Syngap1 MGI Mouse Gene Detail - MGI:3039785 - synaptic Ras GTPase activating protein 1 homolog (rat)

Symbol

Syngap1
Name

synaptic Ras GTPase activating protein 1 homolog (rat)
Synonyms

Syngap

Feature Type

protein coding gene
IDs

MGI:3039785
NCBI Gene: 240057
Alliance

gene page
Transcription Start Sites

12 TSS

Sequence Map

Chr17:27160227-27191408 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 17, 13.60 cM
Mapping Data

1 experiment

SNPs within 2kb

375 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3039785	protein coding gene	Chr17:27160186-27191408 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0023412	protein coding gene	Chr17:26165695-26203612 (+)
A/J	MGP_AJ_G0023369	protein coding gene	Chr17:25371262-25403863 (+)
AKR/J	MGP_AKRJ_G0023335	protein coding gene	Chr17:25504846-25537782 (+)
BALB/cJ	MGP_BALBcJ_G0023374	protein coding gene	Chr17:25613288-25646854 (+)
C3H/HeJ	MGP_C3HHeJ_G0023135	protein coding gene	Chr17:25880263-25913208 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0023817	protein coding gene	Chr17:27271608-27307153 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0021291	protein coding gene	Chr17:22781280-22813507 (+)
CAST/EiJ	MGP_CASTEiJ_G0022636	protein coding gene	Chr17:25807631-25841637 (+)
CBA/J	MGP_CBAJ_G0023109	protein coding gene	Chr17:28223541-28257500 (+)
DBA/2J	MGP_DBA2J_G0023241	protein coding gene	Chr17:24933682-24966065 (+)
FVB/NJ	MGP_FVBNJ_G0023210	protein coding gene	Chr17:24718743-24751744 (+)
LP/J	MGP_LPJ_G0023318	protein coding gene	Chr17:26415629-26452354 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0023228	protein coding gene	Chr17:27738587-27777855 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0023858	protein coding gene	Chr17:25878102-25909572 (+)
PWK/PhJ	MGP_PWKPhJ_G0022386	protein coding gene	Chr17:23732576-23764368 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0022204	protein coding gene	Chr17:23914580-23947735 (+)
WSB/EiJ	MGP_WSBEiJ_G0022699	protein coding gene	Chr17:25900673-25933909 (+)

Human Ortholog

SYNGAP1, synaptic Ras GTPase activating protein 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SYNGAP1, synaptic Ras GTPase activating protein 1
Synonyms

MRD5, RASA1, RASA5, SYNGAP
Links

HGNC:11497

NCBI Gene ID: 8831

neXtProt AC: NX_Q96PV0

UniProt: Q96PV0
Chr Location

6p21.32; chr6:33418167-33453689 (+) GRCh38

MGI Vertebrate Homology

Syngap1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: SYNGAP1
Gene Tree

Syngap1

Diseases

1 with Syngap1 mouse models; 1 with human SYNGAP1 associations

Human Disease

Mouse Models

schizophrenia

IDs

View 1 model

autosomal dominant intellectual developmental disorder 5

IDs

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

43 phenotypes from 4 alleles in 5 genetic backgrounds
8 phenotypes from multigenic genotypes
37 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

18
Endonuclease-mediated

7
Gene trapped

1
Radiation induced

2
Targeted

7
Genomic Mutations

3 involving Syngap1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

49 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutant mice exhibit postnatal lethality, and by P3-P4, exhibit small body size and brain, reduced movement and do not feed.

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All GO Annotations

39
GO References

16

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

798
Tissues

17
cDNA Data

4
Literature Summary

12

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase syngap1

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All Sequences

132
RefSeq

66
UniProt

15
CCDS

CCDS59625.1

Ensembl

ENSMUSG00000067629 (Evidence)
NCBI Gene

240057

			Length	Strain/Species	Flank
genomic	ENSMUSG00000067629	Ensembl Gene Model \| MGI Sequence Detail	31182	C57BL/6J	± kb
transcript	ENSMUST00000194598	Ensembl \| MGI Sequence Detail	6011	Not Applicable
polypeptide	ENSMUSP00000141686	Ensembl \| MGI Sequence Detail	1340	Not Applicable

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UniProt

15 Sequences
Protein Ontology

PR:000015877 Ras/Rap GTPase-activating protein SynGAP

(term hierarchy)
PDB

5JXB, 5JXC
InterPro Domains

IPR000008 C2 domain

IPR035892 C2 domain superfamily

IPR021887 Disabled homolog 2-interacting protein, C-terminal domain

IPR011993 PH-like domain superfamily

IPR001849 Pleckstrin homology domain

IPR001936 Ras GTPase-activating domain

IPR039360 Ras GTPase-activating protein

IPR023152 Ras GTPase-activating protein, conserved site

IPR008936 Rho GTPase activation protein

IPR037779 SynGAP, PH domain
GlyGen

F6SEU4 16 sites, 4 N-linked glycans (4 sites), 1 O-linked glycan (12 sites)

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All nucleic 5

cDNA 4

Primer pair 1

Microarray probesets 6

Summaries

All 73

Developmental Gene Expression 12

Diseases 1

Gene Ontology 16

Phenotypes 37
Earliest

J:98903 Komiyama NH, et al., SynGAP regulates ERK/MAPK signaling, synaptic plasticity, and learning in the complex with postsynaptic density 95 and NMDA receptor. J Neurosci. 2002 Nov 15;22(22):9721-32
Latest

J:353560 Araki Y, et al., SynGAP regulates synaptic plasticity and cognition independently of its catalytic activity. Science. 2024 Mar;383(6686):eadk1291

TSS for Syngap1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr143279	Chr17:27160204-27160244 (+)	-3 bp
Tssr143280	Chr17:27160251-27160290 (+)	44 bp
Tssr143281	Chr17:27160394-27160438 (+)	189 bp
Tssr143282	Chr17:27167375-27167402 (+)	7,162 bp
Tssr143283	Chr17:27167590-27167614 (+)	7,375 bp
Tssr143284	Chr17:27167620-27167660 (+)	7,413 bp
Tssr143285	Chr17:27167895-27167952 (+)	7,697 bp
Tssr143286	Chr17:27170631-27170658 (+)	10,418 bp
Tssr143287	Chr17:27170677-27170694 (+)	10,459 bp
Tssr143288	Chr17:27171811-27171828 (+)	11,593 bp
Tssr143289	Chr17:27171835-27171852 (+)	11,617 bp
Tssr143290	Chr17:27189961-27189968 (+)	29,738 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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