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Aliases for VSX2 Gene

Aliases for VSX2 Gene

  • Visual System Homeobox 2 2 3 5
  • Ceh-10 Homeodomain-Containing Homolog 3 4
  • Homeobox Protein CHX10 3 4
  • CHX10 3 4
  • HOX10 3 4
  • Ceh-10 Homeo Domain Containing Homolog (C. Elegans) 2
  • Ceh-10 Homeodomain Containing Homolog (C. Elegans) 2
  • C Elegans Ceh-10 Homeo Domain-Containing Homolog 2
  • Ceh-10 Homeo Domain Containing Homolog 3
  • MCOPCB3 3
  • MCOP2 3
  • RET1 3

External Ids for VSX2 Gene

Previous HGNC Symbols for VSX2 Gene

  • HOX10
  • CHX10

Previous GeneCards Identifiers for VSX2 Gene

  • GC14P073776
  • GC14P074706
  • GC14P054873

Summaries for VSX2 Gene

Entrez Gene Summary for VSX2 Gene

  • This gene encodes a homeobox protein originally described as a retina-specific transcription factor. Mutations in this gene are associated with microphthalmia, cataracts and iris abnormalities. [provided by RefSeq, Oct 2009]

GeneCards Summary for VSX2 Gene

VSX2 (Visual System Homeobox 2) is a Protein Coding gene. Diseases associated with VSX2 include Microphthalmia, Isolated 2 and Microphthalmia With Coloboma 3. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is VSX1.

UniProtKB/Swiss-Prot for VSX2 Gene

  • Plays a significant role in the specification and morphogenesis of the sensory retina. May also participate in the development of the cells of the inner nuclear layer, particularly bipolar cells (By similarity).

Gene Wiki entry for VSX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VSX2 Gene

Genomics for VSX2 Gene

Regulatory Elements for VSX2 Gene

Enhancers for VSX2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14G074387 0.8 dbSUPER 10.3 +152.6 152632 9.1 ELF3 ZSCAN4 ZSCAN9 RAD21 ZNF366 SCRT2 ZNF143 MIXL1 ZNF654 CEBPB SYNDIG1L ABCD4 VSX2 LTBP2 ENSG00000259005 ENSG00000270000 LIN52 RPS2P2 GC14M074406
GH14G074251 1.1 Ensembl ENCODE 6.7 +12.1 12143 0.8 KLF17 ZNF2 RAD21 RFX5 YY1 SCRT2 ZNF143 ZNF207 EGR2 ZNF654 ABCD4 ENSG00000258559 SYNDIG1L VSX2 ALDH6A1
GH14G074256 1 Ensembl ENCODE 7.1 +18.5 18523 2.0 CTCF SUZ12 ZNF223 RBBP5 RAD21 PATZ1 ZNF143 SMC3 ZNF652 EZH2 VSX2 ALDH6A1 ENSG00000258559
GH14G074239 0.7 Ensembl 8.6 +1.0 999 2.9 RNF2 SUZ12 CHD1 CBX2 BMI1 RBBP5 CBX8 CTBP2 KDM1A ZBTB33 ABCD4 SYNDIG1L VSX2 ENSG00000258559
GH14G074217 1.1 Ensembl ENCODE 0.3 -21.5 -21476 0.9 HDGF PKNOX1 RB1 KLF17 ZNF48 RAD21 ZNF143 IKZF2 REST TBX21 ALDH6A1 LIN52 SYNDIG1L PTGR2 FAM161B ACOT2 LOC105370564 VSX2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VSX2 on UCSC Golden Path with GeneCards custom track

Genomic Location for VSX2 Gene

Chromosome:
14
Start:
74,239,472 bp from pter
End:
74,262,738 bp from pter
Size:
23,267 bases
Orientation:
Plus strand

Genomic View for VSX2 Gene

Genes around VSX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSX2 Gene

Proteins for VSX2 Gene

  • Protein details for VSX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P58304-VSX2_HUMAN
    Recommended name:
    Visual system homeobox 2
    Protein Accession:
    P58304
    Secondary Accessions:
    • A1A4X6

    Protein attributes for VSX2 Gene

    Size:
    361 amino acids
    Molecular mass:
    39411 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VSX2 Gene

Post-translational modifications for VSX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VSX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VSX2 Gene

Domains & Families for VSX2 Gene

Gene Families for VSX2 Gene

Suggested Antigen Peptide Sequences for VSX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P58304

UniProtKB/Swiss-Prot:

VSX2_HUMAN :
  • Belongs to the paired homeobox family.
Family:
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with VSX2: view

Function for VSX2 Gene

Molecular function for VSX2 Gene

UniProtKB/Swiss-Prot Function:
Plays a significant role in the specification and morphogenesis of the sensory retina. May also participate in the development of the cells of the inner nuclear layer, particularly bipolar cells (By similarity).

Gene Ontology (GO) - Molecular Function for VSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with VSX2: view
genes like me logo Genes that share phenotypes with VSX2: view

Human Phenotype Ontology for VSX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VSX2 Gene

MGI Knock Outs for VSX2:

Animal Model Products

Transcription Factor Targets for VSX2 Gene

Selected GeneGlobe predicted Target genes for VSX2

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VSX2

No data available for Enzyme Numbers (IUBMB) , miRNA and HOMER Transcription for VSX2 Gene

Localization for VSX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSX2 Gene

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 VSX2 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for VSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with VSX2: view

Pathways & Interactions for VSX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0007601 visual perception IEA --
GO:0050896 response to stimulus IEA --
genes like me logo Genes that share ontologies with VSX2: view

No data available for Pathways by source and SIGNOR curated interactions for VSX2 Gene

Drugs & Compounds for VSX2 Gene

No Compound Related Data Available

Transcripts for VSX2 Gene

mRNA/cDNA for VSX2 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(17) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VSX2 Gene

Visual system homeobox 2:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VSX2

Alternative Splicing Database (ASD) splice patterns (SP) for VSX2 Gene

No ASD Table

Relevant External Links for VSX2 Gene

GeneLoc Exon Structure for
VSX2
ECgene alternative splicing isoforms for
VSX2

Expression for VSX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VSX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VSX2 Gene

This gene is overexpressed in Testis (x8.0), Brain - Spinal cord (cervical c-1) (x5.1), Brain - Substantia nigra (x4.1), and Brain - Nucleus accumbens (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for VSX2 Gene

This gene is overexpressed in Retina (34.5) and Peripheral blood mononuclear cells (34.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VSX2 Gene



Protein tissue co-expression partners for VSX2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VSX2 Gene:

VSX2

SOURCE GeneReport for Unigene cluster for VSX2 Gene:

Hs.449771

mRNA Expression by UniProt/SwissProt for VSX2 Gene:

P58304-VSX2_HUMAN
Tissue specificity: Abundantly expressed in retinal neuroblasts during eye development and in the inner nuclear layer of the adult retina. Within this layer, expression is stronger in the outer margin where bipolar cells predominate.

Evidence on tissue expression from TISSUES for VSX2 Gene

  • Eye(3.1)
  • Nervous system(2.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VSX2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
Thorax:
  • aorta
  • diaphragm
  • heart
  • heart valve
  • lung
Abdomen:
  • abdominal wall
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • testicle
  • ureter
  • uterus
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with VSX2: view

Primer Products

Orthologs for VSX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for VSX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VSX2 34 35
  • 99.54 (n)
dog
(Canis familiaris)
Mammalia VSX2 34 35
  • 94.83 (n)
mouse
(Mus musculus)
Mammalia Vsx2 34 16 35
  • 91.41 (n)
rat
(Rattus norvegicus)
Mammalia Vsx2 34
  • 91.41 (n)
cow
(Bos Taurus)
Mammalia VSX2 34 35
  • 91.14 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 86 (a)
ManyToMany
chicken
(Gallus gallus)
Aves VSX2 34 35
  • 81.78 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 71 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vsx2 34
  • 67.2 (n)
zebrafish
(Danio rerio)
Actinopterygii vsx2 34 34 35
  • 69.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vsx2 35
  • 21 (a)
ManyToMany
Vsx1 35
  • 15 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-10 35
  • 38 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2804 34
Species where no ortholog for VSX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 VSX2 Gene

ENSEMBL:
Gene Tree for VSX2 (if available)
TreeFam:
Gene Tree for VSX2 (if available)

Paralogs for VSX2 Gene

Paralogs for VSX2 Gene

(1) SIMAP similar genes for VSX2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with VSX2: view

Variants for VSX2 Gene

Sequence variations from dbSNP and Humsavar for VSX2 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs121912543 Pathogenic, Microphthalmia with cataracts and iris abnormalities (MCOPCTI) [MIM:610092], Microphthalmia with cataracts and iris abnormalities (MCOPCTI) [MIM:610092] 74,259,621(+) CCGTC(A/C/G)AGCCA reference, missense
rs121912545 Pathogenic, Microphthalmia, isolated, 2 (MCOP2) [MIM:610093] 74,259,701(+) TGGTG(C/T)GGCAC reference, missense
rs755799430 Pathogenic, Microphthalmia, isolated, with coloboma, 3 (MCOPCB3) [MIM:610092] 74,259,689(+) TCTAC(A/G)GGGCC reference, missense
VAR_067269 Microphthalmia, isolated, 2 (MCOP2) [MIM:610093]
rs869025268 Pathogenic 74,239,632(+) GGGGG(-/G)CGCCC reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for VSX2 Gene

Variant ID Type Subtype PubMed ID
esv3305693 CNV mobile element insertion 20981092
esv3323548 CNV insertion 20981092
nsv565182 CNV loss 21841781

Variation tolerance for VSX2 Gene

Gene Damage Index Score: 3.97; 59.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VSX2 Gene

Human Gene Mutation Database (HGMD)
VSX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSX2 Gene

Disorders for VSX2 Gene

MalaCards: The human disease database

(13) MalaCards diseases for VSX2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, isolated 2
  • isolated microphthalmia 2
microphthalmia with coloboma 3
  • microphthalmia with cataracts and iris abnormalities
colobomatous microphthalmia
  • mac
anophthalmia/microphthalmia
isolated microphthalmia
  • microphthalmia, isolated 6
- elite association - COSMIC cancer census association via MalaCards
Search VSX2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VSX2_HUMAN
  • Microphthalmia with cataracts and iris abnormalities (MCOPCTI) [MIM:610092]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, cataract and other abnormalities like cataract may also be present. {ECO:0000269 PubMed:10932181}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microphthalmia, isolated, 2 (MCOP2) [MIM:610093]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. {ECO:0000269 PubMed:15257456, ECO:0000269 PubMed:21976963}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microphthalmia, isolated, with coloboma, 3 (MCOPCB3) [MIM:610092]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269 PubMed:15257456, ECO:0000269 PubMed:24033328}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VSX2

Genetic Association Database (GAD)
VSX2
Human Genome Epidemiology (HuGE) Navigator
VSX2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VSX2
genes like me logo Genes that share disorders with VSX2: view

No data available for Genatlas for VSX2 Gene

Publications for VSX2 Gene

  1. Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma. (PMID: 20057906) Zhang X. … Zhang Q. (Mol. Vis. 2009) 3 22 46 64
  2. Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes. (PMID: 18648522) Aung T. … Vithana E.N. (Mol. Vis. 2008) 3 22 46 64
  3. CHX10 mutations cause non-syndromic microphthalmia/ anophthalmia in Arab and Jewish kindreds. (PMID: 15257456) Bar-Yosef U. … Birk O.S. (Hum. Genet. 2004) 3 4 22 64
  4. VSX2 mutations in autosomal recessive microphthalmia. (PMID: 21976963) Reis L.M. … Semina E.V. (Mol. Vis. 2011) 3 4 64
  5. Mutational screening of CHX10, GDF6, OTX2, RAX and SOX2 genes in 50 unrelated microphthalmia-anophthalmia-coloboma (MAC) spectrum cases. (PMID: 20494911) Gonzalez-Rodriguez J. … Zenteno J.C. (Br J Ophthalmol 2010) 3 46 64

Products for VSX2 Gene

Sources for VSX2 Gene

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