This gene encodes a Ras GTPase activating protein that is a member of the N-methyl-D-aspartate receptor complex. The N-terminal domain of the protein contains a Ras-GAP domain, a pleckstrin homology domain, and a C2 domain that may be involved in binding of calcium and phospholipids. The C-terminal domain consists of a ten histidine repeat region, serine and tyrosine phosphorylation sites, and a T/SXV motif required for postsynaptic scaffold protein interaction. The encoded protein negatively regulates Ras, Rap and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor trafficking to the postsynaptic membrane to regulate synaptic plasticity and neuronal homeostasis. Allelic variants of this gene are associated with intellectual disability and autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
Transcription factors with Perturb-seq knockdown data for SYNGAP1. 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 = SYNGAP1 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 SYNGAP1, 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 |
|---|---|---|---|---|
| chr6:33,161,505–33,162,100 | 258.5 kb | Distal (>10kb) Multiome | 589 | |
| chr6:33,199,801–33,201,289 | 219.6 kb | Distal (>10kb) Multiome | 1049 | |
| chr6:33,204,263–33,205,422 | 215.6 kb | Distal (>10kb) Multiome | 762 | |
| chr6:33,208,069–33,208,990 | 211.7 kb | Distal (>10kb) Multiome | 858 | |
| chr6:33,248,132–33,249,983 | 172.0 kb | Distal (>10kb) Multiome | 961 | |
| chr6:33,271,370–33,272,508 | 148.3 kb | Distal (>10kb) Multiome | 1058 | |
| chr6:33,276,685–33,277,905 | 142.8 kb | Distal (>10kb) Multiome | 807 | |
| chr6:33,288,941–33,289,881 | 130.9 kb | Distal (>10kb) Multiome | 701 | |
| chr6:33,297,445–33,300,232 | 122.4 kb | Distal (>10kb) Multiome | 1095 | |
| chr6:33,312,436–33,314,207 | 107.4 kb | Distal (>10kb) Multiome | 795 | |
| chr6:33,317,189–33,318,504 | 102.3 kb | Distal (>10kb) Multiome | 649 | |
| chr6:33,322,636–33,323,832 | 97.1 kb | Distal (>10kb) Multiome | 941 | |
| chr6:33,346,609–33,347,126 | 73.5 kb | Distal (>10kb) Multiome | 37 | |
| chr6:33,390,888–33,392,247 | 28.6 kb | Distal (>10kb) Multiome | 993 | |
| chr6:33,409,936–33,411,502 | 9.8 kb | Proximal (<10kb) Multiome | 977 | |
| chr6:33,417,606–33,419,249 | 2.0 kb | Proximal (<10kb) Multiome | 973 | |
| chr6:33,419,793–33,420,532 | 49 bp | At TSS Multiome | 162 | |
| chr6:33,425,590–33,426,362 | 5.6 kb | Proximal (<10kb) Multiome | 665 | |
| chr6:33,427,589–33,428,129 | 7.7 kb | Proximal (<10kb) | 296 | |
| chr6:33,431,024–33,432,096 | 10.9 kb | Distal (>10kb) Multiome | 337 | |
| chr6:33,454,074–33,454,852 | 34.2 kb | Distal (>10kb) Multiome | 906 | |
| chr6:33,547,185–33,548,324 | 127.5 kb | Distal (>10kb) Multiome | 155 | |
| chr6:33,570,899–33,571,638 | 151.1 kb | Distal (>10kb) Multiome | 755 | |
| chr6:33,579,935–33,580,700 | 160.0 kb | Distal (>10kb) Multiome | 639 | |
| chr6:33,592,764–33,593,449 | 172.7 kb | Distal (>10kb) Multiome | 224 | |
| chr6:33,620,828–33,622,474 | 201.8 kb | Distal (>10kb) Multiome | 594 | |
| chr6:33,632,607–33,634,721 | 212.4 kb | Distal (>10kb) Multiome | 600 | |
| chr6:33,711,017–33,712,173 | 291.4 kb | Distal (>10kb) Multiome | 943 |
Genomic view of the SYNGAP1 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.