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

Summary

Go to the top of the page Help

Official Symbol: SYNGAP1provided by HGNC
Official Full Name: synaptic Ras GTPase activating protein 1provided by HGNC
Primary source: HGNC:11497
Locus tag: DASS-97D12.6
See related: Ensembl:ENSG00000197283; HPRD:16018; MIM:603384; Vega:OTTHUMG00000031096
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: The protein encoded by this gene is a major component of the postsynaptic density (PSD), a group of proteins found associated with NMDA receptors at synapses. The encoded protein is phosphorylated by calmodulin-dependent protein kinase II and dephosphorylated by NMDA receptor activation. Defects in this gene are a cause of mental retardation autosomal dominant type 5 (MRD5). [provided by RefSeq, Dec 2009]

Genomic context

Go to the top of the page Help

Location :: 6p21.3

Sequence :: Chromosome: 6; NC_000006.11 (33387847..33421466)

See SYNGAP1 in Epigenomics, MapViewer

Chromosome 6 - NC_000006.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions What's a GeneRIF?

SYNGAP1 is a brain-specific protein that interacts with key components of the proteins involved in experience-dependent changes in glutamate synapses involved in learning.
Title: De novo autosomal dominant mutation in SYNGAP1.
We provide evidence that truncating mutations in SYNGAP1 are common in nonsyndromic intellectual disability and can be also associated with autism.
Title: De novo SYNGAP1 mutations in nonsyndromic intellectual disability and autism.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Functional impact of global rare copy number variation in autism spectrum disorders.
These data suggest that NMDA receptor complex formation, localization, and downstream signaling may be abnormal in schizophrenia as PSD95, SynGAP and MUPP1 expression is altered.
Title: Decreased expression of NMDA receptor-associated proteins in frontal cortex of elderly patients with schizophrenia.
Observational study of gene-disease association. (HuGE Navigator)
Title: [De novo mutations in SYNGAP1 associated with non-syndromic mental retardation].
Results indicate that SYNGAP1 disruption is a cause of autosomal dominant nonsyndromic mental retardation.
Title: Mutations in SYNGAP1 in autosomal nonsyndromic mental retardation.
The C2 domain of SynGAP is essential for stimulation of the Rap GTPase reaction.
Title: The C2 domain of SynGAP is essential for stimulation of the Rap GTPase reaction.
studies show that the regulation of synaptic Ras signaling by SynGAP is important for proper neuronal development and glutamate receptor trafficking and is critical for the induction of LTP
Title: The role of synaptic GTPase-activating protein in neuronal development and synaptic plasticity.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Mental retardation, autosomal dominant 5

MIM: 612621

Genetic Testing Registry

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Source	Pubs	Description
Q96PV0	Q9UQM7	CAMK2A	HPRD	PubMed
Q96PV0	Q92796	DLG3	HPRD	PubMed
Q96PV0	P78352	DLG4	HPRD	PubMed
Q96PV0	Q9Y2H0	DLGAP4	HPRD	PubMed
Q96PV0	Q05586	GRIN1	HPRD	PubMed
Q96PV0	Q13224	GRIN2B	HPRD	PubMed
Q96PV0	O15399	GRIN2D	HPRD	PubMed
Q96PV0	P35968	KDR	HPRD	PubMed
Q96PV0	O75970	MPDZ	HPRD	PubMed
Q96PV0	P09619	PDGFRB	HPRD	PubMed
Q96PV0	Q15654	TRIP6	HPRD	PubMed
Q96PV0	O75385	ULK1	HPRD	PubMed
Q96PV0	Q8IYT8	ULK2	HPRD	PubMed
BioGRID:114358	BioGRID:108085	DLG3	BioGRID	PubMed	Affinity Capture-Western; Two-hybrid
BioGRID:114358	BioGRID:108086	DLG4	BioGRID	PubMed	Two-hybrid
BioGRID:114358	BioGRID:125228	SAAL1	BioGRID	PubMed	Co-fractionation
BioGRID:114358	BioGRID:113996	ULK1	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex; Two-hybrid
BioGRID:114358	BioGRID:115058	ULK2	BioGRID	PubMed	Reconstituted Complex

General gene information

Go to the top of the page Help

Genotypes

See SYNGAP1 SNP Geneview Report
See SYNGAP1 SNP Variation Viewer Report

Homology

Homologs of the SYNGAP1 gene: The SYNGAP1 gene is conserved in chimpanzee, Rhesus monkey, cow, mouse, rat, and zebrafish.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
Rab GTPase activator activity	IEA Inferred from Electronic Annotation more info
Ras GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
SH3 domain binding	IEA Inferred from Electronic Annotation more info
phospholipid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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	IBA Inferred from Biological aspect of Ancestor more info
negative regulation of Ras protein signal transduction	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
negative regulation of axonogenesis	IEA Inferred from Electronic Annotation more info
pattern specification process	IEA Inferred from Electronic Annotation more info
positive regulation of Ras GTPase activity	IBA Inferred from Biological aspect of Ancestor 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 and 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
cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
dendritic shaft	IEA Inferred from Electronic Annotation more info
intrinsic to internal side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: ras GTPase-activating protein SynGAP

Names: ras GTPase-activating protein SynGAP; neuronal RasGAP; synaptic Ras GTPase-activating protein 1; synaptic Ras GTPase activating protein, 135kDa; synaptic Ras GTPase activating protein 1 homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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

NG_016137.1 RefSeqGene

Range

5001..38620

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006772.2 → NP_006763.2 ras GTPase-activating protein SynGAP

Status: REVIEWED

Source sequence(s)

AK094225, AK307888, AL713634, BM354009, BX282051, DA057307

Consensus CDS

CCDS34434.2

UniProtKB/Swiss-Prot

Q96PV0

Related

ENSP00000403636, OTTHUMP00000029119, ENST00000418600, OTTHUMT00000076151

Conserved Domains (4) summary

cd05136
Location:415 – 722
Blast Score: 1249

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 ...

pfam12004
Location:719 – 1309
Blast Score: 917

DUF3498; Domain of unknown function (DUF3498)

cd04013
Location:252 – 414
Blast Score: 558

C2_SynGAP_like; C2 domain present in Ras GTPase activating protein (GAP) family

cl00273
Location:136 – 249
Blast Score: 214

PH-like; Pleckstrin homology-like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

Reference GRCh37.p10 ALT_REF_LOCI_7

Genomic

NT_167249.1 Reference GRCh37.p10 ALT_REF_LOCI_7

Range

4868093..4901710

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000006.11 Reference GRCh37.p10 Primary Assembly

Range

33387847..33421466

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000138.1 Alternate HuRef

Range

33129996..33162361

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018917.1 Alternate CHM1_1.0

Range

33303655..33337214

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001130066.1: Suppressed sequence

Description

NM_001130066.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript and protein.

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01038148.1 (9070..9171)	None
genomic	ABBA01038149.1	None
genomic	ABBA01038150.1	None
genomic	ABBA01038151.1	None
genomic	AL021366.1	CAA16161.1
genomic	AL662799.16 (72438..106057)	None
genomic	AMYH01016245.1 (95126..95301)	None
genomic	AMYH01016246.1	None
genomic	AMYH01016247.1	None
genomic	BX088650.9 (32043..65660)	None
genomic	CH471081.1	EAX03735.1
		EAX03736.1
		EAX03737.1
		EAX03738.1
mRNA	AK094225.1	None
mRNA	AK307888.1	None
mRNA	AL713634.1	CAD28452.1
mRNA	BM354009.1	None
mRNA	BX282051.1	None
mRNA	CN412954.1	None
mRNA	DA057307.1	None
other-genetic	BC148357.1	AAI48358.1