This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]
Transcription factors with Perturb-seq knockdown data for NLGN3. 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 = NLGN3 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 NLGN3, 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 |
|---|---|---|---|---|
| chrX:70,930,282–70,931,432 | 213.8 kb | Distal (>10kb) Multiome | 148 | |
| chrX:71,053,141–71,053,663 | 91.4 kb | Distal (>10kb) Multiome | 90 | |
| chrX:71,067,771–71,068,927 | 76.3 kb | Distal (>10kb) Multiome | 846 | |
| chrX:71,095,671–71,096,651 | 48.8 kb | Distal (>10kb) Multiome | 450 | |
| chrX:71,103,137–71,103,903 | 41.3 kb | Distal (>10kb) Multiome | 375 | |
| chrX:71,181,957–71,182,785 | 37.3 kb | Distal (>10kb) Multiome | 615 | |
| chrX:71,253,749–71,255,053 | 109.3 kb | Distal (>10kb) Multiome | 607 | |
| chrX:71,283,100–71,284,134 | 138.7 kb | Distal (>10kb) Multiome | 633 | |
| chrX:71,365,705–71,366,636 | 221.3 kb | Distal (>10kb) Multiome | 578 |
Genomic view of the NLGN3 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.