VSX1 (visual system homeobox 1)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID 30813
Gene name Visual system homeobox 1
Gene symbol VSX1
Synonyms (NCBI Gene)
CAASDSKTCNKTCN1PPCDPPCD1PPDRINX
Chromosome 20
Chromosome location 20p11.21
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. M
SNPs SNP information provided by dbSNP.
3
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.
7
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
20
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 identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
MIM HGNC e!Ensembl
605020 12723 ENSG00000100987
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
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Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide Unknown Diseases (9)
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Craniofacial anomalies and anterior segment dysgenesis syndrome Uncertain significance; Conflicting classifications of pathogenicity; Likely benign; Benign rs74315435, rs576300014, rs192303122, rs111722263 RCV000005562
RCV002504139
RCV002479019
RCV001200052
Keratoconus Conflicting classifications of pathogenicity rs369865672 RCV000385284
Keratoconus 1 Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity rs6138482, rs74315432, rs74315434, rs74315436, rs576300014, rs148957473, rs192303122 RCV002245216
RCV000005559
RCV000005561
RCV000005563
RCV002504139
RCV000990295
RCV002479019
Long QT syndrome Likely benign rs796052181 RCV000190188
Show/Hide Text Mining Associations (11)
Associations from Text MiningDisease 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