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

Gene ID: 30813, updated on 5-Mar-2024

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
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Genomic context

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Location:
20p11.21
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25070880..25082141, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25127147..25146758, complement)
105.20220307 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 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. Contributions of VSX1 gene to keratoconus. Kalasidou G, et al. J Biol Regul Homeost Agents, 2018 Nov-Dec. PMID 30574758
  3. [A novel VSX1 gene mutation identified in a sporadic keratoconus patient from China]. Guan T, et al. Zhonghua Yan Ke Za Zhi, 2018 Mar 11. PMID 29518881
  4. Analysis of the VSX1 gene in sporadic keratoconus patients from China. Guan T, et al. BMC Ophthalmol, 2017 Sep 26. PMID 28950846, Free PMC Article
  5. Novel visual system homeobox 1 gene mutations in Turkish patients with keratoconus. Bardak H, et al. Genet Mol Res, 2016 Nov 3. PMID 27819732

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)

Genotypes

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 response to stimulus 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
is_active_in cellular_component ND
No biological Data available
more info
  
part_of 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

    See identical proteins and their annotated locations for NP_001243200.1

    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

    See identical proteins and their annotated locations for NP_001243201.1

    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

    See identical proteins and their annotated locations for NP_055403.2

    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

    See identical proteins and their annotated locations for NP_955457.1

    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_2023_10

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

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