This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011] See more...

Aliases for SHROOM3 Gene

Aliases for SHROOM3 Gene

  • Shroom Family Member 3 2 3 5
  • Shroom-Related Protein 3 4
  • Protein Shroom3 3 4
  • KIAA1481 2 4
  • APXL3 2 3
  • ShrmL 2 3
  • SHRM 2 3
  • F-Actin-Binding Protein 3
  • MSTP013 3
  • SHROOM3 5
  • HShrmL 4
  • SHRML 4

External Ids for SHROOM3 Gene

Previous GeneCards Identifiers for SHROOM3 Gene

  • GC04P077575
  • GC04P077356
  • GC04P073108

Summaries for SHROOM3 Gene

Entrez Gene Summary for SHROOM3 Gene

  • This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]

GeneCards Summary for SHROOM3 Gene

SHROOM3 (Shroom Family Member 3) is a Protein Coding gene. Diseases associated with SHROOM3 include Neutrophil Actin Dysfunction and Brachyolmia Type 4 With Mild Epiphyseal And Metaphyseal Changes. Gene Ontology (GO) annotations related to this gene include actin binding and actin filament binding. An important paralog of this gene is SHROOM2.

UniProtKB/Swiss-Prot Summary for SHROOM3 Gene

  • Controls cell shape changes in the neuroepithelium during neural tube closure. Induces apical constriction in epithelial cells by promoting the apical accumulation of F-actin and myosin II, and probably by bundling stress fibers (By similarity). Induces apicobasal cell elongation by redistributing gamma-tubulin and directing the assembly of robust apicobasal microtubule arrays (By similarity).

Gene Wiki entry for SHROOM3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHROOM3 Gene

Genomics for SHROOM3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHROOM3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHROOM3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHROOM3

Top Transcription factor binding sites by QIAGEN in the SHROOM3 gene promoter:
  • c-Myb
  • CUTL1
  • GATA-1
  • HSF1 (long)
  • HSF1short
  • HSF2
  • LCR-F1
  • POU2F1
  • POU2F1a
  • STAT5A

Genomic Locations for SHROOM3 Gene

Genomic Locations for SHROOM3 Gene
chr4:76,435,229-76,783,253
(GRCh38/hg38)
Size:
348,025 bases
Orientation:
Plus strand
chr4:77,356,253-77,704,406
(GRCh37/hg19)
Size:
348,154 bases
Orientation:
Plus strand

Genomic View for SHROOM3 Gene

Genes around SHROOM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHROOM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHROOM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHROOM3 Gene

Proteins for SHROOM3 Gene

  • Protein details for SHROOM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TF72-SHRM3_HUMAN
    Recommended name:
    Protein Shroom3
    Protein Accession:
    Q8TF72
    Secondary Accessions:
    • Q5QTQ3
    • Q6ZRW3
    • Q96IR9
    • Q9P247

    Protein attributes for SHROOM3 Gene

    Size:
    1996 amino acids
    Molecular mass:
    216857 Da
    Quaternary structure:
    • Interacts with F-actin (By similarity). Interacts with ROCK1 (PubMed:22493320).
    SequenceCaution:
    • Sequence=AAQ13515.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB84689.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SHROOM3 Gene

    Alternative splice isoforms for SHROOM3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHROOM3 Gene

Post-translational modifications for SHROOM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SHROOM3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SHROOM3 Gene

Domains & Families for SHROOM3 Gene

Gene Families for SHROOM3 Gene

Protein Domains for SHROOM3 Gene

Suggested Antigen Peptide Sequences for SHROOM3 Gene

GenScript: Design optimal peptide antigens:
  • Shroom-related protein (SHRM3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TF72

UniProtKB/Swiss-Prot:

SHRM3_HUMAN :
  • The ASD1 domain mediates F-actin binding.
  • Belongs to the shroom family.
Domain:
  • The ASD1 domain mediates F-actin binding.
  • The ASD2 domain mediates the interaction with ROCK1 and is required for apical constriction induction.
Family:
  • Belongs to the shroom family.
genes like me logo Genes that share domains with SHROOM3: view

Function for SHROOM3 Gene

Molecular function for SHROOM3 Gene

UniProtKB/Swiss-Prot Function:
Controls cell shape changes in the neuroepithelium during neural tube closure. Induces apical constriction in epithelial cells by promoting the apical accumulation of F-actin and myosin II, and probably by bundling stress fibers (By similarity). Induces apicobasal cell elongation by redistributing gamma-tubulin and directing the assembly of robust apicobasal microtubule arrays (By similarity).

Phenotypes From GWAS Catalog for SHROOM3 Gene

Gene Ontology (GO) - Molecular Function for SHROOM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005515 protein binding IEA --
GO:0051015 actin filament binding IEA,IBA 21873635
genes like me logo Genes that share ontologies with SHROOM3: view
genes like me logo Genes that share phenotypes with SHROOM3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHROOM3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SHROOM3 Gene

Localization for SHROOM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHROOM3 Gene

Cell junction, adherens junction. Cytoplasm, cytoskeleton. Apical cell membrane. Peripheral membrane protein. Note=Colocalizes with F-actin in stress fibers and adherens junctions. {ECO:0000250 UniProtKB:Q9QXN0}.

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 SHROOM3 gene
Compartment Confidence
plasma membrane 4
cytoskeleton 4
nucleus 4
cytosol 4
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SHROOM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton ISS --
GO:0005874 microtubule IEA --
GO:0005886 plasma membrane IEA --
GO:0005912 adherens junction ISS --
genes like me logo Genes that share ontologies with SHROOM3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SHROOM3 Gene

Pathways & Interactions for SHROOM3 Gene

PathCards logo

SuperPathways for SHROOM3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SHROOM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IEA,ISS --
GO:0001843 neural tube closure IEA --
GO:0002064 epithelial cell development IEA --
GO:0007015 actin filament organization IBA 21873635
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with SHROOM3: view

No data available for Pathways by source and SIGNOR curated interactions for SHROOM3 Gene

Drugs & Compounds for SHROOM3 Gene

(2) Drugs for SHROOM3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for SHROOM3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SHROOM3: view

Transcripts for SHROOM3 Gene

mRNA/cDNA for SHROOM3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHROOM3

Alternative Splicing Database (ASD) splice patterns (SP) for SHROOM3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c · 14d ^ 15a · 15b ^ 16a · 16b · 16c ^
SP1: - - - - - - - - - - - - - -
SP2: -
SP3: - - - - - - - - - - - - - - - - -
SP4: - -
SP5: -
SP6: -
SP7:
SP8:
SP9: - -
SP10:
SP11:

ExUns: 17 ^ 18 ^ 19 ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SHROOM3 Gene

GeneLoc Exon Structure for
SHROOM3

Expression for SHROOM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHROOM3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SHROOM3 Gene

This gene is overexpressed in Stomach (41.9), Lung (6.9), and Adrenal (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHROOM3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHROOM3

SOURCE GeneReport for Unigene cluster for SHROOM3 Gene:

Hs.702168

Evidence on tissue expression from TISSUES for SHROOM3 Gene

  • Intestine(4.6)
  • Liver(4.6)
  • Nervous system(4.5)
  • Spleen(4.1)
  • Lung(3.3)
  • Eye(2.9)
  • Blood(2.5)
  • Kidney(2.4)
  • Pancreas(2.4)
  • Skin(2.4)
  • Stomach(2.1)
genes like me logo Genes that share expression patterns with SHROOM3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHROOM3 Gene

Orthologs for SHROOM3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHROOM3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHROOM3 30 31
  • 98.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SHROOM3 30 31
  • 81.36 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SHROOM3 30 31
  • 81.04 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Shroom3 30 17 31
  • 78.43 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shroom3 30
  • 77.92 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SHROOM3 31
  • 68 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SHROOM3 31
  • 54 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SHROOM3 30 31
  • 60.73 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SHROOM3 31
  • 47 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia shroom3 30
  • 50.3 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.5622 30
Zebrafish
(Danio rerio)
Actinopterygii SHROOM3 31
  • 56 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Shroom 31
  • 18 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.5284 31
  • 43 (a)
ManyToMany
-- 31
  • 41 (a)
ManyToMany
Species where no ortholog for SHROOM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)
  • Worm (Caenorhabditis elegans)

Evolution for SHROOM3 Gene

ENSEMBL:
Gene Tree for SHROOM3 (if available)
TreeFam:
Gene Tree for SHROOM3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHROOM3: view image

Paralogs for SHROOM3 Gene

Paralogs for SHROOM3 Gene

(1) SIMAP similar genes for SHROOM3 Gene using alignment to 1 proteins:

  • SHRM3_HUMAN
genes like me logo Genes that share paralogs with SHROOM3: view

Variants for SHROOM3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHROOM3 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
709141 Likely Benign: not provided 76,755,002(+) G/A MISSENSE_VARIANT
714948 Likely Benign: not provided 76,740,326(+) G/A MISSENSE_VARIANT
721106 Benign: not provided 76,756,493(+) T/A MISSENSE_VARIANT
725275 Benign: not provided 76,755,085(+) G/T SYNONYMOUS_VARIANT
730397 Benign: not provided 76,754,924(+) A/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SHROOM3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SHROOM3 Gene

Variant ID Type Subtype PubMed ID
esv2664574 CNV deletion 23128226
esv2727846 CNV deletion 23290073
esv2727847 CNV deletion 23290073
esv275302 CNV loss 21479260
esv2759262 CNV loss 17122850
esv3601055 CNV loss 21293372
esv3601056 CNV loss 21293372
esv3601062 CNV loss 21293372
esv3601063 CNV loss 21293372
esv8702 CNV gain 19470904
nsv1136879 CNV deletion 24896259
nsv1143289 CNV deletion 24896259
nsv289572 CNV insertion 16902084
nsv292270 CNV deletion 16902084
nsv478414 CNV novel sequence insertion 20440878
nsv478526 CNV novel sequence insertion 20440878
nsv594696 CNV gain 21841781
nsv7363 OTHER inversion 18451855
nsv829972 CNV loss 17160897
nsv829973 CNV loss 17160897
nsv967767 CNV duplication 23825009

Variation tolerance for SHROOM3 Gene

Residual Variation Intolerance Score: 93.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.26; 97.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHROOM3 Gene

Human Gene Mutation Database (HGMD)
SHROOM3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHROOM3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHROOM3 Gene

Disorders for SHROOM3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SHROOM3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
neutrophil actin dysfunction
  • nad
brachyolmia type 4 with mild epiphyseal and metaphyseal changes
  • bcym4
neural tube defects
  • neural tube defects, susceptibility to
kuhnt-junius degeneration
  • exudative senile macular degeneration of retina
atrial septal defect 2
  • asd2
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SHROOM3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SHROOM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHROOM3 Gene

Publications for SHROOM3 Gene

  1. A new standard nomenclature for proteins related to Apx and Shroom. (PMID: 16615870) Hagens O … Wallingford JB (BMC cell biology 2006) 2 3 4
  2. New loci associated with kidney function and chronic kidney disease. (PMID: 20383146) Köttgen A … Fox CS (Nature genetics 2010) 3 41
  3. Common variants at 5q22 associate with pediatric eosinophilic esophagitis. (PMID: 20208534) Rothenberg ME … Hakonarson H (Nature genetics 2010) 3 41
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  5. Genetic loci influencing kidney function and chronic kidney disease. (PMID: 20383145) Chambers JC … Kooner JS (Nature genetics 2010) 3 41

Products for SHROOM3 Gene

  • Biorbyt antibodies for SHROOM3

Sources for SHROOM3 Gene