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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 Keratoconus 1 and Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome. 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 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

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 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
GH20F025089 1.3 FANTOM5 Ensembl ENCODE 14.2 -8.8 -8802 2.5 CEBPG ZIC2 RARA GLIS2 POLR2A ZNF600 MAFK NFE2L2 CEBPB CEBPA ACSS1 VSX1 PYGB GINS1 LOC391239
GH20F025077 0.9 ENCODE 16.6 +5.2 5240 0.2 ZNF76 ARID4B SIN3A ZNF48 ZNF335 GLIS2 SCRT2 RCOR1 FOS THAP11 VSX1 ENSG00000275358
GH20F025051 1.1 ENCODE 11.4 +26.5 26493 8.4 HDGF MLX ZFP64 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 ZNF207 VSX1 ACSS1 CST7 ENTPD6 FAM182B ZNF337 NINL PIR53263
GH20F025194 1.1 ENCODE 7.8 -114.0 -113992 3.4 MLX ZFP64 ARID4B SIN3A YBX1 DMAP1 ZNF143 SP3 SP5 MXD4 PYGB ENTPD6 ABHD12 ACSS1 FAM182B VSX1 CST7 NINL LOC101926889
GH20F025067 0.8 FANTOM5 10.4 +14.8 14820 0.7 YBX1 PLRG1 CDC5L ZNF48 ZKSCAN1 ZFHX2 MTA3 CTBP1 HNF4G MNT ZNF337 VSX1 LOC105372582 ENSG00000275358
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VSX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for VSX1 Gene

Chromosome:
20
Start:
25,070,885 bp from pter
End:
25,082,379 bp from pter
Size:
11,495 bases
Orientation:
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:
    Q9NZR4-VSX1_HUMAN
    Recommended name:
    Visual system homeobox 1
    Protein Accession:
    Q9NZR4
    Secondary Accessions:
    • B9EGJ4
    • D1MF28
    • Q0GM60
    • Q0GM61
    • Q0GM62
    • Q0GM63
    • Q0GM64
    • Q0GM65
    • Q5TF40
    • Q5TF41
    • Q9HCU3
    • Q9NU27

    Protein attributes for VSX1 Gene

    Size:
    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

  • 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

Q9NZR4

UniProtKB/Swiss-Prot:

VSX1_HUMAN :
  • Contains 1 CVC domain.
  • Belongs to the paired homeobox family.
Domain:
  • Contains 1 CVC domain.
  • Contains 1 homeobox DNA-binding domain.
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 transcription factor activity, sequence-specific DNA binding 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:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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

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 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 IEA,IBA --
genes like me logo Genes that share ontologies with VSX1: view

Pathways & Interactions for VSX1 Gene

No Data Available

Interacting Proteins for VSX1 Gene

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

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 IEA,TAS --
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

Transcripts for VSX1 Gene

mRNA/cDNA for VSX1 Gene

Unigene Clusters for VSX1 Gene

Visual system homeobox 1:
Representative Sequences:

Inhibitory RNA Products

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
VSX1
ECgene alternative splicing isoforms for
VSX1

Expression for VSX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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 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:

VSX1

SOURCE GeneReport for Unigene cluster for VSX1 Gene:

Hs.274264

mRNA Expression by UniProt/SwissProt for VSX1 Gene:

Q9NZR4-VSX1_HUMAN
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

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
chimpanzee
(Pan troglodytes)
Mammalia VSX1 34 35
  • 99.27 (n)
dog
(Canis familiaris)
Mammalia VSX1 34 35
  • 84.02 (n)
cow
(Bos Taurus)
Mammalia VSX1 34 35
  • 81.59 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VSX1 35
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vsx1 34 16 35
  • 78.25 (n)
rat
(Rattus norvegicus)
Mammalia Vsx1 34
  • 77.59 (n)
oppossum
(Monodelphis domestica)
Mammalia VSX1 35
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves VSX1 34 35
  • 68.83 (n)
lizard
(Anolis carolinensis)
Reptilia VSX1 35
  • 56 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.23560 34
zebrafish
(Danio rerio)
Actinopterygii vsx1 35
  • 51 (a)
OneToOne
-- 34
fruit fly
(Drosophila melanogaster)
Insecta CG15782 36
  • 74 (a)
CG4136 36
  • 57 (a)
Vsx2 35
  • 19 (a)
ManyToMany
Vsx1 35
  • 15 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-10 36 35
  • 73 (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

ENSEMBL:
Gene Tree for VSX1 (if available)
TreeFam:
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
rs74315432 Keratoconus 1 (KTCN1) [MIM:148300], Pathogenic 25,079,443(-) AGCGG(A/C/T)GGCAC nc-transcript-variant, reference, synonymous-codon, missense
rs74315435 Craniofacial anomalies and anterior segment dysgenesis syndrome (CAASDS) [MIM:614195], Pathogenic 25,077,727(-) ACTCC(G/T)CCGAG intron-variant, nc-transcript-variant, reference, missense
rs74315436 Keratoconus 1 (KTCN1) [MIM:148300], Pathogenic 25,082,047(-) GGCGC(C/T)GGTGC nc-transcript-variant, reference, missense
rs771561481 Keratoconus 1 (KTCN1) [MIM:148300] 25,078,931(+) TCCAG(C/G)TGGTG nc-transcript-variant, reference, missense
rs796052181 Likely benign 25,081,787(-) TCCTA(C/G)CGGAC nc-transcript-variant, reference, missense

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)

Relevant External Links for VSX1 Gene

Human Gene Mutation Database (HGMD)
VSX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSX1

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

Disorders for VSX1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
keratoconus 1
  • ktcn1
craniofacial anomalies and anterior segment dysgenesis syndrome
  • caasds
corneal dystrophy, posterior polymorphous, 1
  • corneal endothelial dystrophy 1, autosomal dominant
keratoconus
  • conical cornea
corneal dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search VSX1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VSX1_HUMAN
  • 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.

Relevant External Links for VSX1

Genetic Association Database (GAD)
VSX1
Human Genome Epidemiology (HuGE) Navigator
VSX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VSX1
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. (Invest. Ophthalmol. Vis. Sci. 2005) 3 4 22 46 64
  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 22 64
  3. A novel VSX1 mutation identified in an individual with keratoconus in India. (PMID: 19956409) Paliwal P. … Sharma A. (Mol. Vis. 2009) 3 4 46 64
  4. Three VSX1 gene mutations, L159M, R166W, and H244R, are not associated with keratoconus. (PMID: 18216574) Tang Y.G. … Rabinowitz Y.S. (Cornea 2008) 3 4 46 64
  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 22 64

Products for VSX1 Gene

Sources for VSX1 Gene

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