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Q96PV0 (SYGP1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ras GTPase-activating protein SynGAP
Alternative name(s):
Neuronal RasGAP
Synaptic Ras GTPase-activating protein 1
Short name=Synaptic Ras-GAP 1
Gene names
Name:SYNGAP1
Synonyms:KIAA1938
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length1343 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Major constituent of the PSD essential for postsynaptic signaling. Inhibitory regulator of the Ras-cAMP pathway. Member of the NMDAR signaling complex in excitatory synapses, it may play a role in NMDAR-dependent control of AMPAR potentiation, AMPAR membrane trafficking and synaptic plasticity. Regulates AMPAR-mediated miniature excitatory postsynaptic currents. May be involved in certain forms of brain injury, leading to long-term learning and memory deficits By similarity.

Subunit structure

Interacts KLHL17, CAMK2A and CAMK2B By similarity. Interacts with MPDZ. Ref.4

Post-translational modification

Phosphorylated by CaM-kinase II. Dephosphorylated upon NMDA receptor activation or SYNGAP1/MPDZ complex disruption. Phosphorylation by PLK2 promotes its activity By similarity.

Involvement in disease

Mental retardation, autosomal dominant 5 (MRD5) [MIM:612621]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRD5 patients show global developmental delay with delayed motor development, hypotonia, moderate-to-severe mental retardation, and severe language impairment. Autism can be present in some patients.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.5 Ref.6 Ref.7

Sequence similarities

Contains 1 C2 domain.

Contains 1 PH domain.

Contains 1 Ras-GAP domain.

Caution

It is uncertain whether Met-1 or Met-16 is the initiator methionine.

Sequence caution

The sequence BAB67831.2 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Coding sequence diversityAlternative splicing
Polymorphism
   DiseaseMental retardation
   DomainSH3-binding
   Molecular functionGTPase activation
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRas protein signal transduction

Inferred from electronic annotation. Source: Compara

dendrite development

Inferred from electronic annotation. Source: Compara

negative regulation of Ras protein signal transduction

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of apoptotic process

Inferred from electronic annotation. Source: Compara

negative regulation of axonogenesis

Inferred from electronic annotation. Source: Compara

pattern specification process

Inferred from electronic annotation. Source: Compara

receptor clustering

Inferred from electronic annotation. Source: Compara

regulation of MAPK cascade

Inferred from electronic annotation. Source: Compara

regulation of long-term neuronal synaptic plasticity

Inferred from electronic annotation. Source: Compara

regulation of synapse structure and activity

Inferred from electronic annotation. Source: Compara

regulation of synaptic plasticity

Inferred from sequence or structural similarity. Source: UniProtKB

visual learning

Inferred from electronic annotation. Source: Compara

   Cellular_componentcytoplasm

Inferred from Biological aspect of Ancestor. Source: RefGenome

dendritic shaft

Inferred from electronic annotation. Source: Compara

intrinsic to internal side of plasma membrane

Inferred from Biological aspect of Ancestor. Source: RefGenome

   Molecular_functionRab GTPase activator activity

Inferred from electronic annotation. Source: Compara

Ras GTPase activator activity

Inferred from Biological aspect of Ancestor. Source: RefGenome

phospholipid binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q96PV0-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q96PV0-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1265-1343: RLMLVEEELR...NGEFRNTADH → SPSLQADAGGGGAAPGPPRHG
Isoform 3 (identifier: Q96PV0-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-98: MSRSRASIHR...PVEGRPHGEH → MGLRPPTPSP...RRCSSCCFPG
Isoform 4 (identifier: Q96PV0-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1296-1343: ERQLPPLGPTNPRVTLAPPWNGLAPPAPPPPPRLQITENGEFRNTADH → LLIR

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 13431343Ras GTPase-activating protein SynGAP
PRO_0000056654

Regions

Domain150 – 251102PH
Domain249 – 34799C2
Domain443 – 635193Ras-GAP
Motif785 – 81531SH3-binding Potential

Amino acid modifications

Modified residue3791Phosphoserine By similarity
Modified residue3851Phosphoserine; by PLK2 By similarity
Modified residue4491Phosphoserine; by PLK2 By similarity
Modified residue4661Phosphoserine; by PLK2 By similarity
Modified residue8361Phosphoserine; by PLK2 By similarity
Modified residue8401Phosphoserine; by PLK2 By similarity
Modified residue8421Phosphoserine; by PLK2 By similarity
Modified residue8951Phosphoserine; by PLK2 By similarity

Natural variations

Alternative sequence1 – 9898MSRSR…PHGEH → MGLRPPTPSPSGGSCSGSLP PPSRCQPLRRRCSSCCFPG in isoform 3.
VSP_026376
Alternative sequence1265 – 134379RLMLV…NTADH → SPSLQADAGGGGAAPGPPRH G in isoform 2.
VSP_007973
Alternative sequence1296 – 134348ERQLP…NTADH → LLIR in isoform 4.
VSP_026377
Natural variant2011D → E. Ref.5
VAR_065078
Natural variant7491R → Q. Ref.5
VAR_065079
Natural variant7901T → N. Ref.5
VAR_065080
Natural variant9911G → R. Ref.7
VAR_065081
Natural variant11151I → T. Ref.5 Ref.7
VAR_065082
Natural variant12831P → L. Ref.5
VAR_065083
Natural variant13101T → M. Ref.5
VAR_065084

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 26, 2007. Version 4.
Checksum: D9ABE21054677AA0

FASTA1,343148,284
        10         20         30         40         50         60 
MSRSRASIHR GSIPAMSYAP FRDVRGPSMH RTQYVHSPYD RPGWNPRFCI ISGNQLLMLD 

        70         80         90        100        110        120 
EDEIHPLLIR DRRSESSRNK LLRRTVSVPV EGRPHGEHEY HLGRSRRKSV PGGKQYSMEG 

       130        140        150        160        170        180 
APAAPFRPSQ GFLSRRLKSS IKRTKSQPKL DRTSSFRQIL PRFRSADHDR ARLMQSFKES 

       190        200        210        220        230        240 
HSHESLLSPS SAAEALELNL DEDSIIKPVH SSILGQEFCF EVTTSSGTKC FACRSAAERD 

       250        260        270        280        290        300 
KWIENLQRAV KPNKDNSRRV DNVLKLWIIE ARELPPKKRY YCELCLDDML YARTTSKPRS 

       310        320        330        340        350        360 
ASGDTVFWGE HFEFNNLPAV RALRLHLYRD SDKKRKKDKA GYVGLVTVPV ATLAGRHFTE 

       370        380        390        400        410        420 
QWYPVTLPTG SGGSGGMGSG GGGGSGGGSG GKGKGGCPAV RLKARYQTMS ILPMELYKEF 

       430        440        450        460        470        480 
AEYVTNHYRM LCAVLEPALN VKGKEEVASA LVHILQSTGK AKDFLSDMAM SEVDRFMERE 

       490        500        510        520        530        540 
HLIFRENTLA TKAIEEYMRL IGQKYLKDAI GEFIRALYES EENCEVDPIK CTASSLAEHQ 

       550        560        570        580        590        600 
ANLRMCCELA LCKVVNSHCV FPRELKEVFA SWRLRCAERG REDIADRLIS ASLFLRFLCP 

       610        620        630        640        650        660 
AIMSPSLFGL MQEYPDEQTS RTLTLIAKVI QNLANFSKFT SKEDFLGFMN EFLELEWGSM 

       670        680        690        700        710        720 
QQFLYEISNL DTLTNSSSFE GYIDLGRELS TLHALLWEVL PQLSKEALLK LGPLPRLLND 

       730        740        750        760        770        780 
ISTALRNPNI QRQPSRQSER PRPQPVVLRG PSAEMQGYMM RDLNSSIDLQ SFMARGLNSS 

       790        800        810        820        830        840 
MDMARLPSPT KEKPPPPPPG GGKDLFYVSR PPLARSSPAY CTSSSDITEP EQKMLSVNKS 

       850        860        870        880        890        900 
VSMLDLQGDG PGGRLNSSSV SNLAAVGDLL HSSQASLTAA LGLRPAPAGR LSQGSGSSIT 

       910        920        930        940        950        960 
AAGMRLSQMG VTTDGVPAQQ LRIPLSFQNP LFHMAADGPG PPGGHGGGGG HGPPSSHHHH 

       970        980        990       1000       1010       1020 
HHHHHHRGGE PPGDTFAPFH GYSKSEDLSS GVPKPPAASI LHSHSYSDEF GPSGTDFTRR 

      1030       1040       1050       1060       1070       1080 
QLSLQDNLQH MLSPPQITIG PQRPAPSGPG GGSGGGSGGG GGGQPPPLQR GKSQQLTVSA 

      1090       1100       1110       1120       1130       1140 
AQKPRPSSGN LLQSPEPSYG PARPRQQSLS KEGSIGGSGG SGGGGGGGLK PSITKQHSQT 

      1150       1160       1170       1180       1190       1200 
PSTLNPTMPA SERTVAWVSN MPHLSADIES AHIEREEYKL KEYSKSMDES RLDRVKEYEE 

      1210       1220       1230       1240       1250       1260 
EIHSLKERLH MSNRKLEEYE RRLLSQEEQT SKILMQYQAR LEQSEKRLRQ QQAEKDSQIK 

      1270       1280       1290       1300       1310       1320 
SIIGRLMLVE EELRRDHPAM AEPLPEPKKR LLDAQERQLP PLGPTNPRVT LAPPWNGLAP 

      1330       1340 
PAPPPPPRLQ ITENGEFRNT ADH

« Hide

Isoform 2 [UniParc].

Checksum: A9353354EF091FD6
Show »

FASTA1,285141,248
Isoform 3 [UniParc].

Checksum: 73BCEF16133B6D77
Show »

FASTA1,284140,929
Isoform 4 [UniParc].

Checksum: AC4DC1FF002B7075
Show »

FASTA1,299143,569

References

« Hide 'large scale' references
[1]"Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins."
Nagase T., Kikuno R., Ohara O.
DNA Res. 8:179-187(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Brain.
[2]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 384-1343 (ISOFORM 2).
Tissue: Amygdala.
[4]"SynGAP-MUPP1-CaMKII synaptic complexes regulate p38 MAP kinase activity and NMDA receptor-dependent synaptic AMPA receptor potentiation."
Krapivinsky G., Medina I., Krapivinsky L., Gapon S., Clapham D.E.
Neuron 43:563-574(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH MPDZ.
[5]"Mutations in SYNGAP1 in autosomal nonsyndromic mental retardation."
Synapse to disease group
Hamdan F.F., Gauthier J., Spiegelman D., Noreau A., Yang Y., Pellerin S., Dobrzeniecka S., Cote M., Perreault-Linck E., Carmant L., D'Anjou G., Fombonne E., Addington A.M., Rapoport J.L., Delisi L.E., Krebs M.O., Mouaffak F., Joober R. expand/collapse author list , Mottron L., Drapeau P., Marineau C., Lafreniere R.G., Lacaille J.C., Rouleau G.A., Michaud J.L.
N. Engl. J. Med. 360:599-605(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN MRD5, VARIANTS GLU-201; GLN-749; ASN-790; THR-1115; LEU-1283 AND MET-1310.
[6]"A de novo paradigm for mental retardation."
Vissers L.E., de Ligt J., Gilissen C., Janssen I., Steehouwer M., de Vries P., van Lier B., Arts P., Wieskamp N., del Rosario M., van Bon B.W., Hoischen A., de Vries B.B., Brunner H.G., Veltman J.A.
Nat. Genet. 42:1109-1112(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN MRD5.
[7]"De novo SYNGAP1 mutations in nonsyndromic intellectual disability and autism."
Hamdan F.F., Daoud H., Piton A., Gauthier J., Dobrzeniecka S., Krebs M.O., Joober R., Lacaille J.C., Nadeau A., Milunsky J.M., Wang Z., Carmant L., Mottron L., Beauchamp M.H., Rouleau G.A., Michaud J.L.
Biol. Psychiatry 69:898-901(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN MRD5, VARIANTS ARG-991 AND THR-1115.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB067525 mRNA. Translation: BAB67831.2. Different initiation.
AL021366 Genomic DNA. Translation: CAA16161.1.
AL662799 Genomic DNA. Translation: CAI18276.2.
AL662799 Genomic DNA. Translation: CAM25572.1.
BX088650 Genomic DNA. Translation: CAM26304.1.
BX088650 Genomic DNA. Translation: CAM26305.1.
BX088650 Genomic DNA. Translation: CAM26306.1.
AL713634 mRNA. Translation: CAD28452.1.
IPIIPI00177884.
IPI00337790.
IPI00796859.
IPI00847493.
RefSeqNP_006763.2. NM_006772.2.
UniGeneHs.586264.

3D structure databases

ProteinModelPortalQ96PV0.
ModBaseSearch...

Protein-protein interaction databases

IntActQ96PV0. 6 interactions.
STRING9606.ENSP00000403636.

PTM databases

PhosphoSiteQ96PV0.

Polymorphism databases

DMDM150421676.

Proteomic databases

PaxDbQ96PV0.
PRIDEQ96PV0.

Protocols and materials databases

DNASU8831.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000293748; ENSP00000293748; ENSG00000197283.
ENST00000395071; ENSP00000378509; ENSG00000227460.
ENST00000414753; ENSP00000407995; ENSG00000227460.
ENST00000418600; ENSP00000403636; ENSG00000197283.
ENST00000428982; ENSP00000412475; ENSG00000197283.
ENST00000440474; ENSP00000410023; ENSG00000197283.
ENST00000455687; ENSP00000414259; ENSG00000227460.
ENST00000551507; ENSP00000446753; ENSG00000227460.
GeneID8831.
KEGGhsa:8831.
UCSCuc010juz.3. human.
uc011dri.2. human.

Organism-specific databases

CTD8831.
GeneCardsGC06P033387.
HGNCHGNC:11497. SYNGAP1.
HPAHPA038373.
MIM603384. gene.
612621. phenotype.
neXtProtNX_Q96PV0.
Orphanet178469. Autosomal dominant nonsyndromic intellectual deficit.
PharmGKBPA36279.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG245428.
HOVERGENHBG006492.
InParanoidQ96PV0.
OMANPHIQRQ.
OrthoDBEOG49ZXNH.

Gene expression databases

ArrayExpressQ96PV0.
BgeeQ96PV0.
CleanExHS_SYNGAP1.
GenevestigatorQ96PV0.
GermOnlineENSG00000197283. Homo sapiens.

Family and domain databases

Gene3D1.10.506.10. 1 hit.
2.20.170.10. 1 hit.
2.30.29.30. 2 hits.
InterProIPR000008. C2_Ca-dep.
IPR008973. C2_Ca/lipid-bd_dom_CaLB.
IPR021887. DUF3498.
IPR011993. PH_like_dom.
IPR001849. Pleckstrin_homology.
IPR001936. RasGAP.
IPR023152. RasGAP_CS.
IPR008936. Rho_GTPase_activation_prot.
IPR023315. SynGAP_C2_N.
[Graphical view]
PfamPF00168. C2. 1 hit.
PF12004. DUF3498. 1 hit.
PF00616. RasGAP. 1 hit.
[Graphical view]
SMARTSM00239. C2. 1 hit.
SM00233. PH. 1 hit.
SM00323. RasGAP. 1 hit.
[Graphical view]
SUPFAMSSF49562. C2_CaLB. 1 hit.
SSF48350. Rho_GAP. 1 hit.
PROSITEPS50004. C2. False negative.
PS50003. PH_DOMAIN. 1 hit.
PS00509. RAS_GTPASE_ACTIV_1. 1 hit.
PS50018. RAS_GTPASE_ACTIV_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi8831.
NextBio33144.
SOURCESearch...

Entry information

Entry nameSYGP1_HUMAN
AccessionPrimary (citable) accession number: Q96PV0
Secondary accession number(s): A2AB17 expand/collapse secondary AC list , A2BEL6, A2BEL7, A8MQC4, Q8TCS2, Q9UGE2
Entry history
Integrated into UniProtKB/Swiss-Prot: August 15, 2003
Last sequence update: June 26, 2007
Last modified: May 1, 2013
This is version 99 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

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