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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
  • Visual System Homeobox 1 Homolog, CHX10-Like 3
  • 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 Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome and Keratoconus 1. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is VSX2.

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

Additional gene information for VSX1 Gene

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

Genomics for VSX1 Gene

GeneHancer (GH) Regulatory Elements for VSX1 Gene

Promoters and enhancers for VSX1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I025082 Promoter 0.7 EPDnew 550.8 +0.2 220 0.1 SUZ12 EZH2 VSX1 ACSS1 ENSG00000275358
GH20I025051 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 11.5 +26.5 26493 8.4 HDGF FOXA2 ZFP64 ARID4B SIN3A DMAP1 IRF4 ZNF207 ZNF143 FOS ACSS1 VSX1 CST7 ENTPD6 FAM182B ZNF337 NINL PIR53263
GH20I025194 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 7.8 -114.0 -113992 3.4 MLX ZFP64 ARID4B SIN3A DMAP1 YBX1 ZBTB7B POLR2B ZNF143 SP3 ENTPD6 LOC101926889 PYGB FAM182B NINL ABHD12 ACSS1 VN1R108P VSX1 CST7
GH20I025079 Enhancer 1 Ensembl dbSUPER 17 +4.5 4499 0.7 CTCF ZNF76 CEBPG ZIC2 ZNF644 YY1 ZNF335 ZFHX2 GLIS2 PATZ1 VSX1 ENSG00000275358
GH20I025077 Enhancer 1 ENCODE dbSUPER 16.7 +5.2 5239 0.2 ARID4B SIN3A MZF1 ZNF48 SCRT2 FOS RCOR1 THAP11 REST ZEB2 VSX1 ENSG00000275358
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VSX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VSX1 gene promoter:

Genomic Locations for VSX1 Gene

Genomic Locations for VSX1 Gene
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

Post-translational modifications for VSX1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for VSX1 Gene

Domains & Families for VSX1 Gene

Gene Families for VSX1 Gene

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

Protein Domains for VSX1 Gene

Suggested Antigen Peptide Sequences for VSX1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the paired homeobox family.
  • 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:0003682 chromatin binding IBA --
GO:0003700 DNA binding transcription factor activity NAS 10673340
GO:0043565 sequence-specific DNA binding IEA --
GO:0044212 transcription regulatory region DNA binding IBA --
genes like me logo Genes that share ontologies with VSX1: view
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:

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

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 VSX1 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for VSX1 Gene

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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VSX1 Gene

Pathways & Interactions for VSX1 Gene

No Data Available

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 IBA --
GO:0007275 multicellular organism development IEA --
GO:0007601 visual perception TAS,IEA --
GO:0042551 neuron maturation 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:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, PaxDb, and MOPED for VSX1 Gene

Protein tissue co-expression partners for VSX1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VSX1 Gene:


SOURCE GeneReport for Unigene cluster for VSX1 Gene:


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).

Evidence on tissue expression from TISSUES for VSX1 Gene

  • Eye(4.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VSX1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • ear
  • eye
  • eyelid
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • mouth
  • outer ear
  • skull
  • tooth
  • abdominal wall
  • intestine
genes like me logo Genes that share expression patterns with VSX1: view

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
(Pan troglodytes)
Mammalia VSX1 33 34
  • 99.27 (n)
(Canis familiaris)
Mammalia VSX1 33 34
  • 84.02 (n)
(Bos Taurus)
Mammalia VSX1 33 34
  • 81.59 (n)
(Ornithorhynchus anatinus)
Mammalia VSX1 34
  • 80 (a)
(Mus musculus)
Mammalia Vsx1 33 16 34
  • 78.25 (n)
(Rattus norvegicus)
Mammalia Vsx1 33
  • 77.59 (n)
(Monodelphis domestica)
Mammalia VSX1 34
  • 62 (a)
(Gallus gallus)
Aves VSX1 33 34
  • 68.83 (n)
(Anolis carolinensis)
Reptilia VSX1 34
  • 56 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.23560 33
(Danio rerio)
Actinopterygii vsx1 34
  • 51 (a)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta CG15782 35
  • 74 (a)
CG4136 35
  • 57 (a)
Vsx2 34
  • 19 (a)
Vsx1 34
  • 15 (a)
(Caenorhabditis elegans)
Secernentea ceh-10 34 35
  • 33 (a)
Species where no ortholog for VSX1 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs11427085 benign, Posterior Polymorphous Corneal Dystrophy 25,076,556(-) AAAAAAAAAAA/AAAAAAAAA/AAAAAAAAAA/AAAAAAAAAAAA/AAAAAAAAAAAAA/AAAAAAAAAAAAAA genic_downstream_transcript_variant, intron_variant
rs11478193 benign, Posterior Polymorphous Corneal Dystrophy 25,075,808(-) C/ 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs116022495 likely-benign, Posterior Polymorphous Corneal Dystrophy 25,082,293(-) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, upstream_transcript_variant
rs12480307 benign, not specified, Posterior Polymorphous Corneal Dystrophy 25,078,910(-) T/C coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs139744143 likely-benign, Posterior Polymorphous Corneal Dystrophy 25,075,517(-) G/A/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
esv3645552 CNV gain 21293372
nsv1056345 CNV gain 25217958
nsv522873 CNV gain 19592680

Variation tolerance for VSX1 Gene

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

Additional Variant Information for VSX1 Gene

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

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: HGMD, OMIM, ClinVar, GTR, 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


  • 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:18216574, ECO:0000269 PubMed:19763142, ECO:0000269 PubMed:19956409, ECO:0000269 PubMed:21976959}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VSX1

Genetic Association Database
Human Genome Epidemiology 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. VSX1 mutational analysis in a series of Italian patients affected by keratoconus: detection of a novel mutation. (PMID: 15623752) Bisceglia L … Zelante L (Investigative ophthalmology & visual science 2005) 3 4 22 44 58
  2. Isolation and characterization of a novel human paired-like homeodomain-containing transcription factor gene, VSX1, expressed in ocular tissues. (PMID: 10673340) Semina EV … Murray JC (Genomics 2000) 2 3 4 22 58
  3. A novel VSX1 mutation identified in an individual with keratoconus in India. (PMID: 19956409) Paliwal P … Sharma A (Molecular vision 2009) 3 4 44 58
  4. Three VSX1 gene mutations, L159M, R166W, and H244R, are not associated with keratoconus. (PMID: 18216574) Tang YG … Rabinowitz YS (Cornea 2008) 3 4 44 58
  5. Genetic analysis of chromosome 20-related posterior polymorphous corneal dystrophy: genetic heterogeneity and exclusion of three candidate genes. (PMID: 18253095) Hosseini SM … Héon E (Molecular vision 2008) 3 4 22 58

Products for VSX1 Gene

Sources for VSX1 Gene

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