | 166.6 kb | Distal (>10kb) Multiome | 449 | |
| chr9:91,949,582–91,950,808 | 165.1 kb | Distal (>10kb) Multiome | 453 | |
| chr9:91,994,245–91,995,301 | 120.7 kb | Distal (>10kb) Multiome | 243 | |
| chr9:92,114,946–92,115,785 | 4 bp | At TSS Multiome | 807 | |
| chr9:92,133,789–92,134,516 | 18.7 kb | Distal (>10kb) Multiome | 252 | |
| chr9:92,137,993–92,138,553 | 22.9 kb | Distal (>10kb) Multiome | 237 | |
| chr9:92,140,183–92,140,786 | 25.0 kb | Distal (>10kb) Multiome | 418 | |
| chr9:92,293,467–92,294,114 | 178.4 kb | Distal (>10kb) Multiome | 966 | |
| chr9:92,325,052–92,326,254 | 210.3 kb | Distal (>10kb) Multiome | 999 |
Genomic view of the SPTLC1 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.