This gene encodes a tethering protein and a core subunit of the homotypic fusion and protein sorting (HOPS) complex. The HOPS complex and a second endosomal tethering complex called the class C core vacuole/endosome tethering (CORVET) complex, perform diverse functions in endocytosis including membrane tethering, RabGTPase interaction, activation and proofreading of synaptic-soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) assembly to drive membrane fusion, and endosome-to-cytoskeleton attachment. The HOPS complex controls endosome maturation as well as endosome traffic to the lysosome. This complex is essential for vacuolar fusion and is required for adaptor protein complex 3-dependent transport from the golgi to the vacuole. The encoded protein belongs to the Sec1/Munc18 (SM) family of SNARE-mediated membrane fusion regulators. Naturally occurring mutations in this gene are associated with a novel mucopolysaccharidosis-like disease. [provided by RefSeq, Apr 2017]
Transcription factors with Perturb-seq knockdown data for VPS33A. 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 = VPS33A 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 VPS33A, 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 |
|---|---|---|---|---|
| chr12:122,021,348–122,022,698 | 244.5 kb | Distal (>10kb) Multiome | 537 | |
| chr12:122,063,787–122,064,537 | 202.2 kb | Distal (>10kb) Multiome | 742 | |
| chr12:122,064,878–122,065,312 | 201.2 kb | Distal (>10kb) Multiome | 355 | |
| chr12:122,078,081–122,079,394 | 187.8 kb | Distal (>10kb) Multiome | 952 | |
| chr12:122,097,641–122,098,611 | 168.4 kb | Distal (>10kb) Multiome | 462 | |
| chr12:122,155,564–122,156,340 | 110.5 kb | Distal (>10kb) Multiome | 197 | |
| chr12:122,182,856–122,183,527 | 83.2 kb | Distal (>10kb) Multiome | 228 | |
| chr12:122,203,186–122,204,669 | 62.8 kb | Distal (>10kb) Multiome | 500 | |
| chr12:122,225,485–122,227,116 | 40.2 kb | Distal (>10kb) Multiome | 1019 | |
| chr12:122,265,933–122,267,109 | 117 bp | At TSS Multiome | 1060 | |
| chr12:122,421,844–122,422,754 | 156.0 kb | Distal (>10kb) Multiome | 685 | |
| chr12:122,500,206–122,501,493 | 234.6 kb | Distal (>10kb) Multiome | 955 | |
| chr12:122,526,435–122,527,753 | 260.6 kb | Distal (>10kb) Multiome | 956 |
Genomic view of the VPS33A 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.