Human Gene SHANK2 (ENST00000601538.6_7) from GENCODE V47lift37
  Description: SH3 and multiple ankyrin repeat domains 2, transcript variant 1 (from RefSeq NM_012309.5)
Gencode Transcript: ENST00000601538.6_7
Gencode Gene: ENSG00000162105.21_18
Transcript (Including UTRs)
   Position: hg19 chr11:70,313,959-70,963,623 Size: 649,665 Total Exon Count: 24 Strand: -
Coding Region
   Position: hg19 chr11:70,318,974-70,858,372 Size: 539,399 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:70,313,959-70,963,623)mRNA (may differ from genome)Protein (1784 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SHAN2_HUMAN
DESCRIPTION: RecName: Full=SH3 and multiple ankyrin repeat domains protein 2; Short=Shank2; AltName: Full=Cortactin-binding protein 1; Short=CortBP1; AltName: Full=Proline-rich synapse-associated protein 1;
FUNCTION: Seems to be an adapter protein in the postsynaptic density (PSD) of excitatory synapses that interconnects receptors of the postsynaptic membrane including NMDA-type and metabotropic glutamate receptors, and the actin-based cytoskeleton. May play a role in the structural and functional organization of the dendritic spine and synaptic junction.
SUBUNIT: Interacts with CTTN/cortactin SH3 domain, DLGAP1/GKAP and alpha-latrotoxin receptor 1. Is part of a complex with DLG4/PSD-95 and DLGAP1/GKAP. Interacts with GRID2, SLC9A3, CFTR and PLCB3. Interacts with DBNL (By similarity). Interacts with DNM2. Interacts with BAIAP2.
INTERACTION: P46108:CRK; NbExp=2; IntAct=EBI-1570571, EBI-886; P62993:GRB2; NbExp=2; IntAct=EBI-1570571, EBI-401755; P16333:NCK1; NbExp=6; IntAct=EBI-1570571, EBI-389883; P27986:PIK3R1; NbExp=2; IntAct=EBI-1570571, EBI-79464; P19174:PLCG1; NbExp=4; IntAct=EBI-1570571, EBI-79387;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cell junction, synapse (By similarity). Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity). Note=Cytoplasm, postsynaptic density of neuronal cells (By similarity).
TISSUE SPECIFICITY: Isoform 3 is present in epithelial colonic cells (at protein level).
DOMAIN: The PDZ domain is required for interaction with GRID2, PLCB3, CFTR and SLC9A3 (By similarity).
DISEASE: Defects in SHANK2 are a cause of susceptibility to autism type 17 (AUTS17) [MIM:613436]. Autism is a complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation.
SIMILARITY: Belongs to the SHANK family.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.
SIMILARITY: Contains 1 SH3 domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SHANK2
Diseases sorted by gene-association score: autism susceptibility 17* (975), autism spectrum disorder* (79), pervasive developmental disorder (12), deafness, autosomal recessive 63 (10), secretory diarrhea (5), autistic disorder (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -116.50265-0.440 Picture PostScript Text
3' UTR -1415.105015-0.282 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001478 - PDZ
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR021129 - SAM_type1
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00536 - SAM domain (Sterile alpha motif)
PF00595 - PDZ domain
PF07647 - SAM domain (Sterile alpha motif)
PF07653 - Variant SH3 domain
PF12796 - Ankyrin repeats (3 copies)
PF13637 - Ankyrin repeats (many copies)
PF14604 - Variant SH3 domain
PF17820 - PDZ domain

SCOP Domains:
140860 - Pseudo ankyrin repeat-like
47769 - SAM/Pointed domain
50044 - SH3-domain
50156 - PDZ domain-like
48403 - Ankyrin repeat

ModBase Predicted Comparative 3D Structure on Q9UPX8
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017124 SH3 domain binding
GO:0030160 GKAP/Homer scaffold activity
GO:0035255 ionotropic glutamate receptor binding

Biological Process:
GO:0007416 synapse assembly
GO:0007612 learning
GO:0030534 adult behavior
GO:0035176 social behavior
GO:0060291 long-term synaptic potentiation
GO:0060292 long term synaptic depression
GO:0071625 vocalization behavior

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0001917 photoreceptor inner segment
GO:0005575 cellular_component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030054 cell junction
GO:0030426 growth cone
GO:0031526 brush border membrane
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043197 dendritic spine
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0060170 ciliary membrane
GO:0005883 neurofilament
GO:0008328 ionotropic glutamate receptor complex


-  Descriptions from all associated GenBank mRNAs
  AB208027 - Homo sapiens CORTBP1 mRNA for cortactin-binding protein 1, complete cds.
AB208026 - Homo sapiens PROSAP1 mRNA for proline-rich synapse associated protein 1, complete cds.
AB208025 - Homo sapiens SHANK2 mRNA for SH3 and multiple ankyrin repeat domain2, complete cds.
BC114484 - Homo sapiens SH3 and multiple ankyrin repeat domains 2, mRNA (cDNA clone IMAGE:40054124), complete cds.
BC113876 - Homo sapiens SH3 and multiple ankyrin repeat domains 2, mRNA (cDNA clone IMAGE:40054125).
BC168372 - Synthetic construct Homo sapiens clone IMAGE:100068268, MGC:195885 SH3 and multiple ankyrin repeat domains 2 (SHANK2) mRNA, encodes complete protein.
AF141901 - Homo sapiens GKAP/SAPAP interacting protein (SHANK) mRNA, partial cds.
BC093885 - Homo sapiens SH3 and multiple ankyrin repeat domains 2, mRNA (cDNA clone IMAGE:7939730), complete cds.
BC112097 - Homo sapiens SH3 and multiple ankyrin repeat domains 2, transcript variant 2, mRNA (cDNA clone IMAGE:8327565), complete cds.
BC143389 - Homo sapiens SH3 and multiple ankyrin repeat domains 2, mRNA (cDNA clone IMAGE:9051895), complete cds.
DQ152234 - Homo sapiens Shank2E mRNA, partial cds.
AK095088 - Homo sapiens cDNA FLJ37769 fis, clone BRHIP2025366, highly similar to Rattus norvegicus mRNA for Proline Rich Synapse Associated Protein 1A.
AK096045 - Homo sapiens cDNA FLJ38726 fis, clone KIDNE2010271, moderately similar to Mus musculus mRNA for Shank3b protein.
JD092931 - Sequence 73955 from Patent EP1572962.
AF131790 - Homo sapiens clone 24903 mRNA sequence.
JD086170 - Sequence 67194 from Patent EP1572962.
JD239330 - Sequence 220354 from Patent EP1572962.
JD288851 - Sequence 269875 from Patent EP1572962.
JD122409 - Sequence 103433 from Patent EP1572962.
JD262650 - Sequence 243674 from Patent EP1572962.
JD208151 - Sequence 189175 from Patent EP1572962.
JD500901 - Sequence 481925 from Patent EP1572962.
JD289839 - Sequence 270863 from Patent EP1572962.
JD196874 - Sequence 177898 from Patent EP1572962.
JD147554 - Sequence 128578 from Patent EP1572962.
JD375537 - Sequence 356561 from Patent EP1572962.
BX648718 - Homo sapiens mRNA; cDNA DKFZp686O22113 (from clone DKFZp686O22113).
AB028945 - Homo sapiens mRNA for KIAA1022 protein, partial cds.
BC041371 - Homo sapiens SH3 and multiple ankyrin repeat domains 2, mRNA (cDNA clone IMAGE:5273763).
JD036608 - Sequence 17632 from Patent EP1572962.
AK128563 - Homo sapiens cDNA FLJ46722 fis, clone TRACH3018606, moderately similar to Rattus norvegicus Shank1a mRNA.
JD360310 - Sequence 341334 from Patent EP1572962.
JD245987 - Sequence 227011 from Patent EP1572962.
JD321395 - Sequence 302419 from Patent EP1572962.
JD181765 - Sequence 162789 from Patent EP1572962.
JD309953 - Sequence 290977 from Patent EP1572962.
JD474703 - Sequence 455727 from Patent EP1572962.
JD162509 - Sequence 143533 from Patent EP1572962.
JD286294 - Sequence 267318 from Patent EP1572962.
JD263733 - Sequence 244757 from Patent EP1572962.
JD359973 - Sequence 340997 from Patent EP1572962.
JD036356 - Sequence 17380 from Patent EP1572962.
JD370769 - Sequence 351793 from Patent EP1572962.
JD207151 - Sequence 188175 from Patent EP1572962.
JD299193 - Sequence 280217 from Patent EP1572962.
JD348697 - Sequence 329721 from Patent EP1572962.
JD457785 - Sequence 438809 from Patent EP1572962.
JD172057 - Sequence 153081 from Patent EP1572962.
JD079210 - Sequence 60234 from Patent EP1572962.
JD051579 - Sequence 32603 from Patent EP1572962.
JD476063 - Sequence 457087 from Patent EP1572962.
JD038156 - Sequence 19180 from Patent EP1572962.
JD362963 - Sequence 343987 from Patent EP1572962.
JD362114 - Sequence 343138 from Patent EP1572962.
JD105204 - Sequence 86228 from Patent EP1572962.
JD065886 - Sequence 46910 from Patent EP1572962.
JD368886 - Sequence 349910 from Patent EP1572962.
JD217616 - Sequence 198640 from Patent EP1572962.
JD102810 - Sequence 83834 from Patent EP1572962.
JD094814 - Sequence 75838 from Patent EP1572962.
JD559286 - Sequence 540310 from Patent EP1572962.
JD383283 - Sequence 364307 from Patent EP1572962.
JD111793 - Sequence 92817 from Patent EP1572962.
JD431155 - Sequence 412179 from Patent EP1572962.
JD183057 - Sequence 164081 from Patent EP1572962.
JD201118 - Sequence 182142 from Patent EP1572962.
JD049543 - Sequence 30567 from Patent EP1572962.
JD149708 - Sequence 130732 from Patent EP1572962.
JD533930 - Sequence 514954 from Patent EP1572962.
JD077111 - Sequence 58135 from Patent EP1572962.
JD445842 - Sequence 426866 from Patent EP1572962.
JD243051 - Sequence 224075 from Patent EP1572962.
JD281339 - Sequence 262363 from Patent EP1572962.
JD069013 - Sequence 50037 from Patent EP1572962.
JD230336 - Sequence 211360 from Patent EP1572962.
JD297787 - Sequence 278811 from Patent EP1572962.
JD431521 - Sequence 412545 from Patent EP1572962.
JD167056 - Sequence 148080 from Patent EP1572962.
JD454940 - Sequence 435964 from Patent EP1572962.
JD420808 - Sequence 401832 from Patent EP1572962.
JD240072 - Sequence 221096 from Patent EP1572962.
JD181970 - Sequence 162994 from Patent EP1572962.
JD454989 - Sequence 436013 from Patent EP1572962.
JD105454 - Sequence 86478 from Patent EP1572962.
JD105453 - Sequence 86477 from Patent EP1572962.
JD052871 - Sequence 33895 from Patent EP1572962.
JD095110 - Sequence 76134 from Patent EP1572962.
JD182140 - Sequence 163164 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UPX8 (Reactome details) participates in the following event(s):

R-HSA-6794351 SHARPIN binds SHANK proteins
R-HSA-6794357 SHANK proteins bind GKAPs
R-HSA-6794344 HOMER binds SHANK proteins
R-HSA-6797554 ABP1 binds SHANK proteins
R-HSA-6794361 Neurexins and neuroligins
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: C0SPG8, C0SPG9, CORTBP1, ENST00000601538.1, ENST00000601538.2, ENST00000601538.3, ENST00000601538.4, ENST00000601538.5, KIAA1022, NM_012309, PROSAP1, Q3Y8G9, Q52LK2, Q9UKP1, Q9UPX8, SHAN2_HUMAN, uc327ftn.1, uc327ftn.2
UCSC ID: ENST00000601538.6_7
RefSeq Accession: NM_012309.5
Protein: Q9UPX8 (aka SHAN2_HUMAN or SHK2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.