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VSX1 (visual system homeobox 1)
Gene
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
30813
Gene nameGene Name - the full gene name approved by the HGNC.
Visual system homeobox 1
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
VSX1
SynonymsGene synonyms aliases
CAASDS, KTCN, KTCN1, PPCD, PPCD1, PPD, RINX
ChromosomeChromosome number
20
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
20p11.21
SummarySummary of gene provided in NCBI Entrez 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. M
SNPsSNP information provided by dbSNP.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
SNP ID Visualize variation Clinical significance Consequence
rs74315432 G>A,T Pathogenic Coding sequence variant, upstream transcript variant, genic upstream transcript variant, synonymous variant, non coding transcript variant, missense variant
rs74315435 C>A Pathogenic Coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs74315436 A>G Likely-benign, pathogenic Coding sequence variant, upstream transcript variant, genic upstream transcript variant, non coding transcript variant, missense variant
miRNAmiRNA information provided by mirtarbase database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
miRTarBase ID miRNA Experiments Reference
MIRT1487953 hsa-miR-3685 CLIP-seq
MIRT1487954 hsa-miR-384 CLIP-seq
MIRT1487955 hsa-miR-4461 CLIP-seq
MIRT1487956 hsa-miR-580 CLIP-seq
MIRT1487957 hsa-miR-590-3p CLIP-seq
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000976 Function Transcription regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific ISA
GO:0003700 Function DNA-binding transcription factor activity NAS 10673340
GO:0005515 Function Protein binding IPI 32814053
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
MIM
HGNC
e!Ensembl
Protein
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
UniProt ID Q9NZR4
Protein name Visual system homeobox 1 (Homeodomain protein RINX) (Retinal inner nuclear layer homeobox protein) (Transcription factor VSX1)
Protein function Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster (PubMed:10903837). May regulate the activity of the LCR and the cone opsin genes at earlier stages of development (PubMed:10903837). Dispensab
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00046 Homeodomain
165 → 221
Homeodomain
 Domain
Sequence 
MTGRDSLSDGRTSSRALVPGGSPRGSRPRGFAITDLLGLEAELPAPAGPGQGSGCEGPAV
APCPGPGLDGSSLARGALPLGLGLLCGFGTQPPAAARAPCLLLADVPFLPPRGPEPAAPL
APSRPPPALGRQKRSDSVSTSDEDSQSEDRNDLKASPTLGKRKKRRHRTVFTAHQLEELE
KAFSEAHYPDVYAREMLAVKTELPEDRIQVWFQNRRAKWRKREKRWGGSSVMAEYGLYGA
MVRHCIPLPDSVLNSAEGGLLGSCAPWLLGMHKKSMGMIRKPGSEDKLAGLWGSDHFKEG
SSQSESGSQRGSDKVSPENGLEDVAIDLSSSARQETKKVHPGAGAQGGSNSTALEGPQPG
KVGAT
Sequence length 365
Interactions View interactions
Associated diseases
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Causal
Disease name Disease term dbSNP ID References
Corneal endothelial dystrophy CORNEAL ENDOTHELIAL DYSTROPHY 1, AUTOSOMAL DOMINANT rs267607064, rs1600618680, rs80358191, rs80358192, rs727504229 15051220
Hydrocephalus Hydrocephalus rs387907320, rs369384363, rs387907321, rs372127610, rs770273135, rs797045095, rs797045707, rs769795916, rs781251438, rs922703465, rs376078512, rs1567043467, rs1587149916, rs1586841546
Keratoconus Keratoconus, Keratoconus 1 rs273585637, rs273585632, rs273585616, rs273585618, rs281865144, rs281865150, rs1553500862, rs756938019 15623752, 11978762, 15051220, 21976959, 19763142, 15623752, 19956409, 11978762, 18216574
Macular corneal dystrophy Macular corneal dystrophy rs28937877, rs28937878, rs28937879, rs121917822, rs72547544, rs121917826, rs886052321, rs756036451, rs753928736, rs755563003 11978762
Unknown
Disease name Disease term dbSNP ID References
Astigmatism Astigmatism
Auditory processing disorder Auditory Perceptual Disorders 15051220
Corneal granular dystrophy Granular Dystrophy, Corneal 11978762
Craniofacial anomalies and anterior segment dysgenesis syndrome CRANIOFACIAL ANOMALIES AND ANTERIOR SEGMENT DYSGENESIS SYNDROME rs74315435 15051220

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