This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Transcription factors with Perturb-seq knockdown data for NPHP4. 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 = NPHP4 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 NPHP4, 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 |
|---|---|---|---|---|
| chr1:5,771,235–5,771,777 | 221.0 kb | Distal (>10kb) Multiome | 90 | |
| chr1:5,980,417–5,980,986 | 11.8 kb | Distal (>10kb) Multiome | 282 | |
| chr1:5,991,687–5,993,712 | 87 bp | At TSS Multiome | 829 | |
| chr1:6,127,538–6,128,516 | 135.5 kb | Distal (>10kb) Multiome | 300 | |
| chr1:6,148,503–6,149,108 | 156.4 kb | Distal (>10kb) Multiome | 254 | |
| chr1:6,199,148–6,200,364 | 207.2 kb | Distal (>10kb) Multiome | 992 | |
| chr1:6,204,893–6,206,690 | 212.8 kb | Distal (>10kb) Multiome | 913 | |
| chr1:6,208,737–6,209,635 | 216.9 kb | Distal (>10kb) Multiome | 362 | |
| chr1:6,235,160–6,236,710 | 243.6 kb | Distal (>10kb) Multiome | 673 | |
| chr1:6,241,773–6,242,771 | 249.8 kb | Distal (>10kb) Multiome | 241 | |
| chr1:6,244,532–6,247,144 | 253.6 kb | Distal (>10kb) Multiome | 1073 | |
| chr1:6,248,779–6,250,153 | 257.0 kb | Distal (>10kb) Multiome | 287 | |
| chr1:6,259,688–6,261,954 | 267.7 kb | Distal (>10kb) Multiome | 550 |
Genomic view of the NPHP4 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.