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Aliases for VAX1 Gene

Aliases for VAX1 Gene

  • Ventral Anterior Homeobox 1 2 3 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 Cleft Lip. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin DNA binding. An important paralog of this gene is VAX2.

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

Additional gene information for VAX1 Gene

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

Genomics for VAX1 Gene

GeneHancer (GH) Regulatory Elements for VAX1 Gene

Promoters and enhancers for VAX1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J117138 Promoter/Enhancer 1 EPDnew ENCODE 650.7 -0.5 -514 1.4 ZNF335 SUZ12 ZBTB26 EZH2 VAX1 MIR3663
GH10J117137 Enhancer 0.8 ENCODE 650.7 +0.8 836 0.2 ZSCAN5A ZNF146 ZNF777 SUZ12 SIN3A KLF14 ZIC2 ZNF335 GLIS2 POLR2A VAX1 SHTN1
GH10J117139 Enhancer 0.7 ENCODE 650.7 +1.1 1076 0.2 ZSCAN5A ZNF146 SUZ12 SIN3A KLF14 ZNF335 POLR2A ZBTB48 PRDM10 KLF8 VAX1 SHTN1
GH10J117141 Enhancer 0.7 ENCODE 650.7 +0.5 536 0.2 ZNF777 SUZ12 ZFP37 ZBTB8A ZNF501 ZIC2 PRDM2 ZNF335 ZNF341 CTBP2 VAX1 SHTN1
GH10J117136 Enhancer 0.5 ENCODE 650.7 +1.5 1456 0.2 ZNF202 SUZ12 SP2 CTBP2 ZBTB26 ZFX EZH2 VAX1 ENSG00000231104 SHTN1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VAX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VAX1 gene promoter:
  • Nkx6-1
  • AREB6
  • Olf-1
  • IRF-2
  • Sox5
  • Cart-1
  • Ik-2
  • c-Myb
  • POU6F1 (c2)
  • Pax-5

Genomic Locations for VAX1 Gene

Genomic Locations for VAX1 Gene
9,781 bases
Minus strand
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

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

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for VAX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the EMX homeobox family.
  • 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

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).
GENATLAS Biochemistry:
ventral anterior homeobox 1,specifically expressed in the developing basal forebrain and optic nerve,tightly linked to EMX2 in mouse and human

Phenotypes From GWAS Catalog for VAX1 Gene

Gene Ontology (GO) - Molecular Function for VAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IEA --
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with VAX1: view
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VAX1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with VAX1: view

Pathways & Interactions for VAX1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001764 neuron migration IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development 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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for VAX1 Gene

Protein tissue co-expression partners for VAX1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VAX1 Gene:


SOURCE GeneReport for Unigene cluster for VAX1 Gene:


Evidence on tissue expression from TISSUES for VAX1 Gene

  • Nervous system(4.3)
  • Eye(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VAX1 Gene

Germ Layers:
  • ectoderm
  • digestive
  • integumentary
  • nervous
  • skeleton
Head and neck:
  • brain
  • eye
  • face
  • head
  • lip
  • mouth
  • skull
  • skin
genes like me logo Genes that share expression patterns with VAX1: view

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
(Pan troglodytes)
Mammalia VAX1 34 33
  • 99.3 (n)
(Canis familiaris)
Mammalia VAX1 34 33
  • 93.61 (n)
(Bos Taurus)
Mammalia VAX1 34 33
  • 91.72 (n)
(Mus musculus)
Mammalia Vax1 16 34 33
  • 88.52 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 88 (a)
(Rattus norvegicus)
Mammalia Vax1 33
  • 87.43 (n)
(Gallus gallus)
Aves VAX1 33
  • 82.16 (n)
-- 34
  • 33 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486982 33
  • 81.13 (n)
(Danio rerio)
Actinopterygii vax1 34 33
  • 66.88 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG18599 34
  • 13 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
Species where no ortholog for VAX1 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for VAX1: view image

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 Variation AA Info Type
rs387907252 pathogenic, Microphthalmia, syndromic 11, Microphthalmia, syndromic, 11 (MCOPS11) [MIM:614402] 117,134,559(-) G/T coding_sequence_variant, intron_variant, missense_variant
rs554140675 uncertain-significance, likely-benign, not specified, Microphthalmia, syndromic 11 117,134,371(-) C/T coding_sequence_variant, intron_variant, synonymous_variant
rs794727489 uncertain-significance, not specified 117,134,130(-) T/C coding_sequence_variant, intron_variant, missense_variant
rs794727490 uncertain-significance, not specified 117,134,298(-) C/A/T coding_sequence_variant, intron_variant, missense_variant
rs886042715 uncertain-significance, not specified 117,134,209(-) C/G/T coding_sequence_variant, intron_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
esv3624671 CNV gain 21293372
nsv825577 CNV gain 20364138
nsv832002 CNV gain+loss 17160897

Variation tolerance for VAX1 Gene

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

Additional Variant Information for VAX1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for VAX1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
microphthalmia, syndromic 11
  • mcops11
cleft lip
  • cheiloschisis
  • microphthalmos
coloboma of macula
  • agenesis of macula
cleft palate, isolated
  • cpi
- 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.

Additional Disease Information for VAX1

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 AM … Schorderet DF (Human mutation 2012) 3 4 58
  2. Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. (PMID: 20023658) Mangold E … Nöthen MM (Nature genetics 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for VAX1 Gene

Sources for VAX1 Gene

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