This gene represents the human homolog of Xenopus laevis apical protein (APX) gene, which is implicated in amiloride-sensitive sodium channel activity. It is expressed in endothelial cells and facilitates the formation of a contractile network within endothelial cells. Depletion of this gene results in an increase in endothelial sprouting, migration, and angiogenesis. This gene... See more...

Aliases for SHROOM2 Gene

Aliases for SHROOM2 Gene

  • Shroom Family Member 2 2 3 5
  • Apical-Like Protein 3 4
  • Protein Shroom2 3 4
  • APXL 3 4
  • Apical Protein-Like (Xenopus Laevis) 2
  • Apical Protein, Xenopus Laevis-Like 2
  • APX Homolog Of Xenopus 3
  • Protein APXL 4
  • SHROOM2 5
  • HSAPXL 3

External Ids for SHROOM2 Gene

Previous HGNC Symbols for SHROOM2 Gene

  • APXL

Previous GeneCards Identifiers for SHROOM2 Gene

  • GC0XP009714
  • GC0XP007649

Summaries for SHROOM2 Gene

Entrez Gene Summary for SHROOM2 Gene

  • This gene represents the human homolog of Xenopus laevis apical protein (APX) gene, which is implicated in amiloride-sensitive sodium channel activity. It is expressed in endothelial cells and facilitates the formation of a contractile network within endothelial cells. Depletion of this gene results in an increase in endothelial sprouting, migration, and angiogenesis. This gene is highly expressed in the retina, and is a strong candidate for ocular albinism type 1 syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]

GeneCards Summary for SHROOM2 Gene

SHROOM2 (Shroom Family Member 2) is a Protein Coding gene. Diseases associated with SHROOM2 include Ocular Albinism and Flinders Island Spotted Fever. Gene Ontology (GO) annotations related to this gene include actin binding and actin filament binding. An important paralog of this gene is SHROOM3.

UniProtKB/Swiss-Prot Summary for SHROOM2 Gene

  • May be involved in endothelial cell morphology changes during cell spreading. In the retinal pigment epithelium, may regulate the biogenesis of melanosomes and promote their association with the apical cell surface by inducing gamma-tubulin redistribution (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHROOM2 Gene

Genomics for SHROOM2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHROOM2 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
GH0XJ009785 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 266.1 +1.6 1600 6 CEBPA YY1 SIN3A FOXA2 CTBP1 MAFF RXRA MAFK JUND ZNF217 SHROOM2 GPR143 5EW4_A-054 LOC107985658 piR-32177 CLDN34
GH0XJ009910 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE CraniofacialAtlas 254.4 +126.5 126528 4.1 SIN3A ZNF316 ZSCAN4 MAFK CEBPB SHROOM2 CLDN34 RF00017-7552 HSALNG0136608
GH0XJ009844 Enhancer 0.7 Ensembl ENCODE 24.4 +60.2 60188 3.2 CEBPA CEBPB EP300 SMAD4 SAP130 TEAD3 JUND BCL6 NFE2L2 CEBPG MK280144-697 SHROOM2 GPR143 HSALNG0136606 EIF5P1 RF00017-7552 CLDN34
GH0XJ009829 Enhancer 0.9 Ensembl ENCODE 19.2 +43.4 43395 1.6 BCL11A CEBPB TRIM22 EP300 IRF4 CBFB JUND BHLHE40 BATF ZNF24 SHROOM2 GPR143 EIF5P1 MK280144-697 RF00017-7552 CLDN34
GH0XJ009824 Enhancer 0.6 Ensembl ENCODE 19.8 +39.3 39295 2.2 HNF4A NFIL3 HLF ZNF7 SHROOM2 GPR143 EIF5P1 MK280144-697 RF00017-7552 CLDN34
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHROOM2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHROOM2

Top Transcription factor binding sites by QIAGEN in the SHROOM2 gene promoter:
  • AP-1
  • AP-4
  • Arnt
  • Lmo2
  • NF-kappaB
  • NF-kappaB1
  • POU2F1
  • POU2F1a
  • RelA
  • STAT5B

Genomic Locations for SHROOM2 Gene

Latest Assembly
chrX:9,786,406-9,949,443
(GRCh38/hg38)
Size:
163,038 bases
Orientation:
Plus strand

Previous Assembly
chrX:9,754,469-9,917,483
(GRCh37/hg19 by Entrez Gene)
Size:
163,015 bases
Orientation:
Plus strand

chrX:9,754,496-9,917,483
(GRCh37/hg19 by Ensembl)
Size:
162,988 bases
Orientation:
Plus strand

Genomic View for SHROOM2 Gene

Genes around SHROOM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHROOM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHROOM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHROOM2 Gene

Proteins for SHROOM2 Gene

  • Protein details for SHROOM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13796-SHRM2_HUMAN
    Recommended name:
    Protein Shroom2
    Protein Accession:
    Q13796
    Secondary Accessions:
    • B9EIQ7

    Protein attributes for SHROOM2 Gene

    Size:
    1616 amino acids
    Molecular mass:
    176410 Da
    Quaternary structure:
    • Interacts with F-actin.

    Three dimensional structures from OCA and Proteopedia for SHROOM2 Gene

neXtProt entry for SHROOM2 Gene

Post-translational modifications for SHROOM2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SHROOM2 Gene

Domains & Families for SHROOM2 Gene

Gene Families for SHROOM2 Gene

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

Protein Domains for SHROOM2 Gene

InterPro:
Blocks:
  • PDZ/DHR/GLGF domain

Suggested Antigen Peptide Sequences for SHROOM2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ39277 fis, clone OCBBF2010858, highly similar to APICAL-LIKE PROTEIN (B3KU73_HUMAN)
  • Protein APXL (SHRM2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13796

UniProtKB/Swiss-Prot:

SHRM2_HUMAN :
  • The ASD1 domain mediates F-actin binding.
  • Belongs to the shroom family.
Domain:
  • The ASD1 domain mediates F-actin binding.
Family:
  • Belongs to the shroom family.
genes like me logo Genes that share domains with SHROOM2: view

Function for SHROOM2 Gene

Molecular function for SHROOM2 Gene

UniProtKB/Swiss-Prot Function:
May be involved in endothelial cell morphology changes during cell spreading. In the retinal pigment epithelium, may regulate the biogenesis of melanosomes and promote their association with the apical cell surface by inducing gamma-tubulin redistribution (By similarity).

Phenotypes From GWAS Catalog for SHROOM2 Gene

Gene Ontology (GO) - Molecular Function for SHROOM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding ISS --
GO:0005515 protein binding IPI 17474147
GO:0008013 beta-catenin binding ISS 16684770
GO:0015280 ligand-gated sodium channel activity TAS 7795590
GO:0051015 actin filament binding IEA,ISS 16684770
genes like me logo Genes that share ontologies with SHROOM2: view
genes like me logo Genes that share phenotypes with SHROOM2: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHROOM2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SHROOM2 Gene

Localization for SHROOM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHROOM2 Gene

Apical cell membrane. Cell junction, tight junction. Cytoplasm, cytoskeleton. Note=Associates with cortical F-actin. {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 SHROOM2 gene
Compartment Confidence
plasma membrane 4
extracellular 4
cytoskeleton 4
nucleus 3
cytosol 3
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHROOM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA,ISS --
GO:0005874 microtubule IEA --
GO:0005886 plasma membrane ISS --
GO:0005912 adherens junction IBA,ISS 16684770
genes like me logo Genes that share ontologies with SHROOM2: view

Pathways & Interactions for SHROOM2 Gene

PathCards logo

SuperPathways for SHROOM2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SHROOM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 NOT cell morphogenesis IDA, ISS 16684770
GO:0002089 lens morphogenesis in camera-type eye ISS --
GO:0007015 actin filament organization IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007420 brain development ISS --
genes like me logo Genes that share ontologies with SHROOM2: view

No data available for Pathways by source and SIGNOR curated interactions for SHROOM2 Gene

Drugs & Compounds for SHROOM2 Gene

No Compound Related Data Available

Transcripts for SHROOM2 Gene

mRNA/cDNA for SHROOM2 Gene

3 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
4 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 SHROOM2

Alternative Splicing Database (ASD) splice patterns (SP) for SHROOM2 Gene

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

Relevant External Links for SHROOM2 Gene

GeneLoc Exon Structure for
SHROOM2

Expression for SHROOM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHROOM2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SHROOM2 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.1).

Protein differential expression in normal tissues from HIPED for SHROOM2 Gene

This gene is overexpressed in Fetal Brain (27.4), Breast (16.5), and Fetal testis (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHROOM2 Gene



Protein tissue co-expression partners for SHROOM2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHROOM2

SOURCE GeneReport for Unigene cluster for SHROOM2 Gene:

Hs.567236

mRNA Expression by UniProt/SwissProt for SHROOM2 Gene:

Q13796-SHRM2_HUMAN
Tissue specificity: Abundant in retina and melanoma; also in brain, placenta, lung, kidney and pancreas.

Evidence on tissue expression from TISSUES for SHROOM2 Gene

  • Eye(4.3)
  • Liver(4.1)
  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with SHROOM2: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SHROOM2 Gene

Orthologs for SHROOM2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHROOM2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHROOM2 29
  • 97.16 (n)
Cow
(Bos Taurus)
Mammalia -- 30
  • 93 (a)
OneToMany
-- 30
  • 91 (a)
OneToMany
-- 30
  • 54 (a)
OneToMany
-- 30
  • 47 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia SHROOM2 29 30
  • 78.78 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shroom2 29
  • 74.06 (n)
Mouse
(Mus musculus)
Mammalia Shroom2 29 16 30
  • 73.71 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SHROOM2 30
  • 58 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SHROOM2 30
  • 57 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SHROOM2 29 30
  • 63.5 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SHROOM2 30
  • 78 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia shroom2 29
  • 55.96 (n)
Str.7319 29
Zebrafish
(Danio rerio)
Actinopterygii LOC556551 29
  • 55.88 (n)
SHROOM2 (2 of 2) 30
  • 44 (a)
OneToMany
SHROOM2 (1 of 2) 30
  • 36 (a)
OneToMany
wufj08g11 29
Fruit Fly
(Drosophila melanogaster)
Insecta Shroom 30
  • 15 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.5284 30
  • 43 (a)
ManyToMany
-- 30
  • 43 (a)
ManyToMany
Species where no ortholog for SHROOM2 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SHROOM2 Gene

ENSEMBL:
Gene Tree for SHROOM2 (if available)
TreeFam:
Gene Tree for SHROOM2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHROOM2: view image
Alliance of Genome Resources:
Additional Orthologs for SHROOM2

Paralogs for SHROOM2 Gene

Paralogs for SHROOM2 Gene

(1) SIMAP similar genes for SHROOM2 Gene using alignment to 3 proteins:

  • SHRM2_HUMAN
  • C9IZC6_HUMAN
  • F5H3B6_HUMAN

Pseudogenes.org Pseudogenes for SHROOM2 Gene

genes like me logo Genes that share paralogs with SHROOM2: view

Variants for SHROOM2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHROOM2 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs103360230 A breast cancer sample p.Asp1245His
rs12006769 Benign: not provided 9,896,403(+) C/T
NM_001649.4(SHROOM2):c.2495C>T (p.Ala832Val)
MISSENSE
rs145727348 Benign: not provided 9,896,103(+) T/A
NM_001649.4(SHROOM2):c.2195T>A (p.Leu732Gln)
MISSENSE
rs7881210 Benign: not provided 9,937,320(+) G/C
NM_001649.4(SHROOM2):c.3774G>C (p.Ser1258=)
SYNONYMOUS
rs12012202 -- p.Ile1475Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SHROOM2 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 SHROOM2 Gene

Variant ID Type Subtype PubMed ID
esv1350812 CNV insertion 17803354
esv2147584 CNV deletion 18987734
esv2739957 CNV deletion 23290073
esv2739958 CNV deletion 23290073
esv2739959 CNV deletion 23290073
esv28708 CNV loss 19812545
nsv1075717 CNV deletion 25765185
nsv1122260 CNV deletion 24896259
nsv1142565 CNV tandem duplication 24896259
nsv957824 CNV deletion 24416366

Variation tolerance for SHROOM2 Gene

Residual Variation Intolerance Score: 97.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.86; 58.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHROOM2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHROOM2
Leiden Open Variation Database (LOVD)
SHROOM2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHROOM2 Gene

Disorders for SHROOM2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SHROOM2 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
ocular albinism
  • albinism, ocular
flinders island spotted fever
  • fisf
atrial septal defect 2
  • asd2
atrial septal defect 1
  • asd1
superficial mycosis
  • piedra
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SHROOM2

genes like me logo Genes that share disorders with SHROOM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHROOM2 Gene

Publications for SHROOM2 Gene

  1. Cloning of a human homologue of the Xenopus laevis APX gene from the ocular albinism type 1 critical region. (PMID: 7795590) Schiaffino MV … Ballabio A (Human molecular genetics 1995) 2 3 4 22
  2. A new standard nomenclature for proteins related to Apx and Shroom. (PMID: 16615870) Hagens O … Wallingford JB (BMC cell biology 2006) 2 3 4
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4
  4. CTDP1 regulates breast cancer survival and DNA repair through BRCT-specific interactions with FANCI. (PMID: 31240132) Hu WF … Woods NT (Cell death discovery 2019) 3
  5. Rewiring of RSK-PDZ Interactome by Linear Motif Phosphorylation. (PMID: 30726710) Gógl G … Nyitray L (Journal of molecular biology 2019) 3

Products for SHROOM2 Gene

Sources for SHROOM2 Gene