SHANK1 Gene (Protein Coding)

SH3 And Multiple Ankyrin Repeat Domains 1

GC19M050659
GIFtS:
38
This gene encodes a member of the SHANK (SH3 domain and ankyrin repeat containing) family of proteins. Members of this family act as scaffold proteins that are required for the development and function of neuronal synapses. Deletions in this gene may be associated with autism spectrum disorder in males. [provided by RefSeq, Apr 2016] See more...

Aliases for SHANK1 Gene

Aliases for SHANK1 Gene

  • SH3 And Multiple Ankyrin Repeat Domains 1 2 3 5
  • Somatostatin Receptor-Interacting Protein 2 3 4
  • SSTRIP 2 3 4
  • SH3 And Multiple Ankyrin Repeat Domains Protein 1 3 4
  • SSTR-Interacting Protein 3 4
  • SPANK-1 2 3
  • Synamon 2 3
  • SHANK1 5
  • Shank1 4

External Ids for SHANK1 Gene

Previous GeneCards Identifiers for SHANK1 Gene

  • GC19M051793
  • GC19M051526
  • GC19M055841
  • GC19M055856
  • GC19M055818
  • GC19M051165
  • GC19M047499

Summaries for SHANK1 Gene

Entrez Gene Summary for SHANK1 Gene

  • This gene encodes a member of the SHANK (SH3 domain and ankyrin repeat containing) family of proteins. Members of this family act as scaffold proteins that are required for the development and function of neuronal synapses. Deletions in this gene may be associated with autism spectrum disorder in males. [provided by RefSeq, Apr 2016]

GeneCards Summary for SHANK1 Gene

SHANK1 (SH3 And Multiple Ankyrin Repeat Domains 1) is a Protein Coding gene. Diseases associated with SHANK1 include Schizophrenia 15 and Autism Spectrum Disorder. Among its related pathways are Protein-protein interactions at synapses and Circadian entrainment. Gene Ontology (GO) annotations related to this gene include identical protein binding and protein C-terminus binding. An important paralog of this gene is SHANK2.

UniProtKB/Swiss-Prot Summary for SHANK1 Gene

  • 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 via complexes with GKAP/PSD-95 and Homer, respectively, and the actin-based cytoskeleton. Plays a role in the structural and functional organization of the dendritic spine and synaptic junction.

Gene Wiki entry for SHANK1 Gene

Additional gene information for SHANK1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHANK1 Gene

Genomics for SHANK1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SHANK1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH19J050718 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas 254 +0.7 701 2.2 ZNF513 VEZF1 ZNF148 GLIS1 ZNF398 EGR1 BHLHE40 SIN3A KLF1 ZNF560 SHANK1 lnc-SHANK1-1 CLEC11A SPACA6P-AS FUZ SYT3 LRRC4B ASPDH KCNC3 lnc-SYT3-2
GH19J050716 Promoter 0.3 EPDnew 250.7 +2.9 2911 0.1 SHANK1 lnc-SHANK1-1 lnc-SYT3-2 C19orf81
GH19J050329 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 19.5 +388.8 388801 7.2 TBP ZBTB10 SP1 MXD4 FEZF1 CEBPA SIX5 NR2C1 MNT IKZF1 KCNC3 NR1H2 HSALNG0127087 LOC105372437 lnc-POLD1-3 NUP62 PRR12 POLD1 CPT1C ENSG00000268047
GH19J050510 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 20 +207.3 207301 5 CHD2 TBP SP1 ZBTB10 CEBPA SIX5 NR2C1 MNT DEK BRCA1 ASPDH JOSD2 HSALNG0127111 lnc-ASPDH-1 SHANK1 SYT3 ENSG00000267890 NR1H2 RRAS PRR12
GH19J049764 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 20 +953.0 953039 3.9 CHD2 TBP ZBTB10 SP1 MXD4 CEBPA SIX5 MNT DEK IKZF1 AP2A1 lnc-TSKS-2 NUP62 SHANK1 PTOV1-AS2 SYT3 SNORD35A SNORD35B IRF3 ALDH16A1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHANK1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHANK1

Top Transcription factor binding sites by QIAGEN in the SHANK1 gene promoter:
  • AP-1
  • c-Myc
  • E47
  • Max1
  • NRSF form 1
  • NRSF form 2
  • Pax-5
  • STAT5A
  • Tal-1

Genomic Locations for SHANK1 Gene

Latest Assembly
chr19:50,659,255-50,719,802
(GRCh38/hg38)
Size:
60,548 bases
Orientation:
Minus strand

Previous Assembly
chr19:51,162,512-51,223,059
(GRCh37/hg19 by Entrez Gene)
Size:
60,548 bases
Orientation:
Minus strand

chr19:51,165,084-51,222,707
(GRCh37/hg19 by Ensembl)
Size:
57,624 bases
Orientation:
Minus strand

Genomic View for SHANK1 Gene

Genes around SHANK1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHANK1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHANK1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SHANK1 Gene

Proteins for SHANK1 Gene

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  • Protein details for SHANK1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y566-SHAN1_HUMAN
    Recommended name:
    SH3 and multiple ankyrin repeat domains protein 1
    Protein Accession:
    Q9Y566
    Secondary Accessions:
    • A8MXP5
    • B7WNY6
    • Q9NYW9

    Protein attributes for SHANK1 Gene

    Size:
    2161 amino acids
    Molecular mass:
    224959 Da
    Quaternary structure:
    • May homomultimerize via its SAM domain (By similarity). Interacts with the C-terminus of SSTR2 via the PDZ domain. Interacts with IGSF9, SHARPIN, SPTAN1, HOMER1 and DLGAP1/GKAP isoforms 1 and 2 (By similarity). Part of a complex with DLG4/PSD-95 and DLGAP1/GKAP (By similarity). Interacts with BAIAP2. Interacts with HOMER1 and HOMER3 (By similarity).

    Three dimensional structures from OCA and Proteopedia for SHANK1 Gene

    Alternative splice isoforms for SHANK1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHANK1 Gene

Protein Expression for SHANK1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SHANK1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SHANK1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SHANK1 Gene

Domains & Families for SHANK1 Gene

Gene Families for SHANK1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SHANK1 Gene

InterPro:
Blocks:
  • Ankyrin repeat signature
  • Sterile alpha motif SAM
  • SH3 domain signature
  • PDZ/DHR/GLGF domain
  • Variant SH3
ProtoNet:

Suggested Antigen Peptide Sequences for SHANK1 Gene

GenScript: Design optimal peptide antigens:
  • Somatostatin receptor-interacting protein (SHAN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y566

UniProtKB/Swiss-Prot:

SHAN1_HUMAN :
  • Belongs to the SHANK family.
Family:
  • Belongs to the SHANK family.
genes like me logo Genes that share domains with SHANK1: view

Function for SHANK1 Gene

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  6. Cell Lines for research

Molecular function for SHANK1 Gene

UniProtKB/Swiss-Prot 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 via complexes with GKAP/PSD-95 and Homer, respectively, and the actin-based cytoskeleton. Plays a role in the structural and functional organization of the dendritic spine and synaptic junction.

Phenotypes From GWAS Catalog for SHANK1 Gene

Gene Ontology (GO) - Molecular Function for SHANK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10551867
GO:0008022 protein C-terminus binding ISS --
GO:0017124 SH3 domain binding ISS --
GO:0030159 receptor signaling complex scaffold activity IEA --
GO:0030160 GKAP/Homer scaffold activity ISS --
genes like me logo Genes that share ontologies with SHANK1: view
genes like me logo Genes that share phenotypes with SHANK1: view

Animal Models for SHANK1 Gene

MGI Knock Outs for SHANK1:

Animal Models for research

miRNA for SHANK1 Gene

miRTarBase miRNAs that target SHANK1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHANK1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHANK1 Gene

Localization for SHANK1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHANK1 Gene

Cytoplasm. Cell junction, synapse, postsynaptic density. Cell junction, synapse. Note=Colocalizes with alpha-latrotoxin receptor 1. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SHANK1 gene
Compartment Confidence
plasma membrane 5
cytosol 5
nucleus 4
cytoskeleton 3
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHANK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane ISS --
GO:0008328 colocalizes_with ionotropic glutamate receptor complex IBA,ISS --
GO:0014069 postsynaptic density ISS --
genes like me logo Genes that share ontologies with SHANK1: view

Pathways & Interactions for SHANK1 Gene

genes like me logo Genes that share pathways with SHANK1: view

Pathways by source for SHANK1 Gene

1 KEGG pathway for SHANK1 Gene

SIGNOR curated interactions for SHANK1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SHANK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IEA --
GO:0007610 behavior IBA 21873635
GO:0007616 long-term memory ISS --
GO:0008306 associative learning ISS --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with SHANK1: view

Drugs & Compounds for SHANK1 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for SHANK1 Gene

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mRNA/cDNA for SHANK1 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHANK1

Alternative Splicing Database (ASD) splice patterns (SP) for SHANK1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18
SP1:
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:

Relevant External Links for SHANK1 Gene

GeneLoc Exon Structure for
SHANK1

Expression for SHANK1 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHANK1 Gene

mRNA expression in normal human tissues for SHANK1 Gene
mRNA expression by GTEx for SHANK1 GenemRNA expression by BioGPS for SHANK1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SHANK1 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x8.4), Brain - Amygdala (x7.1), Brain - Hippocampus (x6.9), Brain - Frontal Cortex (BA9) (x6.2), and Brain - Cortex (x5.3).

Protein differential expression in normal tissues from HIPED for SHANK1 Gene

This gene is overexpressed in Cerebrospinal fluid (35.3), Urine (12.8), and Breast (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHANK1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHANK1

SOURCE GeneReport for Unigene cluster for SHANK1 Gene:

Hs.274255

mRNA Expression by UniProt/SwissProt for SHANK1 Gene:

Q9Y566-SHAN1_HUMAN
Tissue specificity: Expressed in brain particularly in the amygdala, hippocampus, substantia nigra and thalamus. Isoform 2 seems to be expressed ubiquitously.

Evidence on tissue expression from TISSUES for SHANK1 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SHANK1: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHANK1 Gene

Orthologs for SHANK1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHANK1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SHANK1 31
  • 98 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia SHANK1 31
  • 93 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SHANK1 30 31
  • 92.29 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SHANK1 30 31
  • 89.32 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Shank1 30 17 31
  • 85.93 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Shank1 30
  • 85.54 (n)
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 55 (a)
 ManyToMany
Lizard
(Anolis carolinensis)
 Reptilia SHANK1 31
  • 67 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia shank1 30
  • 61.64 (n)
Zebrafish
(Danio rerio)
 Actinopterygii SHANK1 (2 of 2) 31
  • 65 (a)
 OneToMany
SHANK1 (1 of 2) 31
  • 50 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta Prosap 31
  • 23 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea C33B4.3 32
  • 44 (a)
shn-1 31
  • 29 (a)
 OneToMany
Species where no ortholog for SHANK1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SHANK1 Gene

ENSEMBL:
Gene Tree for SHANK1 (if available)
TreeFam:
Gene Tree for SHANK1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHANK1: view image

Paralogs for SHANK1 Gene

Paralogs for SHANK1 Gene

(3) SIMAP similar genes for SHANK1 Gene using alignment to 3 proteins:

  • SHAN1_HUMAN
  • H9KV90_HUMAN
  • M0QYB5_HUMAN
genes like me logo Genes that share paralogs with SHANK1: view

Variants for SHANK1 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHANK1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
871353 Uncertain Significance: not provided 50,662,090(-) C/T
NM_016148.5(SHANK1):c.6361G>A (p.Asp2121Asn) 		MISSENSE
931661 Uncertain Significance: See cases 50,666,489(-) G/A
NM_016148.5(SHANK1):c.5471C>T (p.Pro1824Leu) 		MISSENSE
975163 Likely Benign: Intellectual disability 50,697,954(-) G/A
NM_016148.5(SHANK1):c.1750C>T (p.Leu584Phe) 		MISSENSE
978942 Likely Benign: Intellectual disability 50,666,270(-) C/A
NM_016148.5(SHANK1):c.5690G>T (p.Gly1897Val) 		MISSENSE
rs10419507 Benign: not provided 50,704,135(-) G/T
NM_016148.5(SHANK1):c.1207C>A (p.Arg403=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SHANK1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SHANK1 Gene

Variant ID Type Subtype PubMed ID
dgv1801n106 CNV deletion 24896259
esv2718744 CNV deletion 23290073
esv2718745 CNV deletion 23290073
esv2718746 CNV deletion 23290073
esv2718747 CNV deletion 23290073
esv3574587 CNV gain 25503493
esv3583462 CNV loss 25503493
nsv1071941 CNV deletion 25765185
nsv1140251 OTHER inversion 24896259
nsv579950 CNV loss 21841781
nsv828583 CNV loss 20364138
nsv953605 CNV deletion 24416366

Variation tolerance for SHANK1 Gene

Gene Damage Index Score: 5.63; 72.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHANK1 Gene

Human Gene Mutation Database (HGMD)
SHANK1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHANK1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHANK1 Gene

Disorders for SHANK1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for SHANK1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
schizophrenia 15
  • sczd15
autism spectrum disorder
  • asd
phelan-mcdermid syndrome
  • phmds
autism
  • autistic disorder
familial isolated trichomegaly
  • long eyelashes
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SHANK1

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SHANK1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHANK1 Gene

Publications for SHANK1 Gene

  1. Somatostatin receptor interacting protein defines a novel family of multidomain proteins present in human and rodent brain. (PMID: 10551867) Zitzer H … Kreienkamp HJ (The Journal of biological chemistry 1999) 2 3 4 23
  2. Shank1 mRNA: dendritic transport by kinesin and translational control by the 5'untranslated region. (PMID: 19416473) Falley K … Kreienkamp HJ (Traffic (Copenhagen, Denmark) 2009) 3 23
  3. Differential expression and dendritic transcript localization of Shank family members: identification of a dendritic targeting element in the 3' untranslated region of Shank1 mRNA. (PMID: 15121189) Böckers TM … Kreienkamp HJ (Molecular and cellular neurosciences 2004) 3 23
  4. The insulin receptor substrate IRSp53 links postsynaptic shank1 to the small G-protein cdc42. (PMID: 12504591) Soltau M … Kreienkamp HJ (Molecular and cellular neurosciences 2002) 3 4
  5. The Shank family of scaffold proteins. (PMID: 10806096) Sheng M … Kim E (Journal of cell science 2000) 3 4

ExternalLinks

View latest publications for SHANK1 gene in Mastermind

Products for SHANK1 Gene

Sources for SHANK1 Gene