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

Gene ID: 8831, updated on 2-Nov-2024

Summary

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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
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Genomic context

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See SYNGAP1 in Genome Data Viewer
Location:
6p21.32
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33418167..33453689)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33239529..33275052)
RS_2024_09 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Novel SYNGAP1 variant in a patient with intellectual disability and distinctive dysmorphisms. Kimura Y, et al. Congenit Anom (Kyoto), 2018 Nov. PMID 29381230
  2. Differential auditory brain response abnormalities in two intellectual disability conditions: SYNGAP1 mutations and Down syndrome. Côté V, et al. Clin Neurophysiol, 2021 Aug. PMID 34130248
  3. SYNGAP1-DEE: A visual sensitive epilepsy. Lo Barco T, et al. Clin Neurophysiol, 2021 Apr. PMID 33639450
  4. Multi-parametric analysis of 57 SYNGAP1 variants reveal impacts on GTPase signaling, localization, and protein stability. Meili F, et al. Am J Hum Genet, 2021 Jan 7. PMID 33308442, Free PMC Article
  5. Distinct patterns of repetition suppression in Fragile X syndrome, down syndrome, tuberous sclerosis complex and mutations in SYNGAP1. Côté V, et al. Brain Res, 2021 Jan 15. PMID 33189692

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Behavioural and neurodevelopmental characteristics of SYNGAP1.
    Title: Behavioural and neurodevelopmental characteristics of SYNGAP1.
  2. SYNGAP1-related developmental and epileptic encephalopathy: Genotypic and phenotypic characteristics and longitudinal insights.
    Title: SYNGAP1-related developmental and epileptic encephalopathy: Genotypic and phenotypic characteristics and longitudinal insights.
  3. Visual social attention in SYNGAP1-related intellectual disability.
    Title: Visual social attention in SYNGAP1-related intellectual disability.
  4. The Behavioral Profile of SYNGAP1-Related Intellectual Disability.
    Title: The Behavioral Profile of SYNGAP1-Related Intellectual Disability.
  5. Severe behavior problems in SYNGAP1-related disorder: A summary of 11 consecutive patients in a tertiary care specialty clinic.
    Title: Severe behavior problems in SYNGAP1-related disorder: A summary of 11 consecutive patients in a tertiary care specialty clinic.
  6. [Correlation of early neurodevelopmental features of children with SYNGAP1 variants and their genotypes].
    Title: [Correlation of early neurodevelopmental features of children with SYNGAP1 variants and their genotypes].
  7. Discovery of a non-canonical function of SYNGAP1 at early stages of human cortical neurogenesis.
    Title: Discovery of a non-canonical function of SYNGAP1 at early stages of human cortical neurogenesis.
  8. Non-synaptic function of the autism spectrum disorder-associated gene SYNGAP1 in cortical neurogenesis.
    Title: Non-synaptic function of the autism spectrum disorder-associated gene SYNGAP1 in cortical neurogenesis.
  9. Upregulation of SYNGAP1 expression in mice and human neurons by redirecting alternative splicing.
    Title: Upregulation of SYNGAP1 expression in mice and human neurons by redirecting alternative splicing.
  10. The SYNGAP1 3'UTR Variant in ALS Patients Causes Aberrant SYNGAP1 Splicing and Dendritic Spine Loss by Recruiting HNRNPK.
    Title: The SYNGAP1 3'UTR Variant in ALS Patients Causes Aberrant SYNGAP1 Splicing and Dendritic Spine Loss by Recruiting HNRNPK.
Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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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)

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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_001130066.2 → NP_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:415 → 722
    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:1154 → 1266
    Jnk-SapK_ap_N; JNK_SAPK-associated protein-1
    pfam12004
    Location:719 → 1282
    DUF3498; Domain of unknown function (DUF3498)
    cd04013
    Location:252 → 414
    C2_SynGAP_like; C2 domain present in Ras GTPase activating protein (GAP) family
    cl00273
    Location:136 → 249
    PH-like; Pleckstrin homology-like domain

  2. NM_006772.3 → NP_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:252 → 414
    C2_SynGAP_like; C2 domain present in Ras GTPase activating protein (GAP) family
    cd05136
    Location:405 → 728
    RasGAP_DAB2IP; Ras-GTPase Activating Domain of DAB2IP and similar proteins
    cd13375
    Location:122 → 313
    PH_SynGAP; Synaptic Ras-GTPase activating protein Pleckstrin homology (PH) domain
    pfam12004
    Location:718 → 1310
    DUF3498; Domain of unknown function (DUF3498)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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_047419455.1 → XP_047275411.1  ras/Rap GTPase-activating protein SynGAP isoform X5

  2. XM_047419464.1 → XP_047275420.1  ras/Rap GTPase-activating protein SynGAP isoform X9

  3. XM_047419463.1 → XP_047275419.1  ras/Rap GTPase-activating protein SynGAP isoform X9

    Related
    ENSP00000403636.3, ENST00000418600.7

  4. XM_047419450.1 → XP_047275406.1  ras/Rap GTPase-activating protein SynGAP isoform X13

  5. XM_047419451.1 → XP_047275407.1  ras/Rap GTPase-activating protein SynGAP isoform X1

  6. XM_047419457.1 → XP_047275413.1  ras/Rap GTPase-activating protein SynGAP isoform X6

  7. XM_047419452.1 → XP_047275408.1  ras/Rap GTPase-activating protein SynGAP isoform X2

  8. XM_047419453.1 → XP_047275409.1  ras/Rap GTPase-activating protein SynGAP isoform X3

  9. XM_047419454.1 → XP_047275410.1  ras/Rap GTPase-activating protein SynGAP isoform X4

  10. XM_047419465.1 → XP_047275421.1  ras/Rap GTPase-activating protein SynGAP isoform X14

    UniProtKB/TrEMBL
    B7ZCA0

  11. XM_047419461.1 → XP_047275417.1  ras/Rap GTPase-activating protein SynGAP isoform X9

  12. XM_047419458.1 → XP_047275414.1  ras/Rap GTPase-activating protein SynGAP isoform X7

    Related
    ENSP00000486431.1, ENST00000628646.2

  13. XM_047419460.1 → XP_047275416.1  ras/Rap GTPase-activating protein SynGAP isoform X8

  14. XM_047419467.1 → XP_047275423.1  ras/Rap GTPase-activating protein SynGAP isoform X12

  15. XM_047419456.1 → XP_047275412.1  ras/Rap GTPase-activating protein SynGAP isoform X5

  16. XM_047419462.1 → XP_047275418.1  ras/Rap GTPase-activating protein SynGAP isoform X10

    Related
    ENSP00000412475.2, ENST00000428982.4

  17. XM_047419466.1 → XP_047275422.1  ras/Rap GTPase-activating protein SynGAP isoform X11

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_054356657.1 → XP_054212632.1  ras/Rap GTPase-activating protein SynGAP isoform X5

  2. XM_054356665.1 → XP_054212640.1  ras/Rap GTPase-activating protein SynGAP isoform X9

  3. XM_054356664.1 → XP_054212639.1  ras/Rap GTPase-activating protein SynGAP isoform X9

  4. XM_054356653.1 → XP_054212628.1  ras/Rap GTPase-activating protein SynGAP isoform X1

  5. XM_054356659.1 → XP_054212634.1  ras/Rap GTPase-activating protein SynGAP isoform X6

  6. XM_054356654.1 → XP_054212629.1  ras/Rap GTPase-activating protein SynGAP isoform X2

  7. XM_054356655.1 → XP_054212630.1  ras/Rap GTPase-activating protein SynGAP isoform X3

  8. XM_054356656.1 → XP_054212631.1  ras/Rap GTPase-activating protein SynGAP isoform X4

  9. XM_054356662.1 → XP_054212637.1  ras/Rap GTPase-activating protein SynGAP isoform X9

  10. XM_054356660.1 → XP_054212635.1  ras/Rap GTPase-activating protein SynGAP isoform X7

  11. XM_054356661.1 → XP_054212636.1  ras/Rap GTPase-activating protein SynGAP isoform X8

  12. XM_054356667.1 → XP_054212642.1  ras/Rap GTPase-activating protein SynGAP isoform X12

  13. XM_054356658.1 → XP_054212633.1  ras/Rap GTPase-activating protein SynGAP isoform X5

  14. XM_054356663.1 → XP_054212638.1  ras/Rap GTPase-activating protein SynGAP isoform X10

  15. XM_054356666.1 → XP_054212641.1  ras/Rap GTPase-activating protein SynGAP isoform X11

RNA

  1. XR_008487455.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96PV0.4 GenPept UniProtKB/Swiss-Prot:Q96PV0

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