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Aliases for VAX1 Gene

Aliases for VAX1 Gene

  • Ventral Anterior Homeobox 1 2 3 5
  • MCOPS11 3

External Ids for VAX1 Gene

Previous GeneCards Identifiers for VAX1 Gene

  • GC10M117812
  • GC10U900019
  • GC10M118552
  • GC10M118878
  • GC10M112516

Summaries for VAX1 Gene

Entrez Gene Summary for VAX1 Gene

  • This gene encodes a homeo-domain containing protein from a class of homeobox transcription factors which are conserved in vertebrates. Genes of this family are involved in the regulation of body development and morphogenesis. The most conserved genes, called HOX genes are found in special gene clusters. This gene belongs to the VAX subfamily and lies in the vicinity of the EMX homeobox gene family. Another member of VAX family is located on chromosome 2. The encoded protein may play an important role in the development of anterior ventral forebrain and visual system. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for VAX1 Gene

VAX1 (Ventral Anterior Homeobox 1) is a Protein Coding gene. Diseases associated with VAX1 include Microphthalmia, Syndromic 11 and Microphthalmia. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and chromatin DNA binding. An important paralog of this gene is EN2.

UniProtKB/Swiss-Prot for VAX1 Gene

  • Transcription factor that may function in dorsoventral specification of the forebrain. Required for axon guidance and major tract formation in the developing forebrain. May contribute to the differentiation of the neuroretina, pigmented epithelium and optic stalk (By similarity).

Gene Wiki entry for VAX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VAX1 Gene

Genomics for VAX1 Gene

Regulatory Elements for VAX1 Gene

Enhancers for VAX1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around VAX1 on UCSC Golden Path with GeneCards custom track

Promoters for VAX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VAX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for VAX1 Gene

117,128,521 bp from pter
117,138,301 bp from pter
9,781 bases
Minus strand

Genomic View for VAX1 Gene

Genes around VAX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VAX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VAX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VAX1 Gene

Proteins for VAX1 Gene

  • Protein details for VAX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ventral anterior homeobox 1
    Protein Accession:
    Secondary Accessions:
    • B1AVW5
    • Q6ZSX0

    Protein attributes for VAX1 Gene

    334 amino acids
    Molecular mass:
    34713 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for VAX1 Gene


neXtProt entry for VAX1 Gene

Proteomics data for VAX1 Gene at MOPED

Post-translational modifications for VAX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VAX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VAX1 Gene

Domains & Families for VAX1 Gene

Gene Families for VAX1 Gene

Suggested Antigen Peptide Sequences for VAX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the EMX homeobox family.
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the EMX homeobox family.
genes like me logo Genes that share domains with VAX1: view

Function for VAX1 Gene

Molecular function for VAX1 Gene

GENATLAS Biochemistry:
ventral anterior homeobox 1,specifically expressed in the developing basal forebrain and optic nerve,tightly linked to EMX2 in mouse and human
UniProtKB/Swiss-Prot Function:
Transcription factor that may function in dorsoventral specification of the forebrain. Required for axon guidance and major tract formation in the developing forebrain. May contribute to the differentiation of the neuroretina, pigmented epithelium and optic stalk (By similarity).
genes like me logo Genes that share phenotypes with VAX1: view

Human Phenotype Ontology for VAX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VAX1 Gene

MGI Knock Outs for VAX1:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targets and HOMER Transcription for VAX1 Gene

Localization for VAX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAX1 Gene

Subcellular locations from

Jensen Localization Image for VAX1 Gene COMPARTMENTS Subcellular localization image for VAX1 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for VAX1 Gene

Pathways & Interactions for VAX1 Gene

SuperPathways for VAX1 Gene

No Data Available

Interacting Proteins for VAX1 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
Selected Interacting proteins: ENSP00000358207 for VAX1 Gene via STRING

Gene Ontology (GO) - Biological Process for VAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001764 neuron migration IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0007420 brain development IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with VAX1: view

No data available for Pathways by source and SIGNOR curated interactions for VAX1 Gene

Drugs & Compounds for VAX1 Gene

No Compound Related Data Available

Transcripts for VAX1 Gene

mRNA/cDNA for VAX1 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VAX1 Gene

Ventral anterior homeobox 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VAX1 Gene

No ASD Table

Relevant External Links for VAX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VAX1 Gene

mRNA expression in normal human tissues for VAX1 Gene

mRNA differential expression in normal tissues according to GTEx for VAX1 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x12.0), Brain - Caudate (basal ganglia) (x10.7), Brain - Putamen (basal ganglia) (x8.2), and Brain - Hypothalamus (x7.0).

Protein differential expression in normal tissues from HIPED for VAX1 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VAX1 Gene

SOURCE GeneReport for Unigene cluster for VAX1 Gene Hs.441536

genes like me logo Genes that share expression patterns with VAX1: view

Protein tissue co-expression partners for VAX1 Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for VAX1 Gene

Orthologs for VAX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for VAX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia VAX1 35
  • 91.72 (n)
  • 97.9 (a)
VAX1 36
  • 98 (a)
(Canis familiaris)
Mammalia VAX1 35
  • 93.61 (n)
  • 99.1 (a)
VAX1 36
  • 99 (a)
(Mus musculus)
Mammalia Vax1 35
  • 88.52 (n)
  • 94.01 (a)
Vax1 16
Vax1 36
  • 95 (a)
(Pan troglodytes)
Mammalia VAX1 35
  • 99.3 (n)
  • 99.4 (a)
VAX1 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Vax1 35
  • 87.43 (n)
  • 94.01 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 88 (a)
(Gallus gallus)
Aves VAX1 35
  • 82.16 (n)
  • 89.73 (a)
-- 36
  • 33 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486982 35
  • 81.13 (n)
  • 92.65 (a)
(Danio rerio)
Actinopterygii vax1 35
  • 66.88 (n)
  • 70.98 (a)
vax1 36
  • 73 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG18599 36
  • 13 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 35 (a)
Species with no ortholog for VAX1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VAX1 Gene

Gene Tree for VAX1 (if available)
Gene Tree for VAX1 (if available)

Paralogs for VAX1 Gene

Paralogs for VAX1 Gene

(2) SIMAP similar genes for VAX1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with VAX1: view

Variants for VAX1 Gene

Sequence variations from dbSNP and Humsavar for VAX1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
VAR_067307 Microphthalmia, syndromic, 11 (MCOPS11)
rs1871345 -- 117,135,857(-) GGCCA(A/G)TGATG intron-variant
rs751231 -- 117,137,153(-) AGATC(G/T)CCGGG intron-variant
rs751232 -- 117,137,100(-) GACTC(C/G)GGAGG intron-variant
rs751233 -- 117,137,256(-) TGGTG(C/T)TCTGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VAX1 Gene

Variant ID Type Subtype PubMed ID
nsv832002 CNV Gain+Loss 17160897
nsv825577 CNV Gain 20364138

Variation tolerance for VAX1 Gene

Gene Damage Index Score: 0.74; 15.76% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VAX1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VAX1 Gene

Disorders for VAX1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for VAX1 Gene - From: OMIM, ClinVar, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 11
  • microphthalmia, syndromic, 11
  • microphthalmos
cleft lip
  • cheiloschisis
- elite association - COSMIC cancer census association via MalaCards
Search VAX1 in MalaCards View complete list of genes associated with diseases


  • Microphthalmia, syndromic, 11 (MCOPS11) [MIM:614402]: A rare clinical entity including as main characteristics microphthalmia and small optic nerves, cleft lip and palate, absence of corpus callosum, hippocampal malformations, and absence of the pineal gland. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269 PubMed:22095910}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VAX1

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with VAX1: view

No data available for Genatlas for VAX1 Gene

Publications for VAX1 Gene

  1. VAX1 mutation associated with microphthalmia, corpus callosum agenesis, and orofacial clefting: The first description of a VAX1 phenotype in humans. (PMID: 22095910) Slavotinek A.M. … Schorderet D.F. (Hum. Mutat. 2012) 3 4 67
  2. A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. (PMID: 10485894) Barbieri A.M. … Banfi S. (Proc. Natl. Acad. Sci. U.S.A. 1999) 2 3
  3. Vax1 is a novel homeobox-containing gene expressed in the developing anterior ventral forebrain. (PMID: 9636075) Hallonet M. … Gruss P. (Development 1998) 2 3
  4. Replication of genome wide association identified candidate genes confirm the role of common and rare variants in PAX7 and VAX1 in the etiology of nonsyndromic CL(P). (PMID: 23463464) Butali A. … Murray J.C. (Am. J. Med. Genet. A 2013) 3
  5. Polymorphisms in FGF12, VCL, CX43 and VAX1 in Brazilian patients with nonsyndromic cleft lip with or without cleft palate. (PMID: 23679094) de Aquino S.N. … Coletta R.D. (BMC Med. Genet. 2013) 3

Products for VAX1 Gene

Sources for VAX1 Gene