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SYNGAP1 synaptic Ras GTPase activating protein 1 [ Homo sapiens (human) ]

Gene ID: 8831, updated on 24-Nov-2020

Summary

Official Symbol
SYNGAP1provided by HGNC
Official Full Name
synaptic Ras GTPase activating protein 1provided by HGNC
Primary source
HGNC:HGNC:11497
See related
Ensembl:ENSG00000197283 MIM:603384
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRD5; RASA1; RASA5; SYNGAP
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 17.6), ovary (RPKM 8.3) and 23 other tissues See more
Orthologs

Genomic context

See SYNGAP1 in Genome Data Viewer
Location:
6p21.32
Exon count:
19
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (33420065..33453689)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33387847..33421466)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene kinesin family member C1 Neighboring gene ribosomal protein L12 pseudogene 1 Neighboring gene PHD finger protein 1 Neighboring gene cutA divalent cation tolerance homolog Neighboring gene microRNA 5004 Neighboring gene zinc finger and BTB domain containing 9 Neighboring gene uncharacterized LOC107986537

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal dominant 5 Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-06)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1938, DKFZp761G1421

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IEA
Inferred from Electronic Annotation
more info
 
SH3 domain binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
MAPK cascade TAS
Traceable Author Statement
more info
 
Ras protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
dendrite development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of Ras protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of axonogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
pattern specification process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
receptor clustering IEA
Inferred from Electronic Annotation
more info
 
regulation of MAPK cascade IEA
Inferred from Electronic Annotation
more info
 
regulation of long-term neuronal synaptic plasticity IEA
Inferred from Electronic Annotation
more info
 
regulation of synapse structure or activity IEA
Inferred from Electronic Annotation
more info
 
regulation of synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
visual learning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
dendritic shaft IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
ras/Rap GTPase-activating protein SynGAP
Names
Ras GTPase-activating protein SynGAP
neuronal RasGAP
synaptic Ras GTPase activating protein 1 homolog
synaptic Ras GTPase activating protein, 135kDa

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016137.2 RefSeqGene

    Range
    4996..38620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130066.2NP_001123538.1  ras/Rap GTPase-activating protein SynGAP isoform 2

    Status: REVIEWED

    Source sequence(s)
    AK094225, AK124666, AK307888, AL662799, AL713634, DA057307
    UniProtKB/Swiss-Prot
    Q96PV0
    Related
    ENSP00000416519.4, ENST00000449372.7
    Conserved Domains (5) summary
    cd05136
    Location:415722
    RasGAP_DAB2IP; The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated...
    pfam09744
    Location:11541266
    Jnk-SapK_ap_N; JNK_SAPK-associated protein-1
    pfam12004
    Location:7191282
    DUF3498; Domain of unknown function (DUF3498)
    cd04013
    Location:252414
    C2_SynGAP_like; C2 domain present in Ras GTPase activating protein (GAP) family
    cl00273
    Location:136249
    PH-like; Pleckstrin homology-like domain
  2. NM_006772.3NP_006763.2  ras/Rap GTPase-activating protein SynGAP isoform 1

    See identical proteins and their annotated locations for NP_006763.2

    Status: REVIEWED

    Source sequence(s)
    AK094225, AK124666, AK307888, AL662799, AL713634, BX282051, DA057307
    Consensus CDS
    CCDS34434.2
    UniProtKB/Swiss-Prot
    Q96PV0
    UniProtKB/TrEMBL
    A0A1U9X8L0
    Related
    ENSP00000496007.1, ENST00000646630.1
    Conserved Domains (4) summary
    cd04013
    Location:252414
    C2_SynGAP_like; C2 domain present in Ras GTPase activating protein (GAP) family
    cd05136
    Location:405728
    RasGAP_DAB2IP; Ras-GTPase Activating Domain of DAB2IP and similar proteins
    cd13375
    Location:122313
    PH_SynGAP; Synaptic Ras-GTPase activating protein Pleckstrin homology (PH) domain
    pfam12004
    Location:7181310
    DUF3498; Domain of unknown function (DUF3498)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    33420065..33453689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    4868790..4902412
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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