VSX1 (visual system homeobox 1)

Gene

• Entrez ID: 30813
• Gene name: Visual system homeobox 1
• Gene symbol: VSX1
• Synonyms (NCBI Gene): CAASDS, KTCN, KTCN1, PPCD, PPCD1, PPD, RINX
• 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 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

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
MIRT2146853	hsa-miR-4719	CLIP-seq
MIRT2146854	hsa-miR-488	CLIP-seq

Gene ontology (GO)

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
GO:0003700	Function	DNA-binding transcription factor activity	NAS	10673340
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IBA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	10673340
GO:0042551	Process	Neuron maturation	IEA
GO:0048666	Process	Neuron development	IBA
GO:0048666	Process	Neuron development	IEA
GO:0060040	Process	Retinal bipolar neuron differentiation	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 605020
• HGNC: 12723
• e!Ensembl: ENSG00000100987

Protein

• 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

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUDITORY PERCEPTUAL DISORDERS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEAL DYSTROPHIES, HEREDITARY	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEAL DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEAL DYSTROPHY, POSTERIOR POLYMORPHOUS, 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Craniofacial anomalies and anterior segment dysgenesis syndrome	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign; Benign	ClinVar CTD, ClinVar, Disgenet, HPO, Orphanet CTD, ClinVar, Disgenet, HPO, Orphanet CTD, ClinVar, Disgenet, HPO, Orphanet CTD, ClinVar, Disgenet, HPO, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
EYE ABNORMALITIES	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL LONG QT SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY CORNEAL DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Keratoconus	Conflicting classifications of pathogenicity	ClinVar CTD, Disgenet CTD, Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus 1	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long QT syndrome	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYMORPHOUS CORNEAL DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Posterior polymorphous corneal dystrophy	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar HPO, Orphanet HPO, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Posterior polymorphous corneal dystrophy 1	Conflicting classifications of pathogenicity	ClinVar GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VSX1-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	BEFREE	16384943		★☆☆☆☆ Found in Text Mining only
Amyloidosis cutis dyschromia	Amyloidosis Cutis Dyschromia	BEFREE	28889150		★☆☆☆☆ Found in Text Mining only
Anterior encephalocele	Encephalocele	HPO_DG			★☆☆☆☆ Found in Text Mining only
Astigmatism	Astigmatism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Auditory Perceptual Disorders	Auditory processing disorder	CTD_human_DG	15051220		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	BEFREE	11916331		★☆☆☆☆ Found in Text Mining only
Avellino corneal dystrophy	Avellino Corneal Dystrophy	BEFREE	28889150		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	22911819		★☆☆☆☆ Found in Text Mining only
Buruli Ulcer	Buruli Ulcer	BEFREE	10756149		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	36463181	Associate	★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	BEFREE	15899484		★☆☆☆☆ Found in Text Mining only
Congenital hereditary endothelial dystrophy	Congenital Hereditary Endothelial Dystrophy	BEFREE	19574904, 26749309		★☆☆☆☆ Found in Text Mining only
Contact Dermatitis	Dermatitis	BEFREE	7233093		★☆☆☆☆ Found in Text Mining only
Corneal Diseases	Corneal Diseases	BEFREE	30535423		★☆☆☆☆ Found in Text Mining only
Corneal dystrophy	Corneal Dystrophy	BEFREE	11978762, 15623752, 20848555		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corneal Dystrophy Posterior Polymorphous 1	Posterior polymorphous corneal dystrophy	Pubtator	16252232, 18253095, 19997581, 20567203, 23049806, 23592923, 25564336	Associate	★☆☆☆☆ Found in Text Mining only
CORNEAL ENDOTHELIAL DYSTROPHY 1, AUTOSOMAL DOMINANT	CORNEAL ENDOTHELIAL DYSTROPHY	GENOMICS_ENGLAND_DG	15051220		★☆☆☆☆ Found in Text Mining only
CORNEAL ENDOTHELIAL DYSTROPHY 1, AUTOSOMAL DOMINANT	CORNEAL ENDOTHELIAL DYSTROPHY	BEFREE	15623752, 16303937, 20808945, 25564336, 27310661, 30535423		★☆☆☆☆ Found in Text Mining only
CRANIOFACIAL ANOMALIES AND ANTERIOR SEGMENT DYSGENESIS SYNDROME	Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome	UNIPROT_DG	15051220		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CRANIOFACIAL ANOMALIES AND ANTERIOR SEGMENT DYSGENESIS SYNDROME	Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome	GENOMICS_ENGLAND_DG	15051220		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CRANIOFACIAL ANOMALIES AND ANTERIOR SEGMENT DYSGENESIS SYNDROME	Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome	CTD_human_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CRANIOFACIAL ANOMALIES AND ANTERIOR SEGMENT DYSGENESIS SYNDROME	Craniofacial Anomalies And Anterior Segment Dysgenesis Syndrome	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Depression, Postpartum	Mental Depression	BEFREE	31533685		★☆☆☆☆ Found in Text Mining only
Diabetes Gestational	Gestational diabetes	Pubtator	36585686	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	25898945	Associate	★☆☆☆☆ Found in Text Mining only
Empty Sella Syndrome	Empty Sella Syndrome	CTD_human_DG	15051220		★☆☆☆☆ Found in Text Mining only
Empty Sella Syndrome, Primary	Empty Sella Syndrome	CTD_human_DG	15051220		★☆☆☆☆ Found in Text Mining only
Empty Sella Syndrome, Secondary	Empty Sella Syndrome	CTD_human_DG	15051220		★☆☆☆☆ Found in Text Mining only
FG syndrome	FG Syndrome	BEFREE	9475086		★☆☆☆☆ Found in Text Mining only
Fibrosis, Liver	Liver Fibrosis	BEFREE	29929367		★☆☆☆☆ Found in Text Mining only
Fuchs Endothelial Dystrophy	Fuchs Endothelial Dystrophy	BEFREE	23662738		★☆☆☆☆ Found in Text Mining only
Granular Dystrophy, Corneal	Corneal Granular Dystrophy	CTD_human_DG	11978762		★☆☆☆☆ Found in Text Mining only
Greig cephalopolysyndactyly syndrome	Greig Cephalopolysyndactyly Syndrome	BEFREE	22903559		★☆☆☆☆ Found in Text Mining only
Groenouw`s Dystrophies	Groenouw`s Dystrophies	CTD_human_DG	11978762		★☆☆☆☆ Found in Text Mining only
Hereditary corneal dystrophy	Hereditary Corneal Dystrophy	CTD_human_DG	11978762		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypercholesterolemia, Familial	Hypercholesterolemia	BEFREE	15026427, 15899484		★☆☆☆☆ Found in Text Mining only
Hyperlipoproteinemia Type IIa	Hyperlipoproteinemia	BEFREE	15026427, 15899484		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	BEFREE	11978762, 15623752, 16799019, 17960127, 18216574, 18484309, 18626569, 19011015, 19763142, 19956409, 20023586, 21139977, 21365019, 21403853, 21528002, 21976959, 22171159, 22531431, 23289806, 23592923, 23599324, 24099280, 24644548, 24940934, 25675348, 25963163, 27819732, 28950846, 30535423, 30574758, 30809473		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus	Keratoconus	LHGDN	11978762, 18216574		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus	Keratoconus	CTD_human_DG	11978762, 15623752		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus	Keratoconus	Pubtator	17960127, 18253095, 19011015, 19956409, 20664914, 21139977, 21365019, 21403853, 21976959, 22171159, 23592923, 27819732, 28950846, 37322657	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus	Keratoconus	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus 1	Keratoconus	UNIPROT_DG	11978762, 15623752, 18216574, 19763142, 19956409, 21976959		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus 1	Keratoconus	GENOMICS_ENGLAND_DG	15051220		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus 1	Keratoconus	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Keratoconus 1	Keratoconus	CTD_human_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Leukocyte adhesion deficiency type 1	Leukocyte adhesion deficiency	Pubtator	26339660	Associate	★☆☆☆☆ Found in Text Mining only
Lymphadenitis	Lymphadenitis	BEFREE	30055739		★☆☆☆☆ Found in Text Mining only
Macular corneal dystrophy	Macular Corneal Dystrophy	CTD_human_DG	11978762		★☆☆☆☆ Found in Text Mining only
Macular degeneration	Macular Degeneration	BEFREE	16384943		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	22911819		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	19203832		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	18253123		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	26428367		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	31382131		★☆☆☆☆ Found in Text Mining only
Mood Disorders	Mood Disorder	BEFREE	8297808		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	18253123, 29473838, 31571900		★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Isolated keratoconus	Isolated Keratoconus	Orphanet			★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	31571900		★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	BEFREE	29843053, 30389428		★☆☆☆☆ Found in Text Mining only
Pallister-Hall syndrome	Pallister-Hall Syndrome	BEFREE	10441570, 22903559		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	19203832		★☆☆☆☆ Found in Text Mining only
Paratuberculosis	Paratuberculosis	BEFREE	29483289		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	23485738		★☆☆☆☆ Found in Text Mining only
Periodontal Diseases	Periodontal Diseases	BEFREE	25280920, 27727278		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	BEFREE	12837695		★☆☆☆☆ Found in Text Mining only
POLYDACTYLY, POSTAXIAL	Polydactyly	BEFREE	15811011		★☆☆☆☆ Found in Text Mining only
Polymorphous corneal dystrophy	Polymorphous corneal dystrophy	ORPHANET_DG	11978762		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Polymorphous corneal dystrophy	Polymorphous corneal dystrophy	BEFREE	15623752, 15725882, 16303937, 16384943, 18253095, 19574904, 20567203, 20808945, 23559851, 23592923, 25564336, 27310661, 28046031, 28414732, 30535423, 31194824, 31233731		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Posterior polymorphous corneal dystrophy	Polymorphous corneal dystrophy	Orphanet			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Progressive pseudorheumatoid dysplasia	Progressive Pseudorheumatoid Dysplasia	BEFREE	28802407, 29312328, 30096296		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	18253123		★☆☆☆☆ Found in Text Mining only
Radial polydactyly	Radial Polydactyly	BEFREE	15811011		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	CTD_human_DG	15051220		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	8297808		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	26428367		★☆☆☆☆ Found in Text Mining only
Stromal Dystrophies, Corneal	Stromal corneal dystrophy	CTD_human_DG	11978762		★☆☆☆☆ Found in Text Mining only
Syndactyly	Syndactyly	BEFREE	15811011		★☆☆☆☆ Found in Text Mining only