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Aliases for VSX1 Gene

Aliases for VSX1 Gene

  • Visual System Homeobox 1 2 3 5
  • Retinal Inner Nuclear Layer Homeobox Protein 3 4
  • Transcription Factor VSX1 3 4
  • Homeodomain Protein RINX 3 4
  • RINX 3 4
  • Visual System Homeobox 1 Homolog, CHX10-Like (Zebrafish) 2
  • Posterior Polymorphous Corneal Dystrophy 2
  • CAASDS 3
  • PPCD1 3
  • KTCN1 3
  • PPCD 3
  • KTCN 3
  • PPD 3

External Ids for VSX1 Gene

Previous HGNC Symbols for VSX1 Gene

  • PPCD

Previous GeneCards Identifiers for VSX1 Gene

  • GC20M025044
  • GC20M025051
  • GC20M025004

Summaries for VSX1 Gene

Entrez Gene Summary for VSX1 Gene

  • The protein encoded by this gene contains a paired-like homeodomain and binds to the core of the locus control region of the red/green visual pigment gene cluster. The encoded protein may regulate expression of the cone opsin genes early in development. Mutations in this gene can cause posterior polymorphous corneal dystrophy and keratoconus. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for VSX1 Gene

VSX1 (Visual System Homeobox 1) is a Protein Coding gene. Diseases associated with VSX1 include Keratoconus 1 and Corneal Dystrophy, Posterior Polymorphous, 1. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and sequence-specific DNA binding. An important paralog of this gene is UNCX.

UniProtKB/Swiss-Prot for VSX1 Gene

  • Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster. May regulate the activity of the LCR and the cone opsin genes at earlier stages of development.

Gene Wiki entry for VSX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VSX1 Gene

Genomics for VSX1 Gene

Regulatory Elements for VSX1 Gene

Enhancers for VSX1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around VSX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for VSX1 Gene

25,070,885 bp from pter
25,082,379 bp from pter
11,495 bases
Minus strand

Genomic View for VSX1 Gene

Genes around VSX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSX1 Gene

Proteins for VSX1 Gene

  • Protein details for VSX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Visual system homeobox 1
    Protein Accession:
    Secondary Accessions:
    • B9EGJ4
    • D1MF28
    • Q0GM60
    • Q0GM61
    • Q0GM62
    • Q0GM63
    • Q0GM64
    • Q0GM65
    • Q5TF40
    • Q5TF41
    • Q9HCU3
    • Q9NU27

    Protein attributes for VSX1 Gene

    365 amino acids
    Molecular mass:
    38431 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for VSX1 Gene

neXtProt entry for VSX1 Gene

Proteomics data for VSX1 Gene at MOPED

Post-translational modifications for VSX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VSX1 Gene

Domains & Families for VSX1 Gene

Gene Families for VSX1 Gene

Protein Domains for VSX1 Gene

Suggested Antigen Peptide Sequences for VSX1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 CVC domain.
  • Belongs to the paired homeobox family.
  • Contains 1 CVC domain.
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with VSX1: view

Function for VSX1 Gene

Molecular function for VSX1 Gene

UniProtKB/Swiss-Prot Function:
Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster. May regulate the activity of the LCR and the cone opsin genes at earlier stages of development.
genes like me logo Genes that share phenotypes with VSX1: view

Human Phenotype Ontology for VSX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VSX1 Gene

MGI Knock Outs for VSX1:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for VSX1 Gene

Localization for VSX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSX1 Gene

Subcellular locations from

Jensen Localization Image for VSX1 Gene COMPARTMENTS Subcellular localization image for VSX1 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for VSX1 Gene

Pathways & Interactions for VSX1 Gene

SuperPathways for VSX1 Gene

No Data Available

Interacting Proteins for VSX1 Gene

Selected Interacting proteins: Q9NZR4-VSX1_HUMAN for VSX1 Gene via I2D

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for VSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042551 neuron maturation IEA --
GO:0060040 retinal bipolar neuron differentiation IEA --
genes like me logo Genes that share ontologies with VSX1: view

No data available for Pathways by source and SIGNOR curated interactions for VSX1 Gene

Drugs & Compounds for VSX1 Gene

No Compound Related Data Available

Transcripts for VSX1 Gene

mRNA/cDNA for VSX1 Gene

Unigene Clusters for VSX1 Gene

Visual system homeobox 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VSX1 Gene

No ASD Table

Relevant External Links for VSX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VSX1 Gene

mRNA expression in normal human tissues for VSX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VSX1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x14.9) and Brain - Cerebellum (x12.5).

Protein differential expression in normal tissues from HIPED for VSX1 Gene

This gene is overexpressed in Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VSX1 Gene

SOURCE GeneReport for Unigene cluster for VSX1 Gene Hs.274264

mRNA Expression by UniProt/SwissProt for VSX1 Gene

Tissue specificity: In the adult eye, expressed in lens, iris, ciliary body, choroid, optical nerve head and, most strongly, in retina, but not expressed in sclera and cornea. According to PubMed 11978762, expressed in adult retina but not in lens and cornea. Within adult retina, found exclusively in the inner nuclear layer. Isoform 1, isoform 2, isoform 3 and isoform 4 expressed in adult retina, but not in brain, heart, kidney, liver, lung, pancreas, placenta and skeletal muscle. Not expressed in thymus and spleen. Expressed in embryonic craniofacial tissue. Expressed in fetal (week 14) retina. Strongly expressed in neonatal retina (day 0), weakly in neonatal lens (day 0), choroid (day 0) and cornea (day 0, 4; month 9).
genes like me logo Genes that share expression patterns with VSX1: view

Protein tissue co-expression partners for VSX1 Gene

- Elite partner

Primer Products

Orthologs for VSX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for VSX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia VSX1 35
  • 81.59 (n)
  • 81.87 (a)
VSX1 36
  • 82 (a)
(Canis familiaris)
Mammalia VSX1 35
  • 84.02 (n)
  • 82.92 (a)
VSX1 36
  • 83 (a)
(Mus musculus)
Mammalia Vsx1 35
  • 78.25 (n)
  • 76.84 (a)
Vsx1 16
Vsx1 36
  • 75 (a)
(Pan troglodytes)
Mammalia VSX1 35
  • 99.27 (n)
  • 99.18 (a)
VSX1 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Vsx1 35
  • 77.59 (n)
  • 74.1 (a)
(Monodelphis domestica)
Mammalia VSX1 36
  • 62 (a)
(Ornithorhynchus anatinus)
Mammalia VSX1 36
  • 80 (a)
(Gallus gallus)
Aves VSX1 35
  • 68.83 (n)
  • 65.19 (a)
VSX1 36
  • 63 (a)
(Anolis carolinensis)
Reptilia VSX1 36
  • 56 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.23560 35
(Danio rerio)
Actinopterygii -- 35
vsx1 36
  • 51 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG15782 37
  • 74 (a)
CG4136 37
  • 57 (a)
Vsx1 36
  • 15 (a)
Vsx2 36
  • 19 (a)
(Caenorhabditis elegans)
Secernentea ceh-10 37
  • 73 (a)
ceh-10 36
  • 33 (a)
Species with no ortholog for VSX1:
  • A. gosspyii yeast (Ashbya 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 squirt (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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for VSX1 Gene

Gene Tree for VSX1 (if available)
Gene Tree for VSX1 (if available)

Paralogs for VSX1 Gene

Paralogs for VSX1 Gene

(2) SIMAP similar genes for VSX1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with VSX1: view

Variants for VSX1 Gene

Sequence variations from dbSNP and Humsavar for VSX1 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs140122268 Corneal dystrophy, posterior polymorphous, 1 (PPCD1), Keratoconus 1 (KTCN1) 25,079,507(+) TGGCT(C/G)TCCTC nc-transcript-variant, reference, missense
VAR_014244 Keratoconus 1 (KTCN1)
rs74315433 - 25,079,460(-) CTTGG(A/G/T)CAAGA nc-transcript-variant, reference, missense
VAR_014246 Keratoconus 1 (KTCN1)
rs148957473 - 25,077,762(+) TGCAG(C/T)GGCGC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for VSX1 Gene

Variant ID Type Subtype PubMed ID
nsv522873 CNV Gain 19592680
nsv912826 CNV Loss 21882294

Variation tolerance for VSX1 Gene

Gene Damage Index Score: 3.89; 59.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VSX1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSX1 Gene

Disorders for VSX1 Gene

MalaCards: The human disease database

(14) MalaCards diseases for VSX1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search VSX1 in MalaCards View complete list of genes associated with diseases


  • Corneal dystrophy, posterior polymorphous, 1 (PPCD1) [MIM:122000]: A rare corneal disorder characterized by small aggregates of apparent vesicles bordered by a gray haze at the level of Descemet membrane, an altered corneal endothelial cell structure, and an unusual proliferation of endothelial cells. Symptoms can range from very aggressive to asymptomatic and non-progressive, even within the same family. {ECO:0000269 PubMed:11978762}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Craniofacial anomalies and anterior segment dysgenesis syndrome (CAASDS) [MIM:614195]: A disorder with extremely variable expressivity. Clinical features include wide interpupillary distance, abnormal corneal endothelium, unusual pinnae, partially to completely empty sella turcica, posterior fossa cyst, anterior encephalocele, and/or hydrocephalus. {ECO:0000269 PubMed:15051220}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Keratoconus 1 (KTCN1) [MIM:148300]: Frequent corneal dystrophy with an incidence that varies from 50 to 230 per 100000. The cornea assumes a conical shape as a result of a progressive non-inflammatory thinning of the corneal stroma. Keratoconus is most often an isolated sporadic condition with cases of autosomal dominant and autosomal recessive transmission. {ECO:0000269 PubMed:11978762, ECO:0000269 PubMed:15623752, ECO:0000269 PubMed:19956409}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VSX1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with VSX1: view

No data available for Genatlas for VSX1 Gene

Publications for VSX1 Gene

  1. Isolation and characterization of a novel human paired-like homeodomain-containing transcription factor gene, VSX1, expressed in ocular tissues. (PMID: 10673340) Semina E.V. … Murray J.C. (Genomics 2000) 2 3 4 23 67
  2. [Mutational analysis of VSX-1 in one patient with posterior polymorphous corneal dystrophy and in three families with hereditary Fuchs endothelial dystrophy]. (PMID: 19507099) Clausen I. … GrA1nauer-Kloevekorn C. (Klin Monbl Augenheilkd 2009) 3 23
  3. Genetic analysis of chromosome 20-related posterior polymorphous corneal dystrophy: genetic heterogeneity and exclusion of three candidate genes. (PMID: 18253095) Hosseini S.M. … Heon E. (Mol. Vis. 2008) 3 23
  4. VSX1 gene variants are associated with keratoconus in unrelated Korean patients. (PMID: 18626569) Mok J.W. … Joo C.K. (J. Hum. Genet. 2008) 3 23
  5. No VSX1 gene mutations associated with keratoconus. (PMID: 16799019) Aldave A.J. … Rabinowitz Y.S. (Invest. Ophthalmol. Vis. Sci. 2006) 3 23

Products for VSX1 Gene

Sources for VSX1 Gene