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FLASH GENE
Symbol VSX1 contributors: npt/mct/shn - updated : 19-03-2019
HGNC name visual system homeobox 1
HGNC id 12723
Corresponding disease
CAASDS craniofacial anomalies and anterior segment dysgenesis syndrome
KTCN1 keratoconus 1
Location 20p11.21      Physical location : 25.056.099 - 25.062.767
Synonym name
  • retinal inner nuclear layer homeobox
  • paired-like homeobox containing-gene
  • visual system homeobox 1 homolog
  • CHX10-like (zebrafish)
  • transcription factor VSX1
  • homeodomain protein RINX
  • posterior polymorphous corneal dystrophy
  • Synonym symbol(s) RINX, PPD, PPCD, P5-1025A1.1, CAASDS, KTCN, KTCN1, PPCD1
    DNA
    TYPE functioning gene
    STRUCTURE 12.44 kb     5 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status confirmed
    Map pter - D20S486 - D20S844 - VSX1 - D20S191 - cen
    Authors Hayashi (00)
    Physical map
    CST3 20p11.22-p11.21 cystatin C (amyloid angiopathy and cerebral hemorrhage) CST4 20p11.2 cystatin S CST1 20p11.2 cystatin SN CSTP2 20p11.2 cystatin pseudogene 2 CST2 20p11.2 cystatin SA CST5 20p11.21 cystatin D CSTP1 20p11.2 cystatin pseudogene 1 GGTLA4 20p11.1 gamma-glutamyltransferase-like activity 4 LOC284796 20p11.21 similar to hypothetical protein DKFZp434P211.1 - human (fragments) C20orf39 20p11.21 chromosome 20 open reading frame 39 LOC391238 20 LOC391238 CST7 20p11.22-p11.21 cystatin F (leukocystatin) C20orf3 20p11.22-p11.21 chromosome 20 open reading frame 3 ACAS2L 20p11.23-p11.21 acetyl-Coenzyme A synthetase 2 (AMP forming)-like VSX1 20p11.23-p11.22 visual system homeobox 1 homolog, CHX10-like (zebrafish) LOC391239 20 similar to immune costimulatory protein B7-H4 LOC391240 20 similar to nodulin ENTPD6 20q11.2 ectonucleoside triphosphate diphosphohydrolase 6 (putative function) PYGB 20p11.2 phosphorylase, glycogen; brain C20orf22 20 chromosome 20 open reading frame 22 PPIAP2 20 peptidylprolyl isomerase A (cyclophilin A) pseudogene 2 KIAA0186 20pter-cen peptidylprolyl isomerase A (cyclophilin A) pseudogene 2 KIAA0980 20p11.2-p11.1 peptidylprolyl isomerase A (cyclophilin A) pseudogene 2 C20orf147 20p11.1 chromosome 20 open reading frame 147 ZNF337 20p11.1 zinc finger protein 337 C20orf189 20 chromosome 20 open reading frame 189 FLJ38374 20p11.21 hypothetical protein FLJ38374 LOC149934 20p11.21 similar to bB329D4.2.1 (novel protein similar to a truncated nuclear receptor co-repressor 1 (NCOR1) (retinoid X receptor interacting protein 13), isoform 1)
    RNA
    TRANSCRIPTS type messenger
    text two major alternatively spliced forms L1 and S1 and four alternative forms truncated L2, L3 and S3, one with alternative splicing
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    3 splicing 943 24 239 - 2005 15647262
  • three exons transcript
  • containing exon 3a (longer than 3b)
  • lacking the 156 C-terminal amino acid of L1, replaced by a stretch of 30 residues
  • encoding for the shortest product
  • 5 splicing 1956 38 365 visual system 2005 15647262
  • five exons transcript
  • containing exon 3b (shorter than 3a)
  • encoding for the largest product
  • 4 - 2055 - 236 - 2005 15647262
    5 - 2236 - 301 - 2005 15647262
    EXPRESSION
    Type restricted
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Visualeyeretina  highly Homo sapiens
     eyeanterior segmentcornea highly Homo sapiens
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Connective   moderately
    Epithelial    
    Nervouscentral   
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Visualbipolar cell
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    physiological period embryo, fetal
    Text craniofacial, corneal tissue, fetal eyes
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • an octapeptide, a proline-rich
  • an acid rich region
  • a nuclear localization signal (NLS)
  • the helix-turn helix homeodomain
  • a CVC domain (goldfish ca-Vsx1, Vsx2)
  • a C terminal conserved RV (RINX-VSX1) domain
  • HOMOLOGY
    interspecies ortholog to Vsx1, Mus musculus
    ortholog to vsx1, Danio rerio
    ortholog to Vsx1, Rattus norvegicus
    ortholog to VSX1, Pan troglodytes
    intraspecies homolog to CHX10,CRX
    Homologene
    FAMILY
  • vertebrate paired-like homeodomain transcription factor family
  • paired homeobox family
  • CATEGORY regulatory , transcription factor
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus,nucleolus
    basic FUNCTION
  • playing a role in the development of cone cells
  • required for the late differentiation and function of OFF-cone bipolar cells and associated with a heritable OFF visual pathway-specific retinal defect
  • with IRX5, control specific aspects of visual function in circuits of the mammalian retina (Kerschensteiner 2008)
  • may have an important role in the pathogenesis of keratoconus (
  • CELLULAR PROCESS nucleotide, transcription, regulation
    PHYSIOLOGICAL PROCESS development
    PATHWAY
    metabolism
    signaling sensory transduction/vision
    a component
    INTERACTION
    DNA binding to locus control region of the cone pigment cluster LCR-RGCP@
    RNA
    small molecule
    protein
  • VSX2
  • VSX1 has likely a partial inhibitory effect on the expression of IRX6
  • IRX6 can activate or repress transcription through Iroquois-binding sites found proximal to RCVRN, VSX1 and TACR3
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) CAASDS , KTCN1
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS