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    VSX1 visual system homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 30813, updated on 4-Jan-2025

    Summary

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    Official Symbol
    VSX1provided by HGNC
    Official Full Name
    visual system homeobox 1provided by HGNC
    Primary source
    HGNC:HGNC:12723
    See related
    Ensembl:ENSG00000100987 MIM:605020; AllianceGenome:HGNC:12723
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PPD; KTCN; PPCD; RINX; KTCN1; PPCD1; CAASDS
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See VSX1 in Genome Data Viewer
    Location:
    20p11.21
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25070880..25082141, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25127147..25146758, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (25051516..25062777, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene acyl-CoA synthetase short chain family member 1 Neighboring gene Sharpr-MPRA regulatory region 14776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25038651-25039256 Neighboring gene uncharacterized LOC124904882 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:25052223-25052743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25062766-25063295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25064059-25064663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25064664-25065269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25085805-25086741 Neighboring gene VTCN1 pseudogene 1 Neighboring gene uncharacterized LOC284798

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The association between VSX1 exon3 gene variants and keratoconus in Malaysian patients. Deva JP, et al. Indian J Ophthalmol, 2023 Jun. PMID 37322657, Free PMC Article
    2. A novel VSX1 mutation identified in an individual with keratoconus in India. Paliwal P, et al. Mol Vis, 2009 Nov 28. PMID 19956409, Free PMC Article
    3. Mutational screening of VSX1 in keratoconus patients from the European population. Dash DP, et al. Eye (Lond), 2010 Jun. PMID 19763142
    4. [Mutational analysis of VSX-1 in one patient with posterior polymorphous corneal dystrophy and in three families with hereditary Fuchs endothelial dystrophy]. Clausen I, et al. Klin Monbl Augenheilkd, 2009 Jun. PMID 19507099
    5. VSX1 gene analysis in keratoconus. Tanwar M, et al. Mol Vis, 2010 Nov 16. PMID 21139977, Free PMC Article

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The association between VSX1 exon3 gene variants and keratoconus in Malaysian patients.
      Title: The association between VSX1 exon3 gene variants and keratoconus in Malaysian patients.
    2. High VSX1 expression promotes the aggressiveness of clear cell renal cell carcinoma by transcriptionally regulating FKBP10.
      Title: High VSX1 expression promotes the aggressiveness of clear cell renal cell carcinoma by transcriptionally regulating FKBP10.
    3. Sequence variants of the VSX1 gene were identified for the first time in Chinese patients with sporadic keratoconus
      Title: [A novel VSX1 gene mutation identified in a sporadic keratoconus patient from China].
    4. VSX1 is involved in keratoconus and other corneal pathologies
      Title: Contributions of VSX1 gene to keratoconus.
    5. In this study, we added one novel missense sequence variation (p.Arg131Pro) in the coding region of the VSX1 gene to the range of VSX1 coding region variations observed in patients with sporadic keratoconus from China.
      Title: Analysis of the VSX1 gene in sporadic keratoconus patients from China.
    6. The aim of this study was to screen the visual system homeobox 1 (VSX1) gene in Turkish patients with keratoconus
      Title: Novel visual system homeobox 1 gene mutations in Turkish patients with keratoconus.
    7. We cannot confirm the previously reported association of the polymorphism in the VSX1 gene with keratoconus (KC). Our results suggest a possible causative role of SOD1 in the pathogenesis of KC.
      Title: Polymorphism Analysis of VSX1 and SOD1 Genes in Greek Patients with Keratoconus.
    8. novel missense substitutions in the VSX1 gene: clinical and genetic analysis of families with Keratoconus from India
      Title: Two novel missense substitutions in the VSX1 gene: clinical and genetic analysis of families with Keratoconus from India.
    9. Our findings confirmed previous reports that polymorphisms of VSX1 and IL1A genes were associated with risk of keratoconus in the Chinese population
      Title: Common single nucleotide polymorphisms and keratoconus in the Han Chinese population.
    10. Our investigation showed that Keratoconus-related VSX1 mutations were found in a very small proportion of the studied patients from Iran.
      Title: Study of VSX1 mutations in patients with keratoconus in southwest Iran using PCR-single-strand conformation polymorphism/heteroduplex analysis and sequencing method.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Craniofacial anomalies and anterior segment dysgenesis syndrome
    MedGen: C3280099 OMIM: 614195 GeneReviews: Not available
    		Compare labs
    Keratoconus 1
    MedGen: C1835677 OMIM: 148300 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in neuron development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retinal bipolar neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    visual system homeobox 1
    Names
    homeodomain protein RINX
    retinal inner nuclear layer homeobox protein
    transcription factor VSX1
    visual system homeobox 1 homolog, CHX10-like

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008101.3 RefSeqGene

      Range
      5041..11719
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256271.2 → NP_001243200.1  visual system homeobox 1 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL080312
      Consensus CDS
      CCDS58766.1
      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000387720.2, ENST00000444511.6
      Conserved Domains (1) summary
      pfam00046
      Location:167 → 209
      Homeobox; Homeobox domain

    2. NM_001256272.2 → NP_001243201.1  visual system homeobox 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL080312
      Consensus CDS
      CCDS58767.1
      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000401690.3, ENST00000429762.7
      Conserved Domains (1) summary
      pfam00046
      Location:167 → 220
      Homeobox; Homeobox domain

    3. NM_001378633.1 → NP_001365562.1  visual system homeobox 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL080312

    4. NM_014588.6 → NP_055403.2  visual system homeobox 1 isoform a

      Status: REVIEWED

      Source sequence(s)
      AF176797, DQ854807
      Consensus CDS
      CCDS13168.1
      UniProtKB/Swiss-Prot
      B9EGJ4, D1MF28, Q0GM60, Q0GM61, Q0GM62, Q0GM63, Q0GM64, Q0GM65, Q5TF40, Q5TF41, Q9HCU3, Q9NU27, Q9NZR4
      Related
      ENSP00000365899.3, ENST00000376709.9
      Conserved Domains (2) summary
      pfam00046
      Location:167 → 220
      Homeobox; Homeobox domain
      cl26247
      Location:47 → 149
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    5. NM_199425.3 → NP_955457.1  visual system homeobox 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL080312
      Consensus CDS
      CCDS13169.1
      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000365897.3, ENST00000376707.4
      Conserved Domains (1) summary
      pfam00046
      Location:167 → 210
      Homeobox; Homeobox domain

    RNA

    1. NR_045948.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312

    2. NR_045951.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312

    3. NR_165181.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312

    4. NR_165182.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312

    5. NR_165183.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      25070880..25082141 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027838.2 → XP_016883327.1  visual system homeobox 1 isoform X2

      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000387069.2, ENST00000409958.6
      Conserved Domains (1) summary
      pfam00046
      Location:167 → 209
      Homeobox; Homeobox domain

    2. XM_017027837.2 → XP_016883326.1  visual system homeobox 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000386612.2, ENST00000409285.6
      Conserved Domains (1) summary
      pfam00046
      Location:167 → 220
      Homeobox; Homeobox domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      25127147..25146758 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323401.1 → XP_054179376.1  visual system homeobox 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZR4.2 GenPept UniProtKB/Swiss-Prot:Q9NZR4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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