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Aliases for VSX1 Gene

Aliases for VSX1 Gene

  • Visual System Homeobox 1 2 3
  • RINX 3 4 6
  • Retinal Inner Nuclear Layer Homeobox Protein 3 4
  • Transcription Factor VSX1 3 4
  • Homeodomain Protein RINX 3 4
  • CAASDS 3 6
  • KTCN1 3 6
  • PPCD 3 6
  • PPD 3 6
  • Visual System Homeobox 1 Homolog, CHX10-Like (Zebrafish) 2
  • Posterior Polymorphous Corneal Dystrophy 2
  • PPCD1 3
  • KTCN 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 sequence-specific DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is PITX3.

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 for VSX1 Gene

Gene Families for VSX1 Gene

  • PRD :Homeoboxes / PRD class

Protein Domains for VSX1 Gene

Suggested Antigen Peptide Sequences for VSX1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Q9NZR4
  • 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

Gene Ontology (GO) - Molecular Function for VSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity NAS 10673340
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with VSX1: view
genes like me logo Genes that share phenotypes with VSX1: view

Animal Models for VSX1 Gene

MGI Knock Outs for VSX1:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting 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 3
extracellular 2

Gene Ontology (GO) - Cellular Components for VSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with VSX1: view

Pathways for VSX1 Gene

SuperPathways for VSX1 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

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:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007601 visual perception IEA --
GO:0042551 neuron maturation IEA --
GO:0048666 neuron development --
genes like me logo Genes that share ontologies with VSX1: view

No data available for Pathways by source for VSX1 Gene

Transcripts for VSX1 Gene

mRNA/cDNA for VSX1 Gene

Unigene Clusters for VSX1 Gene

Visual system homeobox 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VSX1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for VSX1

Flow Cytometry Products

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 (14.9) and Brain - Cerebellum (12.5).

Integrated Proteomics: protein expression 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 expressions with VSX1: view

In Situ Assay 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
(Pan troglodytes)
Mammalia VSX1 35
  • 99.27 (n)
  • 99.18 (a)
VSX1 36
  • 99 (a)
(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)
(Monodelphis domestica)
Mammalia VSX1 36
  • 62 (a)
(Ornithorhynchus anatinus)
Mammalia VSX1 36
  • 80 (a)
(Rattus norvegicus)
Mammalia Vsx1 35
  • 77.59 (n)
  • 74.1 (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 Vsx1 36
  • 15 (a)
Vsx2 36
  • 19 (a)
CG4136 37
  • 57 (a)
CG15782 37
  • 74 (a)
(Caenorhabditis elegans)
Secernentea ceh-10 36
  • 33 (a)
ceh-10 37
  • 73 (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

Selected 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 MAF
rs743017 -- 25,072,307(+) TGTGA(A/G)GTACA intron-variant
rs743018 -- 25,072,469(-) AGTAT(C/T)GGCCT intron-variant
rs2207632 -- 25,074,809(+) AGGAA(A/G)TGTGT intron-variant
rs2207633 -- 25,078,483(+) AAAGT(A/G)GAGAA intron-variant, downstream-variant-500B
rs4508671 -- 25,079,102(+) GATTA(G/T)CTGAT intron-variant

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

Relevant External Links for VSX1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

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

Disorders for VSX1 Gene

(3) OMIM Diseases for VSX1 Gene (605020)


  • 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.
  • 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.
  • 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.

(2) Novoseek inferred disease relationships for VSX1 Gene

Disease -log(P) Hits PubMed IDs
posterior polymorphous corneal dystrophy 97.5 4
keratoconus 81 11

Relevant External Links for VSX1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with VSX1: view

Publications for VSX1 Gene

  1. VSX1 mutational analysis in a series of Italian patients affected by keratoconus: detection of a novel mutation. (PMID: 15623752) Bisceglia L. … Zelante L. (Invest. Ophthalmol. Vis. Sci. 2005) 3 4 23 48
  2. 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
  3. RINX(VSX1), a novel homeobox gene expressed in the inner nuclear layer of the adult retina. (PMID: 10903837) Hayashi T. … Deeb S.S. (Genomics 2000) 3 4 23
  4. VSX1 (RINX) mutation with craniofacial anomalies, empty sella, corneal endothelial changes, and abnormal retinal and auditory bipolar cells. (PMID: 15051220) Mintz-Hittner H.A. … Murray J.C. (Ophthalmology 2004) 3 4 23
  5. 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 4 23

Products for VSX1 Gene

Sources for VSX1 Gene

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