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Aliases for SYNGAP1 Gene

Aliases for SYNGAP1 Gene

  • Synaptic Ras GTPase Activating Protein 1 2 3 5
  • Neuronal RasGAP 3 4
  • Synaptic Ras GTPase Activating Protein 1 Homolog (Rat) 2
  • Synaptic Ras GTPase Activating Protein 1 Homolog 3
  • Synaptic Ras GTPase Activating Protein, 135kDa 3
  • Synaptic Ras GTPase-Activating Protein 1 4
  • Ras/Rap GTPase-Activating Protein SynGAP 3
  • Ras GTPase-Activating Protein SynGAP 3
  • Synaptic Ras-GAP 1 4
  • KIAA1938 4
  • SYNGAP 3
  • RASA1 3
  • RASA5 3
  • MRD5 3

External Ids for SYNGAP1 Gene

Previous GeneCards Identifiers for SYNGAP1 Gene

  • GC06U990169
  • GC06P033384
  • GC06P033434
  • GC06P033495
  • GC06P033129

Summaries for SYNGAP1 Gene

Entrez Gene Summary for SYNGAP1 Gene

  • 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]

GeneCards Summary for SYNGAP1 Gene

SYNGAP1 (Synaptic Ras GTPase Activating Protein 1) is a Protein Coding gene. Diseases associated with SYNGAP1 include Autosomal Dominant Non-Syndromic Intellectual Disability and Intellectual Disability. Among its related pathways are RET signaling and Immune System. GO annotations related to this gene include GTPase activator activity and SH3 domain binding. An important paralog of this gene is RASAL2.

UniProtKB/Swiss-Prot for SYNGAP1 Gene

  • Major constituent of the PSD essential for postsynaptic signaling. Inhibitory regulator of the Ras-cAMP pathway. Member of the NMDAR signaling complex in excitatory synapses, it may play a role in NMDAR-dependent control of AMPAR potentiation, AMPAR membrane trafficking and synaptic plasticity. Regulates AMPAR-mediated miniature excitatory postsynaptic currents. Exhibits dual GTPase-activating specificity for Ras and Rap. May be involved in certain forms of brain injury, leading to long-term learning and memory deficits (By similarity).

Gene Wiki entry for SYNGAP1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNGAP1 Gene

Genomics for SYNGAP1 Gene

Regulatory Elements for SYNGAP1 Gene

Enhancers for SYNGAP1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F033341 1.2 FANTOM5 Ensembl ENCODE 10.9 -75.7 -75689 4.0 HDGF PKNOX1 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 FEZF1 ZNF2 DAXX TAPBP PHF1 WDR46 RGL2 ZBTB22 MIR6834 MIR6873 PFDN6 KIFC1
GH06F033287 0.2 ENCODE 10.8 -130.1 -130144 3.1 PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF207 TAPBP ZBTB22 KIFC1 PHF1 RPL35AP4 CUTA MIR5004 SYNGAP1 VPS52 RPS18
GH06F033362 0.2 ENCODE 10.6 -57.3 -57343 0.2 CUX1 DAXX KIFC1 RPL35AP4 HLA-DMA MIR5004 SYNGAP1 CUTA LYPLA2P1 MYL8P
GH06F033428 0.7 FANTOM5 ENCODE 6.1 +9.5 9450 1.7 HDGF ATF1 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 YBX1 GLIS2 SMARCA4 ZBTB9 C6orf1 RPL35AP4 KIFC1 CUTA BAK1 SYNGAP1 MIR5004
GH06F032524 1 FANTOM5 Ensembl 5.4 -895.1 -895061 0.4 HLA-DRB1 HLA-DRB5 HLA-DQA2 HLA-DRB6 HLA-DQA1 SYNGAP1 CFB PSMB8 HLA-DMA HLA-DMB
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SYNGAP1 on UCSC Golden Path with GeneCards custom track

Promoters for SYNGAP1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001703179 839 1401 PKNOX1 ARNT GLI4 CBX5 GATA2 ZNF263 NCOA1 REST ZNF518A MBD2
ENSR00001188811 -1961 1801 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1

Genomic Location for SYNGAP1 Gene

Chromosome:
6
Start:
33,419,661 bp from pter
End:
33,457,541 bp from pter
Size:
37,881 bases
Orientation:
Plus strand

Genomic View for SYNGAP1 Gene

Genes around SYNGAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNGAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNGAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNGAP1 Gene

Proteins for SYNGAP1 Gene

  • Protein details for SYNGAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96PV0-SYGP1_HUMAN
    Recommended name:
    Ras/Rap GTPase-activating protein SynGAP
    Protein Accession:
    Q96PV0
    Secondary Accessions:
    • A2AB17
    • A2BEL6
    • A2BEL7
    • A8MQC4
    • Q8TCS2
    • Q9UGE2

    Protein attributes for SYNGAP1 Gene

    Size:
    1343 amino acids
    Molecular mass:
    148284 Da
    Quaternary structure:
    • Interacts KLHL17, CAMK2A and CAMK2B (By similarity). Interacts with MPDZ.
    • Interacts KLHL17, CAMK2A and CAMK2B (By similarity). Interacts with MPDZ.
    SequenceCaution:
    • Sequence=BAB67831.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for SYNGAP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNGAP1 Gene

Post-translational modifications for SYNGAP1 Gene

  • Phosphorylated by CaM-kinase II. Dephosphorylated upon NMDA receptor activation or SYNGAP1/MPDZ complex disruption. Phosphorylation by PLK2 promotes its activity (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SYNGAP1 Gene

Domains & Families for SYNGAP1 Gene

Gene Families for SYNGAP1 Gene

Suggested Antigen Peptide Sequences for SYNGAP1 Gene

Graphical View of Domain Structure for InterPro Entry

Q96PV0

UniProtKB/Swiss-Prot:

SYGP1_HUMAN :
  • The C2 domain is required for RapGAP activity.
Domain:
  • The C2 domain is required for RapGAP activity.
  • Contains 1 C2 domain.
  • Contains 1 PH domain.
  • Contains 1 Ras-GAP domain.
genes like me logo Genes that share domains with SYNGAP1: view

Function for SYNGAP1 Gene

Molecular function for SYNGAP1 Gene

GENATLAS Biochemistry:
synaptic Ras-GTPase activating protein 1,homolog of rat,in the flanking region of KNSL2
UniProtKB/Swiss-Prot Function:
Major constituent of the PSD essential for postsynaptic signaling. Inhibitory regulator of the Ras-cAMP pathway. Member of the NMDAR signaling complex in excitatory synapses, it may play a role in NMDAR-dependent control of AMPAR potentiation, AMPAR membrane trafficking and synaptic plasticity. Regulates AMPAR-mediated miniature excitatory postsynaptic currents. Exhibits dual GTPase-activating specificity for Ras and Rap. May be involved in certain forms of brain injury, leading to long-term learning and memory deficits (By similarity).

Gene Ontology (GO) - Molecular Function for SYNGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA,IBA --
GO:0017124 SH3 domain binding IEA --
genes like me logo Genes that share ontologies with SYNGAP1: view
genes like me logo Genes that share phenotypes with SYNGAP1: view

Human Phenotype Ontology for SYNGAP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYNGAP1 Gene

MGI Knock Outs for SYNGAP1:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SYNGAP1 Gene

Localization for SYNGAP1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SYNGAP1 Gene COMPARTMENTS Subcellular localization image for SYNGAP1 gene
Compartment Confidence
cytosol 3
nucleus 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SYNGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane IBA --
genes like me logo Genes that share ontologies with SYNGAP1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SYNGAP1 Gene

Pathways & Interactions for SYNGAP1 Gene

SuperPathways for SYNGAP1 Gene

SuperPathway Contained pathways
1 RET signaling
2 Developmental Biology
3 Cytokine Signaling in Immune system
4 HIV Life Cycle
.45
5 Immune System
genes like me logo Genes that share pathways with SYNGAP1: view

Pathways by source for SYNGAP1 Gene

1 Cell Signaling Technology pathway for SYNGAP1 Gene
1 KEGG pathway for SYNGAP1 Gene
1 GeneGo (Thomson Reuters) pathway for SYNGAP1 Gene
1 Qiagen pathway for SYNGAP1 Gene

Gene Ontology (GO) - Biological Process for SYNGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade TAS --
GO:0007165 signal transduction IEA --
GO:0007265 Ras protein signal transduction IEA --
GO:0007389 pattern specification process IEA --
GO:0008542 visual learning IEA --
genes like me logo Genes that share ontologies with SYNGAP1: view

No data available for SIGNOR curated interactions for SYNGAP1 Gene

Drugs & Compounds for SYNGAP1 Gene

(2) Drugs for SYNGAP1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
cyclic amp Experimental Pharma 0
genes like me logo Genes that share compounds with SYNGAP1: view

Transcripts for SYNGAP1 Gene

mRNA/cDNA for SYNGAP1 Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(29) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SYNGAP1 Gene

Synaptic Ras GTPase activating protein 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNGAP1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^
SP1:
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

ExUns: 19a · 19b · 19c ^ 20a · 20b · 20c ^ 21a · 21b ^ 22
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9: - - -
SP10: -
SP11:
SP12:
SP13: -

Relevant External Links for SYNGAP1 Gene

GeneLoc Exon Structure for
SYNGAP1
ECgene alternative splicing isoforms for
SYNGAP1

Expression for SYNGAP1 Gene

mRNA expression in normal human tissues for SYNGAP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SYNGAP1 Gene

This gene is overexpressed in Frontal cortex (30.5), Brain (19.0), and Cervix (12.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SYNGAP1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SYNGAP1 Gene:

SYNGAP1

SOURCE GeneReport for Unigene cluster for SYNGAP1 Gene:

Hs.586264
genes like me logo Genes that share expression patterns with SYNGAP1: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SYNGAP1 Gene

Orthologs for SYNGAP1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SYNGAP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYNGAP1 34 35
  • 99.73 (n)
oppossum
(Monodelphis domestica)
Mammalia SYNGAP1 35
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SYNGAP1 34 35
  • 92.26 (n)
mouse
(Mus musculus)
Mammalia Syngap1 34 16 35
  • 91.84 (n)
cow
(Bos Taurus)
Mammalia SYNGAP1 34 35
  • 91.51 (n)
rat
(Rattus norvegicus)
Mammalia Syngap1 34
  • 91.47 (n)
lizard
(Anolis carolinensis)
Reptilia SYNGAP1 35
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia syngap1 34
  • 74.34 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100151149 34
  • 66.56 (n)
SYNGAP1 (2 of 2) 35
  • 65 (a)
OneToMany
SYNGAP1 (1 of 2) 35
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG42684 35
  • 19 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea gap-2 35
  • 24 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BUD2 35
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6146 35
  • 33 (a)
OneToMany
Species where no ortholog for SYNGAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SYNGAP1 Gene

ENSEMBL:
Gene Tree for SYNGAP1 (if available)
TreeFam:
Gene Tree for SYNGAP1 (if available)

Paralogs for SYNGAP1 Gene

Paralogs for SYNGAP1 Gene

(4) SIMAP similar genes for SYNGAP1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SYNGAP1: view

Variants for SYNGAP1 Gene

Sequence variations from dbSNP and Humsavar for SYNGAP1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs397514670 Mental retardation, autosomal dominant 5 (MRD5) [MIM:612621], Pathogenic 33,440,737(+) GTTCC(C/T)GAGGG reference, missense
VAR_069232 Mental retardation, autosomal dominant 5 (MRD5) [MIM:612621]
rs121918315 Pathogenic 33,432,709(+) GGCTA(A/T)AAAGC reference, stop-gained
rs121918316 Pathogenic 33,440,787(+) CAGAG(C/T)GAGGC reference, stop-gained
rs397514741 Pathogenic 33,432,724(+) TCAAA(C/T)GAACG reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for SYNGAP1 Gene

Variant ID Type Subtype PubMed ID
esv3608630 CNV gain 21293372
nsv1019212 CNV gain 25217958
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv437503 CNV loss 16327808
nsv602832 CNV loss 21841781
nsv830635 CNV loss 17160897
nsv830637 CNV loss 17160897

Variation tolerance for SYNGAP1 Gene

Residual Variation Intolerance Score: 1.36% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.95; 79.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYNGAP1 Gene

Human Gene Mutation Database (HGMD)
SYNGAP1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYNGAP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNGAP1 Gene

Disorders for SYNGAP1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SYNGAP1 Gene - From: ClinVar, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SYGP1_HUMAN
  • Mental retardation, autosomal dominant 5 (MRD5) [MIM:612621]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD5 patients show global developmental delay with delayed motor development, hypotonia, moderate-to-severe mental retardation, and severe language impairment. Epilepsy and autism can be present in some patients. {ECO:0000269 PubMed:19196676, ECO:0000269 PubMed:21076407, ECO:0000269 PubMed:21237447, ECO:0000269 PubMed:23161826}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SYNGAP1

Genetic Association Database (GAD)
SYNGAP1
Human Genome Epidemiology (HuGE) Navigator
SYNGAP1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYNGAP1
genes like me logo Genes that share disorders with SYNGAP1: view

No data available for Genatlas for SYNGAP1 Gene

Publications for SYNGAP1 Gene

  1. Mutations in SYNGAP1 in autosomal nonsyndromic mental retardation. (PMID: 19196676) Hamdan F.F. … Michaud J.L. (N. Engl. J. Med. 2009) 3 4 46 64
  2. SynGAP: a synaptic RasGAP that associates with the PSD-95/SAP90 protein family. (PMID: 9581761) Kim J.H. … Huganir R.L. (Neuron 1998) 2 3 22 64
  3. Mutations in SYNGAP1 cause intellectual disability, autism, and a specific form of epilepsy by inducing haploinsufficiency. (PMID: 23161826) Berryer M.H. … Di Cristo G. (Hum. Mutat. 2013) 3 4 64
  4. De novo SYNGAP1 mutations in nonsyndromic intellectual disability and autism. (PMID: 21237447) Hamdan F.F. … Michaud J.L. (Biol. Psychiatry 2011) 3 4 64
  5. [De novo mutations in SYNGAP1 associated with non-syndromic mental retardation]. (PMID: 20188038) Hamdan F.F. … Michaud J.L. (Med Sci (Paris) 2010) 3 46 64

Products for SYNGAP1 Gene

Sources for SYNGAP1 Gene

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