This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2 motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to the X-linked Stocco dos Santos syndrome characterized by cognitive disabilities. Alternatively spliced transcript variants have been described. [provi... See more...

Aliases for SHROOM4 Gene

Aliases for SHROOM4 Gene

  • Shroom Family Member 4 2 3 5
  • Second Homolog Of Apical Protein 3 4
  • Protein Shroom4 3 4
  • KIAA1202 2 4
  • SHAP 3 4
  • SHROOM4 5
  • Shrm4 3

External Ids for SHROOM4 Gene

Previous GeneCards Identifiers for SHROOM4 Gene

  • GC0XM050351
  • GC0XM047778
  • GC0XM050591

Summaries for SHROOM4 Gene

Entrez Gene Summary for SHROOM4 Gene

  • This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2 motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to the X-linked Stocco dos Santos syndrome characterized by cognitive disabilities. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2017]

GeneCards Summary for SHROOM4 Gene

SHROOM4 (Shroom Family Member 4) is a Protein Coding gene. Diseases associated with SHROOM4 include Stocco Dos Santos X-Linked Mental Retardation Syndrome and Stocco Dos Santos Syndrome. Gene Ontology (GO) annotations related to this gene include actin filament binding. An important paralog of this gene is SHROOM3.

UniProtKB/Swiss-Prot Summary for SHROOM4 Gene

  • Probable regulator of cytoskeletal architecture that plays an important role in development. May regulate cellular and cytoskeletal architecture by modulating the spatial distribution of myosin II (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHROOM4 Gene

Genomics for SHROOM4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHROOM4 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
GH0XJ050812 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas 605.9 +0.1 148 3.5 POLR2A SP1 EZH2 SHROOM4 FJ601684-486 DGKK
GH0XJ050768 Enhancer 0.6 Ensembl ENCODE 11.6 +44.2 44201 3.8 PRDM10 FOXA1 NFIA TCF7L2 SHROOM4 FJ601684-486 DGKK
GH0XJ050798 Enhancer 0.5 ENCODE 7.6 +14.7 14662 1.8 ZNF7 SCRT2 TCF7 ATF2 HLF ZNF644 BMP15 SHROOM4 FJ601684-486 DGKK
GH0XJ050779 Enhancer 0.2 Ensembl 13.2 +34.5 34501 0.4 SHROOM4 FJ601684-486 DGKK
GH0XJ050775 Enhancer 0.2 Ensembl 13 +38.6 38601 1 SHROOM4 FJ601684-486 DGKK
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHROOM4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHROOM4

Top Transcription factor binding sites by QIAGEN in the SHROOM4 gene promoter:
  • NF-kappaB
  • NF-kappaB1
  • Nkx2-2
  • Nkx2-5
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • RelA

Genomic Locations for SHROOM4 Gene

Genomic Locations for SHROOM4 Gene
chrX:50,575,534-50,814,302
(GRCh38/hg38)
Size:
238,769 bases
Orientation:
Minus strand
chrX:50,334,642-50,557,302
(GRCh37/hg19)
Size:
222,661 bases
Orientation:
Minus strand

Genomic View for SHROOM4 Gene

Genes around SHROOM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHROOM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHROOM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHROOM4 Gene

Proteins for SHROOM4 Gene

  • Protein details for SHROOM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9ULL8-SHRM4_HUMAN
    Recommended name:
    Protein Shroom4
    Protein Accession:
    Q9ULL8
    Secondary Accessions:
    • A7E2X9
    • D6RFW0
    • Q96LA0

    Protein attributes for SHROOM4 Gene

    Size:
    1493 amino acids
    Molecular mass:
    164857 Da
    Quaternary structure:
    • Interacts directly with F-actin.
    SequenceCaution:
    • Sequence=BAA86516.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SHROOM4 Gene

    Alternative splice isoforms for SHROOM4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHROOM4 Gene

Post-translational modifications for SHROOM4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SHROOM4 Gene

Domains & Families for SHROOM4 Gene

Gene Families for SHROOM4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SHROOM4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SHROOM4 Gene

GenScript: Design optimal peptide antigens:
  • Second homolog of apical protein (SHRM4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9ULL8

UniProtKB/Swiss-Prot:

SHRM4_HUMAN :
  • Belongs to the shroom family.
Family:
  • Belongs to the shroom family.
genes like me logo Genes that share domains with SHROOM4: view

Function for SHROOM4 Gene

Molecular function for SHROOM4 Gene

UniProtKB/Swiss-Prot Function:
Probable regulator of cytoskeletal architecture that plays an important role in development. May regulate cellular and cytoskeletal architecture by modulating the spatial distribution of myosin II (By similarity).

Phenotypes From GWAS Catalog for SHROOM4 Gene

Gene Ontology (GO) - Molecular Function for SHROOM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005515 protein binding IEA --
GO:0045159 myosin II binding IEA,ISS --
GO:0051015 actin filament binding ISS --
genes like me logo Genes that share ontologies with SHROOM4: view
genes like me logo Genes that share phenotypes with SHROOM4: view

Human Phenotype Ontology for SHROOM4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SHROOM4 Gene

MGI Knock Outs for SHROOM4:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHROOM4

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SHROOM4 Gene

Localization for SHROOM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHROOM4 Gene

Cytoplasm, cytoskeleton. Note=Shows partial colocalization with the cytoplasmic pool of F-actin.

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 SHROOM4 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
nucleus 3
cytosol 3
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Focal adhesion sites (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHROOM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 colocalizes_with stress fiber IEA,ISS --
GO:0005737 cytoplasm ISS --
GO:0005856 cytoskeleton IEA --
GO:0005884 actin filament IDA 16249884
GO:0005912 adherens junction IBA 21873635
genes like me logo Genes that share ontologies with SHROOM4: view

Pathways & Interactions for SHROOM4 Gene

PathCards logo

SuperPathways for SHROOM4 Gene

No Data Available

Interacting Proteins for SHROOM4 Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000365188 Q9ULL8-SHRM4_HUMAN for SHROOM4 Gene via STRING IID

Gene Ontology (GO) - Biological Process for SHROOM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 NOT cell morphogenesis IDA 16684770
GO:0007015 actin filament organization IEA,ISS --
GO:0007275 multicellular organism development IEA --
GO:0007420 brain development IDA 16249884
GO:0030036 actin cytoskeleton organization NAS 16684770
genes like me logo Genes that share ontologies with SHROOM4: view

No data available for Pathways by source and SIGNOR curated interactions for SHROOM4 Gene

Drugs & Compounds for SHROOM4 Gene

No Compound Related Data Available

Transcripts for SHROOM4 Gene

mRNA/cDNA for SHROOM4 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
5 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 SHROOM4

Alternative Splicing Database (ASD) splice patterns (SP) for SHROOM4 Gene

No ASD Table

Relevant External Links for SHROOM4 Gene

GeneLoc Exon Structure for
SHROOM4

Expression for SHROOM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHROOM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SHROOM4 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.2) and Lung (x4.1).

Protein differential expression in normal tissues from HIPED for SHROOM4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (41.1), Placenta (20.4), and Adipocyte (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SHROOM4 Gene



Protein tissue co-expression partners for SHROOM4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHROOM4

SOURCE GeneReport for Unigene cluster for SHROOM4 Gene:

Hs.420541

mRNA Expression by UniProt/SwissProt for SHROOM4 Gene:

Q9ULL8-SHRM4_HUMAN
Tissue specificity: Expressed in all fetal and adult tissues investigated. Expressed in adult heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. In brain regions detected in cerebellum, cerebral cortex, medulla, spinal cord, occipital pole, frontal lobe, temporal lobe and putamen. The expression is strongest in the medulla and weakest in the cerebral cortex.

Evidence on tissue expression from TISSUES for SHROOM4 Gene

  • Nervous system(4.4)
  • Heart(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SHROOM4 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeleton
Regions:
Head and neck:
  • brain
  • head
Pelvis:
  • pelvis
Limb:
  • femur
  • hip
  • lower limb
  • thigh
genes like me logo Genes that share expression patterns with SHROOM4: view

Orthologs for SHROOM4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHROOM4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHROOM4 30 31
  • 99.13 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SHROOM4 30 31
  • 89.47 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SHROOM4 30 31
  • 88.33 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shroom4 30
  • 83.04 (n)
Mouse
(Mus musculus)
Mammalia Shroom4 30 17 31
  • 82.65 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SHROOM4 31
  • 54 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SHROOM4 31
  • 47 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LOC777072 30
  • 59.17 (n)
SHROOM4 31
  • 51 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SHROOM4 31
  • 43 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii shroom4 31
  • 25 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Shroom 31
  • 15 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 41 (a)
ManyToMany
CSA.5284 31
  • 41 (a)
ManyToMany
Species where no ortholog for SHROOM4 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)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SHROOM4 Gene

ENSEMBL:
Gene Tree for SHROOM4 (if available)
TreeFam:
Gene Tree for SHROOM4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHROOM4: view image

Paralogs for SHROOM4 Gene

Paralogs for SHROOM4 Gene

(1) SIMAP similar genes for SHROOM4 Gene using alignment to 1 proteins:

  • SHRM4_HUMAN
genes like me logo Genes that share paralogs with SHROOM4: view

Variants for SHROOM4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHROOM4 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
635462 Uncertain Significance: X-linked intellectual disability, Stocco dos Santos type 50,634,077(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
638434 Uncertain Significance: X-linked intellectual disability, Stocco dos Santos type 50,608,071(-) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
769179 Likely Benign: not provided 50,633,901(-) A/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
784432 Benign: not provided 50,633,576(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
810600 Likely Benign: not provided 50,596,889(-) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for SHROOM4 Gene

Structural Variations from Database of Genomic Variants (DGV) for SHROOM4 Gene

Variant ID Type Subtype PubMed ID
esv1223545 CNV deletion 17803354
esv2351992 CNV deletion 18987734
esv3573961 CNV loss 25503493
esv3573962 CNV loss 25503493
esv3573963 CNV loss 25503493
nsv1141064 CNV deletion 24896259
nsv1146756 CNV deletion 26484159
nsv508772 CNV insertion 20534489
nsv527767 CNV gain 19592680

Variation tolerance for SHROOM4 Gene

Residual Variation Intolerance Score: 99.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.29; 70.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHROOM4 Gene

Human Gene Mutation Database (HGMD)
SHROOM4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHROOM4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHROOM4 Gene

Disorders for SHROOM4 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SHROOM4 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
stocco dos santos x-linked mental retardation syndrome
  • sdsx
stocco dos santos syndrome
  • x-linked intellectual disability, stocco dos santos type
santos syndrome
  • fibular agenesis/hypoplasia, oligodactylous clubfeet, and anonychia/nail hypoplasia syndrome
atrial septal defect 2
  • asd2
syndromic x-linked intellectual disability turner type
  • mental retardation, x-linked, syndromic, turner type
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SHRM4_HUMAN
  • Mental retardation, X-linked, syndromic, Stocco dos Santos type (SDSX) [MIM:300434]: A syndrome characterized by severe mental retardation with hyperactivity, aggressive behavior, delayed or no speech, and seizures. Additional features include congenital bilateral hip luxation, short stature, and kyphosis. {ECO:0000269 PubMed:16249884}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving SHROOM4 is a cause of X-linked mental retardation (XLMR). Translocation t(X;8)(p11.22;p23.3) with FBXO25.
  • Note=A chromosomal aberration involving SHROOM4 is a cause of X-linked mental retardation (XLMR). Translocation t(X;19).

Additional Disease Information for SHROOM4

genes like me logo Genes that share disorders with SHROOM4: view

No data available for Genatlas for SHROOM4 Gene

Publications for SHROOM4 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. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10574462) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  3. Differential actin-dependent localization modulates the evolutionarily conserved activity of Shroom family proteins. (PMID: 16684770) Dietz ML … Hildebrand JD (The Journal of biological chemistry 2006) 3 4
  4. Disruptions of the novel KIAA1202 gene are associated with X-linked mental retardation. (PMID: 16249884) Hagens O … Hanauer A (Human genetics 2006) 3 4
  5. Heterozygous deletion of chromosome 17p renders prostate cancer vulnerable to inhibition of RNA polymerase II. (PMID: 30349055) Li Y … Lu X (Nature communications 2018) 3

Products for SHROOM4 Gene

Sources for SHROOM4 Gene