Details for: SYNGAP1

Gene ID: 8831

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: SYNGAP1

Ensembl ID: ENSG00000197283

Description: synaptic Ras GTPase activating protein 1

Cell Significance Landscape

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 7.75
    rCSI 13.69%
    PRS 76.73
  • sst GABAergic cortical interneuron CL4023017
    CSI 4.87
    rCSI 6.28%
    PRS 78.36
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 3.94
    rCSI 14.18%
    PRS 75.23
  • mature astrocyte CL0002627
    CSI 3.24
    rCSI 13.77%
    PRS 83.28
  • melanocyte CL0000148
    CSI 3.11
    rCSI 2.3%
    PRS 86.63
  • interneuron CL0000099
    CSI 3.03
    rCSI 6.09%
    PRS 84.12
  • choroid plexus epithelial cell CL0000706
    CSI 2.89
    rCSI 4.73%
    PRS 83.21
  • early lymphoid progenitor CL0000936
    CSI 2.8
    rCSI 2.46%
    PRS 93.19
  • multi-ciliated epithelial cell CL0005012
    CSI 2.75
    rCSI 2.74%
    PRS 84.76
  • central memory CD8-positive, alpha-beta T cell CL0000907
    CSI 2.63
    rCSI 1.77%
    PRS 97.58
  • hepatic stellate cell CL0000632
    CSI 2.59
    rCSI 9.72%
    PRS 85.56
  • ciliated cell CL0000064
    CSI 2.51
    rCSI 4.07%
    PRS 84.58
  • cerebellar granule cell CL0001031
    CSI 2.35
    rCSI 3.46%
    PRS 85.06
  • retina horizontal cell CL0000745
    CSI 2.29
    rCSI 3.49%
    PRS 87.03
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.28
    rCSI 2.84%
    PRS 75.1
  • vascular leptomeningeal cell CL4023051
    CSI 2.2
    rCSI 3.86%
    PRS 86.5
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 2.19
    rCSI 2.24%
    PRS 95.02
  • chondrocyte CL0000138
    CSI 2.15
    rCSI 3.42%
    PRS 85.53
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.11
    rCSI 2.52%
    PRS 77.35
  • enteric smooth muscle cell CL0002504
    CSI 2.1
    rCSI 3%
    PRS 90.38
  • ependymal cell CL0000065
    CSI 2.09
    rCSI 4.24%
    PRS 72.76
  • adventitial cell CL0002503
    CSI 2.06
    rCSI 4.92%
    PRS 92.44
  • mesodermal cell CL0000222
    CSI 2.04
    rCSI 2.45%
    PRS 89.07
  • cerebral cortex neuron CL0010012
    CSI 1.94
    rCSI 7.9%
    PRS 83.14
  • ciliated epithelial cell CL0000067
    CSI 1.91
    rCSI 1.68%
    PRS 81.68
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 1.91
    rCSI 2.2%
    PRS 83.17
  • amacrine cell CL0000561
    CSI 1.83
    rCSI 5.32%
    PRS 81.82
  • inhibitory interneuron CL0000498
    CSI 1.81
    rCSI 4.17%
    PRS 81.01
  • lung ciliated cell CL1000271
    CSI 1.79
    rCSI 2.07%
    PRS 84.77
  • lung pericyte CL0009089
    CSI 1.61
    rCSI 4.25%
    PRS 93.9
  • peripheral nervous system neuron CL2000032
    CSI 1.58
    rCSI 2.16%
    PRS 83.97
  • direct pathway medium spiny neuron CL4023026
    CSI 1.48
    rCSI 35.32%
    PRS 74.96
  • indirect pathway medium spiny neuron CL4023029
    CSI 1.45
    rCSI 34.97%
    PRS 75.11
  • L6b glutamatergic cortical neuron CL4023038
    CSI 1.44
    rCSI 4.51%
    PRS 78.64
  • deuterosomal cell CL4033044
    CSI 1.23
    rCSI 4.17%
    PRS 85.22
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 1.19
    rCSI 2.84%
    PRS 79.85
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.18
    rCSI 2.87%
    PRS 75.04
  • astrocyte of the cerebral cortex CL0002605
    CSI 1.16
    rCSI 2.61%
    PRS 77.73
  • sncg GABAergic cortical interneuron CL4023015
    CSI 1.12
    rCSI 1.81%
    PRS 78.22
  • L5/6 near-projecting glutamatergic neuron CL4030067
    CSI 1.08
    rCSI 3.55%
    PRS 78.78
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 1.03
    rCSI 3.89%
    PRS 77.48
  • blood vessel smooth muscle cell CL0019018
    CSI 1
    rCSI 8.11%
    PRS 87.44
  • retinal ganglion cell CL0000740
    CSI 0.97
    rCSI 2.15%
    PRS 79.7
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 0.94
    rCSI 2.15%
    PRS 83.49
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.93
    rCSI 5.47%
    PRS 77.72
  • dopaminergic neuron CL0000700
    CSI 0.93
    rCSI 5.25%
    PRS 79.49
  • central nervous system neuron CL2000029
    CSI 0.67
    rCSI 4.96%
    PRS 81.77
  • medium spiny neuron CL1001474
    CSI 0.38
    rCSI 3.23%
    PRS 82.19

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.

Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

Loading network (please wait)...

Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [SYNGAP1](/details-gene/8831) encodes the Synaptic Ras GTPase Activating Protein 1, a critical regulator of synaptic plasticity and neuronal development. This protein is predominantly localized to the postsynaptic density of glutamatergic synapses, where it negatively regulates Ras-GTP signaling and the downstream MAPK/ERK pathway. **Overall**, expression data reveals that [SYNGAP1](/details-gene/8831) is a highly significant gene in various neuronal subtypes, particularly inhibitory interneurons such as the `[caudal ganglionic eminence derived cortical interneuron](/details-cell/CL4023064)`. Its essential role in brain function is underscored by numerous studies linking heterozygous loss-of-function mutations to a spectrum of neurodevelopmental disorders, including intellectual disability, autism spectrum disorder, and epilepsy [Link](https://doi.org/10.1056/nejmoa0805392), [Link](https://doi.org/10.1002/humu.22248). ## Cellular Roles and Expression Landscape The expression profile of [SYNGAP1](/details-gene/8831) firmly establishes its central role within the nervous system. The gene exhibits its highest significance in specific inhibitory neuronal populations, including `[caudal ganglionic eminence derived cortical interneuron](/details-cell/CL4023064)` (CSI: 7.75) and `[sst GABAergic cortical interneuron](/details-cell/CL4023017)` (CSI: 4.87), suggesting a specialized function in regulating cortical inhibitory circuits. Its importance extends to excitatory neurons, as evidenced by its high significance in `[L5 extratelencephalic projecting glutamatergic cortical neuron](/details-cell/CL4023041)` (CSI: 3.94) and `[cerebellar granule cell](/details-cell/CL0001031)` (CSI: 2.35). Beyond neurons, [SYNGAP1](/details-gene/8831) also shows notable significance in glial cells like the `[mature astrocyte](/details-cell/CL0002627)` (CSI: 3.24) and specialized epithelial cells such as the `[choroid plexus epithelial cell](/details-cell/CL0000706)` (CSI: 2.89). This suggests its functions may not be exclusively restricted to the synapse but could also involve neuron-glia interactions or cerebrospinal fluid homeostasis. Minor but significant expression is also detected in unexpected cell types, including `[melanocyte](/details-cell/CL0000148)` and `[central memory CD8-positive, alpha-beta T cell](/details-cell/CL0000907)`, hinting at broader, though less understood, roles outside the central nervous system. ## Pathways and Molecular Function Functionally, [SYNGAP1](/details-gene/8831) is a key modulator of intracellular signaling cascades. As a GTPase-activating protein, its primary molecular function is to stimulate the hydrolysis of GTP bound to Ras-family proteins, thereby inactivating them `[GO:0005096]`. This activity places it as a crucial negative regulator of `[Ras protein signal transduction](/details-ontology/GO:0007265)` and downstream pathways such as the `[Raf/map kinase cascade](/details-ontology/R-HSA-5673001)`. This regulatory role is fundamental to its biological functions in `[Regulation of synaptic plasticity](/details-ontology/GO:0048167)` and `[Dendrite development](/details-ontology/GO:0016358)`. By controlling MAPK signaling at the synapse, [SYNGAP1](/details-gene/8831) influences NMDA receptor-dependent processes that are essential for learning and memory [Link](https://doi.org/10.1016/j.neuron.2004.08.003). Its localization to the `[Postsynaptic density](/details-ontology/GO:0014069)` positions it perfectly to integrate signals from neurotransmitter receptors and modulate the structural and functional changes that underpin long-term synaptic potentiation and depression. ## Research Directions The established role of [SYNGAP1](/details-gene/8831) haploinsufficiency in causing severe neurodevelopmental disorders provides a clear direction for future research. Understanding how the loss of one functional copy of the gene disrupts specific neural circuits is a primary goal. The high significance of [SYNGAP1](/details-gene/8831) in distinct interneuron subtypes suggests that deficits in cortical inhibition may be a core pathogenic mechanism. Based on the available data, several testable hypotheses can be proposed: 1. Haploinsufficiency of [SYNGAP1](/details-gene/8831) disproportionately impairs the maturation, connectivity, or function of specific cortical interneurons, such as Sst- and Pvalb-positive cells, leading to an excitatory/inhibitory imbalance that underlies the seizure susceptibility observed in patients [Link](https://doi.org/10.1038/ng.2646). 2. The significant expression of [SYNGAP1](/details-gene/8831) in `[mature astrocyte](/details-cell/CL0002627)` indicates a non-cell-autonomous role. Astrocytic [SYNGAP1](/details-gene/8831) may regulate synapse formation or elimination, and its reduction could contribute to the synaptic deficits observed in related disorders. A key experiment to test the first hypothesis would involve the use of patient-derived induced pluripotent stem cells (iPSCs) with a heterozygous [SYNGAP1](/details-gene/8831) mutation. These iPSCs could be differentiated into cortical organoids. Subsequent single-cell RNA sequencing and electrophysiological analysis (e.g., patch-clamp) on specific neuronal subtypes within the organoids would allow for a direct assessment of whether inhibitory interneuron development and function are more severely compromised compared to their excitatory counterparts. Given that SYNGAP1-related disorders are caused by haploinsufficiency, the therapeutic goal would be to restore protein function, representing a strategy of **activation or replacement** rather than inhibition. Potential therapeutic avenues include AAV-based gene therapy to deliver a functional copy of the [SYNGAP1](/details-gene/8831) gene or the development of small-molecule drugs that enhance the activity or stability of the protein produced from the remaining healthy allele. The widespread expression in the brain presents a significant delivery challenge, but its critical role makes it a high-priority target for novel neurodevelopmental therapeutics.

Genular Protein ID: 1849853993

Symbol: SYGP1_HUMAN

Name: Ras/Rap GTPase-activating protein SynGAP

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 11572484

Title: Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins.

PubMed ID: 11572484

DOI: 10.1093/dnares/8.4.179

PubMed ID: 14574404

Title: The DNA sequence and analysis of human chromosome 6.

PubMed ID: 14574404

DOI: 10.1038/nature02055

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 15312654

Title: SynGAP-MUPP1-CaMKII synaptic complexes regulate p38 MAP kinase activity and NMDA receptor-dependent synaptic AMPA receptor potentiation.

PubMed ID: 15312654

DOI: 10.1016/j.neuron.2004.08.003

PubMed ID: 19196676

Title: Mutations in SYNGAP1 in autosomal nonsyndromic mental retardation.

PubMed ID: 19196676

DOI: 10.1056/nejmoa0805392

PubMed ID: 21076407

Title: A de novo paradigm for mental retardation.

PubMed ID: 21076407

DOI: 10.1038/ng.712

PubMed ID: 21237447

Title: De novo SYNGAP1 mutations in nonsyndromic intellectual disability and autism.

PubMed ID: 21237447

DOI: 10.1016/j.biopsych.2010.11.015

PubMed ID: 23161826

Title: Mutations in SYNGAP1 cause intellectual disability, autism, and a specific form of epilepsy by inducing haploinsufficiency.

PubMed ID: 23161826

DOI: 10.1002/humu.22248

PubMed ID: 23708187

Title: Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1.

PubMed ID: 23708187

DOI: 10.1038/ng.2646

PubMed ID: 27864847

Title: Diagnostic targeted resequencing in 349 patients with drug-resistant pediatric epilepsies identifies causative mutations in 30 different genes.

PubMed ID: 27864847

DOI: 10.1002/humu.23149

Sequence Information:

  • Length: 1343
  • Mass: 148284
  • Checksum: D9ABE21054677AA0
  • Sequence:
  • MSRSRASIHR GSIPAMSYAP FRDVRGPSMH RTQYVHSPYD RPGWNPRFCI ISGNQLLMLD 
    EDEIHPLLIR DRRSESSRNK LLRRTVSVPV EGRPHGEHEY HLGRSRRKSV PGGKQYSMEG 
    APAAPFRPSQ GFLSRRLKSS IKRTKSQPKL DRTSSFRQIL PRFRSADHDR ARLMQSFKES 
    HSHESLLSPS SAAEALELNL DEDSIIKPVH SSILGQEFCF EVTTSSGTKC FACRSAAERD 
    KWIENLQRAV KPNKDNSRRV DNVLKLWIIE ARELPPKKRY YCELCLDDML YARTTSKPRS 
    ASGDTVFWGE HFEFNNLPAV RALRLHLYRD SDKKRKKDKA GYVGLVTVPV ATLAGRHFTE 
    QWYPVTLPTG SGGSGGMGSG GGGGSGGGSG GKGKGGCPAV RLKARYQTMS ILPMELYKEF 
    AEYVTNHYRM LCAVLEPALN VKGKEEVASA LVHILQSTGK AKDFLSDMAM SEVDRFMERE 
    HLIFRENTLA TKAIEEYMRL IGQKYLKDAI GEFIRALYES EENCEVDPIK CTASSLAEHQ 
    ANLRMCCELA LCKVVNSHCV FPRELKEVFA SWRLRCAERG REDIADRLIS ASLFLRFLCP 
    AIMSPSLFGL MQEYPDEQTS RTLTLIAKVI QNLANFSKFT SKEDFLGFMN EFLELEWGSM 
    QQFLYEISNL DTLTNSSSFE GYIDLGRELS TLHALLWEVL PQLSKEALLK LGPLPRLLND 
    ISTALRNPNI QRQPSRQSER PRPQPVVLRG PSAEMQGYMM RDLNSSIDLQ SFMARGLNSS 
    MDMARLPSPT KEKPPPPPPG GGKDLFYVSR PPLARSSPAY CTSSSDITEP EQKMLSVNKS 
    VSMLDLQGDG PGGRLNSSSV SNLAAVGDLL HSSQASLTAA LGLRPAPAGR LSQGSGSSIT 
    AAGMRLSQMG VTTDGVPAQQ LRIPLSFQNP LFHMAADGPG PPGGHGGGGG HGPPSSHHHH 
    HHHHHHRGGE PPGDTFAPFH GYSKSEDLSS GVPKPPAASI LHSHSYSDEF GPSGTDFTRR 
    QLSLQDNLQH MLSPPQITIG PQRPAPSGPG GGSGGGSGGG GGGQPPPLQR GKSQQLTVSA 
    AQKPRPSSGN LLQSPEPSYG PARPRQQSLS KEGSIGGSGG SGGGGGGGLK PSITKQHSQT 
    PSTLNPTMPA SERTVAWVSN MPHLSADIES AHIEREEYKL KEYSKSMDES RLDRVKEYEE 
    EIHSLKERLH MSNRKLEEYE RRLLSQEEQT SKILMQYQAR LEQSEKRLRQ QQAEKDSQIK 
    SIIGRLMLVE EELRRDHPAM AEPLPEPKKR LLDAQERQLP PLGPTNPRVT LAPPWNGLAP 
    PAPPPPPRLQ ITENGEFRNT ADH

Genular Protein ID: 890057780

Symbol: B7ZCA0_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 14574404

Title: The DNA sequence and analysis of human chromosome 6.

PubMed ID: 14574404

DOI: 10.1038/nature02055

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

Sequence Information:

  • Length: 1292
  • Mass: 142865
  • Checksum: 32B08188D2840287
  • Sequence:
  • MSRSRASIHR GSIPAMSYAP FRDVRGPSMH RTQYVHSPYD RPGWNPRFCI ISGNQLLMLD 
    EDEIHPLLIR DRRSESSRNK LLRRTVSVPV EGRPHGEHEY HLGRSRRKSV PGGKQYSMEG 
    APAAPFRPSQ GFLSRRLKSS IKRTKSQPKL DRTSSFRQIL PRFRSADHDR ARLMQSFKES 
    HSHESLLSPS SAAEALELNL DEDSIIKPVH SSILGQEFCF EVTTSSGTKC FACRSAAERD 
    KWIENLQRAV KPNKDNSRRV DNVLKLWIIE ARELPPKKRY YCELCLDDML YARTTSKPRS 
    ASGDTVFWGE HFEFNNLPAV RALRLHLYRD SDKKRKKDKA GYVGLVTVPV ATLAGRHFTE 
    QWYPVTLPTG SGGSGGMGSG GGGGSGGGSG GKGKGGCPAV RLKARYQTMS ILPMELYKEF 
    AEYVTNHYRM LCAVLEPALN VKGKEEVASA LVHILQSTGK AKDFLSDMAM SEVDRFMERE 
    HLIFRENTLA TKAIEEYMRL IGQKYLKDAI GEFIRALYES EENCEVDPIK CTASSLAEHQ 
    ANLRMCCELA LCKVVNSHCV FPRELKEVFA SWRLRCAERG REDIADRLIS ASLFLRFLCP 
    AIMSPSLFGL MQEYPDEQTS RTLTLIAKVI QNLANFSKFT SKEDFLGFMN EFLELEWGSM 
    QQFLYEISNL DTLTNSSSFE GYIDLGRELS TLHALLWEVL PQLSKEALLK LGPLPRLLND 
    ISTALRNPNI QRQPSRQSER PRPQPVVLRG PSAEMQGYMM RDLNSSMDMA RLPSPTKEKP 
    PPPPPGGGKD LFYVSRPPLA RSSPAYCTSS SDITEPEQKM LSVNKSVSML DLQGDGPGGR 
    LNSSSVSNLA AVGDLLHSSQ ASLTAALGLR PAPAGRLSQG SGSSITAAGM RLSQMGVTTD 
    GVPAQQLRIP LSFQNPLFHM AADGPGPPGG HGGGGGHGPP SSHHHHHHHH HHRGGEPPGD 
    TFAPFHGYSK SEDLSSGVPK PPAASILHSH SYSDEFGPSG TDFTRRQLSL QDNLQHMLSP 
    PQITIGPQRP APSGPGGGSG GGSGGGGGGQ PPPLQRGKSQ QLTVSAAQKP RPSSGNLLQS 
    PEPSYGPARP RQQSLSKEGS IGGSGGSGGG GGGGLKPSIT KQHSQTPSTL NPTMPASERT 
    VAWVSNMPHL SADIESAHIE REEYKLKEYS KSMDESRLDR EYEEEIHSLK ERLHMSNRKL 
    EEYERRLLSQ EEQTSKILMQ YQARLEQSEK RLRQQQAEKD SQIKSIIGRL MLVEEELRRD 
    HPAMAEPLPE PKKRLLDAQR GSFPPWVQQT RV