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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SYNGAP1
synaptic Ras GTPase activating protein 1
Chromosome 6 Β· 6p21.32
NCBI Gene: 8831Ensembl: ENSG00000197283.18HGNC: HGNC:11497UniProt: A0A1U9X8L0
83PubMed Papers
21Diseases
0Drugs
426Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingnegative regulation of Ras protein signal transductionregulation of synaptic plasticityGTPase activator activityintellectual disability, autosomal dominant 5complex neurodevelopmental disorderIntellectual disabilitygenetic disorder
✦AI Summary

SYNGAP1 encodes a synaptic Ras GTPase-activating protein (RASGAP) that functions as a major postsynaptic density constituent essential for synaptic plasticity and neuronal signaling 1. As a dual GTPase-activating protein for Ras and Rap, SYNGAP1 inhibits the Ras-cAMP pathway and integrates into NMDAR signaling complexes, regulating AMPAR membrane trafficking and miniature excitatory postsynaptic currents through mechanisms involving molecular condensate formation rather than solely catalytic activity 2. Beyond synaptic functions, SYNGAP1 is expressed in radial glia cells where it regulates cytoskeletal dynamics critical for cortical neurogenesis 3. De novo SYNGAP1 mutations are among the most frequent genetic causes of autism spectrum disorder and intellectual disability 4, with male-biased enrichment in some populations 5. SYNGAP1 haploinsufficiency causes developmental and epileptic encephalopathy (DEE) characterized by generalized seizures with distinctive eyelid myoclonia, moderate-to-severe intellectual disability, autism spectrum features, and developmental delay 6. Current therapeutic approaches under investigation include splice-switching oligonucleotides to upregulate functional SYNGAP1 isoforms, taurine supplementation, and ketogenic diet intervention 1, though no FDA-approved treatments currently exist for SYNGAP1-related disorders.

Sources cited
1
SYNGAP1 encodes a GTPase-activating protein critical for synaptic plasticity and neuronal excitability; mutations cause intellectual disability, epilepsy, and behavioral abnormalities; current therapeutic approaches under investigation
PMID: 40282364
2
SynGAP regulates synaptic plasticity and cognition through molecular condensate formation with scaffolding proteins, independent of catalytic GAP activity
PMID: 38422154
3
SYNGAP1 is expressed in radial glia and regulates cytoskeletal dynamics essential for cortical neurogenesis; haploinsufficiency disrupts lamination and neuronal maturation
PMID: 37946050
4
De novo SYNGAP1 mutations are among the most frequent causes of autism and intellectual disability; alternative splicing induces nonsense-mediated decay; splice-switching oligonucleotides can restore SYNGAP1 expression
PMID: 36917980
5
SYNGAP1 mutations cause developmental and epileptic encephalopathy with generalized seizures including eyelid myoclonia and myoclonic-atonic seizures; 55/57 patients had intellectual disability and 54% had autism spectrum disorder
PMID: 30541864
6
SYNGAP1 shows male-biased enrichment of de novo mutations in neurodevelopmental disorder-affected individuals
PMID: 31785789
Disease Associationsβ“˜21
intellectual disability, autosomal dominant 5Open Targets
0.82Strong
complex neurodevelopmental disorderOpen Targets
0.62Moderate
Intellectual disabilityOpen Targets
0.58Moderate
genetic disorderOpen Targets
0.56Moderate
SeizureOpen Targets
0.49Moderate
Epileptic encephalopathyOpen Targets
0.45Moderate
Neurodevelopmental disorderOpen Targets
0.41Moderate
Global developmental delayOpen Targets
0.37Weak
epilepsy with myoclonic atonic seizuresOpen Targets
0.37Weak
developmental disorder of mental healthOpen Targets
0.37Weak
Delayed speech and language developmentOpen Targets
0.36Weak
Neurodevelopmental delayOpen Targets
0.35Weak
Atypical behaviorOpen Targets
0.33Weak
infantile epilepsy syndromeOpen Targets
0.33Weak
Motor delayOpen Targets
0.33Weak
aggressive behaviorOpen Targets
0.27Weak
Downslanted palpebral fissuresOpen Targets
0.27Weak
Floppy infantOpen Targets
0.27Weak
Pointed chinOpen Targets
0.27Weak
Wide nasal bridgeOpen Targets
0.27Weak
Intellectual developmental disorder, autosomal dominant 5UniProt
Pathogenic Variants426
NM_006772.3(SYNGAP1):c.2755C>T (p.Gln919Ter)Pathogenic
Intellectual disability, autosomal dominant 5|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 919
NM_006772.3(SYNGAP1):c.928G>A (p.Glu310Lys)Pathogenic
Intellectual disability, autosomal dominant 5|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 310
NM_006772.3(SYNGAP1):c.1685C>T (p.Pro562Leu)Pathogenic
Intellectual disability, autosomal dominant 5|not provided|Inborn genetic diseases|Complex neurodevelopmental disorder|Autosomal dominant epilepsy
β˜…β˜…β˜†β˜†2026β†’ Residue 562
NM_006772.3(SYNGAP1):c.490C>T (p.Arg164Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 5|Complex neurodevelopmental disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 164
NM_006772.3(SYNGAP1):c.2438del (p.Leu813fs)Pathogenic
Intellectual disability, autosomal dominant 5|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 813
NM_006772.3(SYNGAP1):c.2059C>T (p.Arg687Ter)Pathogenic
Intellectual disability, autosomal dominant 5|not provided|13 conditions|See cases|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 687
NM_006772.3(SYNGAP1):c.3583-1G>ALikely pathogenic
Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025
NM_006772.3(SYNGAP1):c.403C>T (p.Arg135Ter)Pathogenic
Intellectual disability, autosomal recessive 5|Inborn genetic diseases|Intellectual disability, autosomal dominant 5|not provided|Intellectual disability
β˜…β˜…β˜†β˜†2025β†’ Residue 135
NM_006772.3(SYNGAP1):c.1082A>C (p.Gln361Pro)Likely pathogenic
Seizure|Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025β†’ Residue 361
NM_006772.3(SYNGAP1):c.68-1G>APathogenic
not provided|Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025
NM_006772.3(SYNGAP1):c.1717C>T (p.Arg573Trp)Pathogenic
not provided|Intellectual disability, autosomal dominant 5|Intellectual disability
β˜…β˜…β˜†β˜†2025β†’ Residue 573
NM_006772.3(SYNGAP1):c.1716G>A (p.Trp572Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025β†’ Residue 572
NM_006772.3(SYNGAP1):c.1726T>C (p.Cys576Arg)Pathogenic
Intellectual disability, autosomal dominant 5|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 576
NM_006772.3(SYNGAP1):c.1167_1168del (p.Gly391fs)Pathogenic
Intellectual disability, autosomal dominant 5|not provided|Inborn genetic diseases|SYNGAP1-related complex neurodevelopmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 391
NM_006772.3(SYNGAP1):c.2916del (p.Asp974fs)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 974
NM_006772.3(SYNGAP1):c.2764C>T (p.Arg922Ter)Pathogenic
Intellectual disability, autosomal dominant 5|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 922
NM_006772.3(SYNGAP1):c.3415C>T (p.Gln1139Ter)Pathogenic
Complex neurodevelopmental disorder|not provided|Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025β†’ Residue 1139
NM_006772.3(SYNGAP1):c.2970del (p.Val992fs)Pathogenic
Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025β†’ Residue 992
NM_006772.3(SYNGAP1):c.387G>A (p.Ser129=)Likely pathogenic
Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025β†’ Residue 129
NM_006772.3(SYNGAP1):c.3277C>T (p.Gln1093Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 5
β˜…β˜…β˜†β˜†2025β†’ Residue 1093
View on ClinVar β†—
Related Genes
ULK2Protein interaction100%DLGAP1Protein interaction100%HRASProtein interaction99%HOMER1Protein interaction98%SHANK3Protein interaction98%SHANK2Protein interaction97%
Tissue Expression6 tissues
Ovary
100%
Brain
62%
Bone Marrow
44%
Lung
39%
Heart
20%
Liver
13%
Gene Interaction Network
Click a node to explore
SYNGAP1ULK2DLGAP1HRASHOMER1SHANK3SHANK2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96PV0
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.13Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.07 [0.04–0.13]
RankingsWhere SYNGAP1 stands among ~20K protein-coding genes
  • #5,760of 20,598
    Most Researched83
  • #130of 5,498
    Most Pathogenic Variants426 Β· top 5%
  • #130of 17,882
    Most Constrained (LOEUF)0.13 Β· top 1%
Genes detectedSYNGAP1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders.
PMID: 31785789
Am J Hum Genet Β· 2019
1.00
2
Upregulation of SYNGAP1 expression in mice and human neurons by redirecting alternative splicing.
PMID: 36917980
Neuron Β· 2023
0.90
3
Prevalence and architecture of de novo mutations in developmental disorders.
PMID: 28135719
Nature Β· 2017
0.80
4
Autism spectrum disorder: neuropathology and animal models.
PMID: 28584888
Acta Neuropathol Β· 2017
0.70
5
SYNGAP1 Syndrome and the Brain Gene Registry.
PMID: 40282364
Genes (Basel) Β· 2025
0.60