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 name Gene Name - the full gene name approved by the HGNC.
Visual system homeobox 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
VSX1
Synonyms (NCBI Gene) Gene synonyms aliases
CAASDS, KTCN, KTCN1, PPCD, PPCD1, PPD, RINX
Chromosome Chromosome number
20
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
20p11.21
Summary Summary 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
SNPs SNP information provided by dbSNP.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all(3)
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
miRNA miRNA information provided by mirtarbase database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all(7)
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
Show/Hide all(20)
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000976 Function Transcription cis-regulatory region binding IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IEA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific ISA
GO:0003677 Function DNA binding IEA
Other IDs Other 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
605020 12723 ENSG00000100987
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
Tissue specificity TISSUE SPECIFICITY: In the adult eye, expressed in lens, iris, ciliary body, choroid, optical nerve head and, most strongly, in retina, but not expressed in sclera and cornea. According to PubMed:11978762, expressed in adult retina but not in lens and cor
Sequence 
MTGRDSLSDGRTSSRALVPGGSPRGSRPRGFAITDLLGLEAELPAPAGPGQGSGCEGPAV
APCPGPGLDGSSLARGALPLGLGLLCGFGTQPPAAARAPCLLLADVPFLPPRGPEPAAPL
APSRPPPALGRQKRSDSVSTSDEDSQSEDRNDLKASPTLGKRKKRRHRTVFTAHQLEELE
KAFSEAHYPDVYAREMLAVKTELPEDRIQVWFQNRRAKWRKREKRWGGSSVMAEYGLYGA
MVRHCIPLPDSVLNSAEGGLLGSCAPWLLGMHKKSMGMIRKPGSEDKLAGLWGSDHFKEG
SSQSESGSQRGSDKVSPENGLEDVAIDLSSSARQETKKVHPGAGAQGGSNSTALEGPQPG
KVGAT
Sequence length 365
Interactions View interactions
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide Unknown Diseases (4)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome craniofacial anomalies and anterior segment dysgenesis syndrome N/A N/A GenCC, ClinVar
Keratoconus keratoconus 1, keratoconus N/A N/A ClinVar
Long QT Syndrome long qt syndrome N/A N/A ClinVar
Polymorphous corneal dystrophy posterior polymorphous corneal dystrophy 1, Posterior polymorphous corneal dystrophy 1 N/A N/A GenCC, ClinVar
Show/Hide Text Mining Associations (11)
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Carcinoma Renal Cell Associate 36463181
Conjunctivitis Allergic Associate 21365019
Corneal Dystrophy Posterior Polymorphous 1 Associate 16252232, 18253095, 19997581, 20567203, 23049806, 23592923, 25564336
Diabetes Gestational Associate 36585686
Diabetes Mellitus Associate 25898945
Fetal Diseases Associate 36585686
Keratoconus Associate 17960127, 18253095, 19011015, 19956409, 20664914, 21139977, 21365019, 21403853, 21976959, 22171159, 23592923, 27819732, 28950846, 37322657
Leukocyte adhesion deficiency type 1 Associate 26339660
Neoplasms Associate 26929985
Non Muscle Invasive Bladder Neoplasms Associate 26929985