This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]
Transcription factors with Perturb-seq knockdown data for NPHP3. 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 = NPHP3 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 NPHP3, 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 |
|---|---|---|---|---|
| chr3:132,644,811–132,645,749 | 77.1 kb | Distal (>10kb) Multiome | 191 | |
| chr3:132,659,118–132,660,967 | 62.0 kb | Distal (>10kb) Multiome | 872 | |
| chr3:132,721,513–132,723,554 | 326 bp | At TSS Multiome | 756 | |
| chr3:132,726,408–132,726,622 | 4.0 kb | Proximal (<10kb) | 74 | |
| chr3:132,730,992–132,731,388 | 8.6 kb | Proximal (<10kb) | 69 | |
| chr3:133,037,636–133,039,245 | 315.9 kb | Distal (>10kb) Multiome HiCAR | 446 | |
| chr3:133,327,859–133,328,993 | 606.2 kb | Distal (>10kb) Multiome HiCAR | 143 | |
| chr3:133,384,300–133,384,776 | 662.2 kb | Distal (>10kb) Multiome HiCAR | 247 | |
| chr3:133,661,440–133,662,508 | 939.5 kb | Distal (>10kb) Multiome HiCAR | 728 | |
| chr3:133,927,020–133,928,082 | 1205.3 kb | Distal (>10kb) Multiome HiCAR | 363 |
Genomic view of the NPHP3 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.