GeneBe

VSX1

visual system homeobox 1, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 20:25070885-25082141

Previous symbols: [ "PPCD" ]

Links

ENSG00000100987 ∙ NCBI:30813 ∙ OMIM:605020 ∙ HGNC:12723 ∙ Uniprot:Q9NZR4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • keratoconus 1 (Limited), mode of inheritance: AD
  • posterior polymorphous corneal dystrophy (Supportive), mode of inheritance: AD
  • craniofacial anomalies and anterior segment dysgenesis syndrome (Limited), mode of inheritance: AD
  • keratoconus 1 (Limited), mode of inheritance: AD
  • posterior polymorphous corneal dystrophy 1 (Limited), mode of inheritance: Unknown
  • keratoconus 1 (Limited), mode of inheritance: Unknown
  • craniofacial anomalies and anterior segment dysgenesis syndrome (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Craniofacial anomalies and anterior segment dysgenesis syndrome; Keratoconus 1; Corneal dystrophy, posterior polymorphousADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Ophthalmologic11978762; 15051220; 15623752; 16735990; 18216574; 18626569; 19763142; 19956409; 20664914; 21365019; 21976959; 26045363

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VSX1 gene.

  • not_provided (57 variants)
  • Inborn_genetic_diseases (51 variants)
  • Posterior_polymorphous_corneal_dystrophy (35 variants)
  • VSX1-related_disorder (10 variants)
  • Keratoconus_1 (9 variants)
  • Craniofacial_anomalies_and_anterior_segment_dysgenesis_syndrome (7 variants)
  • not_specified (4 variants)
  • Keratoconus (1 variants)
  • Long_QT_syndrome (1 variants)
  • Congenital_long_QT_syndrome (1 variants)
  • Posterior_polymorphous_corneal_dystrophy_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014588.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
17
clinvar
4
clinvar
 24
missense
69
clinvar
13
clinvar
5
clinvar
 87
nonsense
3
clinvar
 3
start loss
1
 1
frameshift
1
clinvar
1
clinvar
 2
splice donor/acceptor (+/-2bp)
0
Total 0 0 76 32 9
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VSX1protein_codingprotein_codingENST00000376709 511476
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.03590.932125739071257460.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4821812000.9040.000009882281
Missense in Polyphen4963.6660.76964723
Synonymous-0.9179786.21.130.00000426788
Loss of Function1.85410.50.3825.35e-7108

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.000.00
South Asian0.00009800.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster. May regulate the activity of the LCR and the cone opsin genes at earlier stages of development.;
Disease
DISEASE: Craniofacial anomalies and anterior segment dysgenesis syndrome (CAASDS) [MIM:614195]: A disorder with extremely variable expressivity. Clinical features include wide interpupillary distance, abnormal corneal endothelium, unusual pinnae, partially to completely empty sella turcica, posterior fossa cyst, anterior encephalocele, and/or hydrocephalus. {ECO:0000269|PubMed:15051220}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.137

Haploinsufficiency Scores

pHI
0.115
hipred
N
hipred_score
0.209
ghis
0.428

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.349

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Vsx1
Phenotype
vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
vsx1
Affected structure
ventricular system
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

Biological process
regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;visual perception;neuron maturation;neuron development;response to stimulus;retinal bipolar neuron differentiation
Cellular component
cellular_component;nucleus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;sequence-specific DNA binding;transcription regulatory region DNA binding