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

    Gene ID: 8831, updated on 22-Jan-2024

    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; AllianceGenome:HGNC:11497
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SYNGAP1 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33418167..33453689)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33239529..33275052)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33387842..33421466)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene PHD finger protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33393157-33393699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33396849-33397470 Neighboring gene cutA divalent cation tolerance homolog Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33405630-33405807 Neighboring gene SYNGAP1 antisense RNA 1 Neighboring gene microRNA 5004 Neighboring gene zinc finger and BTB domain containing 9 Neighboring gene uncharacterized LOC107986537 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33499692-33500296 Neighboring gene RNA, 7SL, cytoplasmic 26, pseudogene

    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-11-09)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-11-09)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1938, DKFZp761G1421

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables SH3 domain binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Ras protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axonogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in maintenance of postsynaptic specialization structure IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of Ras protein signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of axonogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in pattern specification process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in receptor clustering IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of MAPK cascade IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of long-term neuronal synaptic plasticity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synapse structure or activity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in visual learning IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in dendritic shaft IEA
    Inferred from Electronic Annotation
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in 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
    Ras/Rap GTPase-activating protein 1
    neuronal RasGAP
    synaptic Ras GTPase activating protein 1 homolog
    synaptic Ras GTPase activating protein, 135kDa

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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), LRG_1193

    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
      Consensus CDS
      CCDS93894.1
      UniProtKB/TrEMBL
      A0A2R8Y6T2, B7ZCA0
      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
      A2AB17, A2BEL6, A2BEL7, A8MQC4, Q8TCS2, Q96PV0, Q9UGE2
      UniProtKB/TrEMBL
      A0A1U9X8L0, A0A2R8Y6T2
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33418167..33453689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419455.1XP_047275411.1  ras/Rap GTPase-activating protein SynGAP isoform X5

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    2. XM_047419464.1XP_047275420.1  ras/Rap GTPase-activating protein SynGAP isoform X9

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    3. XM_047419463.1XP_047275419.1  ras/Rap GTPase-activating protein SynGAP isoform X9

      UniProtKB/TrEMBL
      A0A2R8Y6T2
      Related
      ENSP00000403636.3, ENST00000418600.7
    4. XM_047419450.1XP_047275406.1  ras/Rap GTPase-activating protein SynGAP isoform X13

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    5. XM_047419451.1XP_047275407.1  ras/Rap GTPase-activating protein SynGAP isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    6. XM_047419457.1XP_047275413.1  ras/Rap GTPase-activating protein SynGAP isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    7. XM_047419452.1XP_047275408.1  ras/Rap GTPase-activating protein SynGAP isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    8. XM_047419453.1XP_047275409.1  ras/Rap GTPase-activating protein SynGAP isoform X3

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    9. XM_047419454.1XP_047275410.1  ras/Rap GTPase-activating protein SynGAP isoform X4

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    10. XM_047419465.1XP_047275421.1  ras/Rap GTPase-activating protein SynGAP isoform X14

      UniProtKB/TrEMBL
      A0A2R8Y6T2, B7ZCA0
    11. XM_047419461.1XP_047275417.1  ras/Rap GTPase-activating protein SynGAP isoform X9

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    12. XM_047419458.1XP_047275414.1  ras/Rap GTPase-activating protein SynGAP isoform X7

      UniProtKB/TrEMBL
      A0A0A0MQZ2
      Related
      ENSP00000486431.1, ENST00000628646.2
    13. XM_047419460.1XP_047275416.1  ras/Rap GTPase-activating protein SynGAP isoform X8

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    14. XM_047419467.1XP_047275423.1  ras/Rap GTPase-activating protein SynGAP isoform X12

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    15. XM_047419456.1XP_047275412.1  ras/Rap GTPase-activating protein SynGAP isoform X5

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    16. XM_047419462.1XP_047275418.1  ras/Rap GTPase-activating protein SynGAP isoform X10

      UniProtKB/TrEMBL
      A0A2R8YDS2
      Related
      ENSP00000412475.2, ENST00000428982.4
    17. XM_047419466.1XP_047275422.1  ras/Rap GTPase-activating protein SynGAP isoform X11

      UniProtKB/TrEMBL
      A0A2R8YDS2

    RNA

    1. XR_007059351.1 RNA Sequence

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      33239529..33275052
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356657.1XP_054212632.1  ras/Rap GTPase-activating protein SynGAP isoform X5

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    2. XM_054356665.1XP_054212640.1  ras/Rap GTPase-activating protein SynGAP isoform X9

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    3. XM_054356664.1XP_054212639.1  ras/Rap GTPase-activating protein SynGAP isoform X9

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    4. XM_054356653.1XP_054212628.1  ras/Rap GTPase-activating protein SynGAP isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    5. XM_054356659.1XP_054212634.1  ras/Rap GTPase-activating protein SynGAP isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    6. XM_054356654.1XP_054212629.1  ras/Rap GTPase-activating protein SynGAP isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    7. XM_054356655.1XP_054212630.1  ras/Rap GTPase-activating protein SynGAP isoform X3

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    8. XM_054356656.1XP_054212631.1  ras/Rap GTPase-activating protein SynGAP isoform X4

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    9. XM_054356662.1XP_054212637.1  ras/Rap GTPase-activating protein SynGAP isoform X9

      UniProtKB/TrEMBL
      A0A2R8Y6T2
    10. XM_054356660.1XP_054212635.1  ras/Rap GTPase-activating protein SynGAP isoform X7

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    11. XM_054356661.1XP_054212636.1  ras/Rap GTPase-activating protein SynGAP isoform X8

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    12. XM_054356667.1XP_054212642.1  ras/Rap GTPase-activating protein SynGAP isoform X12

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    13. XM_054356658.1XP_054212633.1  ras/Rap GTPase-activating protein SynGAP isoform X5

      UniProtKB/TrEMBL
      A0A0A0MQZ2
    14. XM_054356663.1XP_054212638.1  ras/Rap GTPase-activating protein SynGAP isoform X10

      UniProtKB/TrEMBL
      A0A2R8YDS2
    15. XM_054356666.1XP_054212641.1  ras/Rap GTPase-activating protein SynGAP isoform X11

      UniProtKB/TrEMBL
      A0A2R8YDS2

    RNA

    1. XR_008487455.1 RNA Sequence