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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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VSX1
visual system homeobox 1
Chromosome 20 · 20p11.21
NCBI Gene: 30813Ensembl: ENSG00000100987.15HGNC: HGNC:12723UniProt: Q9NZR4
53PubMed Papers
22Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingprotein bindingtranscription cis-regulatory region bindingDNA-binding transcription factor activity, RNA polymerase II-specifickeratoconus 1craniofacial anomalies and anterior segment dysgenesis syndromeposterior polymorphous corneal dystrophyneurodegenerative disease
✦AI Summary

VSX1 (visual system homeobox 1) is a paired-like homeodomain transcription factor that binds to the 37-bp core of the locus control region of the red/green visual pigment gene cluster and regulates cone opsin genes during retinal development 1. The gene is expressed in embryonic craniofacial tissues and adult ocular tissues, particularly in the retinal inner nuclear layer 23. VSX1 plays a critical role in ocular development through its DNA-binding transcription factor activity 2. Regarding disease relevance, VSX1 variants show population-specific associations with keratoconus. In Malaysian patients, the p.A182A and p.P237P variants were significantly associated with keratoconus susceptibility, while p.R217H appeared protective 4. A novel variant p.Leu268His identified in Indian families co-segregated with keratoconus and was predicted deleterious 5. However, multiple studies in other populations (Korean and white American cohorts) failed to confirm VSX1 mutations as pathogenic in keratoconus, suggesting population-specific genetic heterogeneity 67. Clinically, VSX1 is implicated in craniofacial anomalies and anterior segment dysgenesis syndrome. Additionally, recent evidence indicates VSX1 functions as an oncogenic transcription factor in clear cell renal cell carcinoma, where high expression promotes cell proliferation and invasion through FKBP10 transcriptional regulation 8.

Sources cited
1
VSX1 binds to the locus control region of red/green visual pigment genes and regulates cone opsin genes during development
PMID: 10903837
2
VSX1 is a paired-like homeodomain transcription factor expressed in embryonic craniofacial and adult ocular tissues
PMID: 10673340
3
Mouse Vsx1 is expressed during embryogenesis and in the retinal inner nuclear layer
PMID: 11485319
4
VSX1 variants p.A182A and p.P237P are associated with keratoconus susceptibility in Malaysian patients, while p.R217H is protective
PMID: 37322657
5
Novel VSX1 variant p.Leu268His co-segregates with keratoconus in Indian families and is predicted to be deleterious
PMID: 25963163
6
VSX1 gene mutations do not show significant association with keratoconus in Korean patients
PMID: 22531431
7
VSX1 mutations L159M, R166W, and H244R are not associated with keratoconus in white sporadic and familial panels
PMID: 18216574
8
High VSX1 expression promotes clear cell renal cell carcinoma aggressiveness through transcriptional activation of FKBP10 and other oncogenic genes
PMID: 36463181
Disease Associationsⓘ22
keratoconus 1Open Targets
0.75Strong
craniofacial anomalies and anterior segment dysgenesis syndromeOpen Targets
0.53Moderate
posterior polymorphous corneal dystrophyOpen Targets
0.42Moderate
neurodegenerative diseaseOpen Targets
0.25Weak
paralytic strabismusOpen Targets
0.24Weak
posterior polymorphous corneal dystrophy 1Open Targets
0.21Weak
thyroiditisOpen Targets
0.21Weak
genetic disorderOpen Targets
0.19Weak
retinal degenerationOpen Targets
0.18Weak
Townes-Brocks syndromeOpen Targets
0.11Weak
familial long QT syndromeOpen Targets
0.11Weak
Romano-Ward syndromeOpen Targets
0.11Weak
neoplasmOpen Targets
0.10Weak
keratoconusOpen Targets
0.09Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.08Suggestive
tuberculosisOpen Targets
0.08Suggestive
non-small cell lung carcinomaOpen Targets
0.07Suggestive
sarcoidosisOpen Targets
0.07Suggestive
breast cancerOpen Targets
0.07Suggestive
pulmonary tuberculosisOpen Targets
0.06Suggestive
Craniofacial anomalies and anterior segment dysgenesis syndromeUniProt
Keratoconus 1UniProt
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
COL8A2Protein interaction90%NXNL1Protein interaction86%ATOH7Protein interaction78%COL4A3Protein interaction72%ALX3Shared pathway50%DRGXShared pathway50%
Tissue Expression6 tissues
Brain
100%
Ovary
61%
Heart
44%
Liver
17%
Bone Marrow
4%
Lung
0%
Gene Interaction Network
Click a node to explore
VSX1COL8A2NXNL1ATOH7COL4A3ALX3DRGX
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9NZR4
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.69LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.21 [0.87–1.69]
RankingsWhere VSX1 stands among ~20K protein-coding genes
  • #8,514of 20,598
    Most Researched53
  • #16,051of 17,882
    Most Constrained (LOEUF)1.69
Genes detectedVSX1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
The association between
PMID: 37322657
Indian J Ophthalmol · 2023
1.00
2
VSX1 gene and keratoconus: genetic analysis in Korean patients.
PMID: 22531431
Cornea · 2012
0.90
3
Visual System Homeobox 1 (VSX1) Gene Analysis in Keratoconus: Design of Specific Primers and DNA Amplification Protocols for Accurate Molecular Characterization.
PMID: 28164597
Clin Lab · 2016
0.80
4
Three VSX1 gene mutations, L159M, R166W, and H244R, are not associated with keratoconus.
PMID: 18216574
Cornea · 2008
0.70
5
Isolation and characterization of a novel human paired-like homeodomain-containing transcription factor gene, VSX1, expressed in ocular tissues.
PMID: 10673340
Genomics · 2000
0.60