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VAX1 ventral anterior homeobox 1 [ Homo sapiens (human) ]

Gene ID: 11023, updated on 8-Mar-2025

Summary

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Official Symbol
VAX1provided by HGNC
Official Full Name
ventral anterior homeobox 1provided by HGNC
Primary source
HGNC:HGNC:12660
See related
Ensembl:ENSG00000148704 MIM:604294; AllianceGenome:HGNC:12660
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MCOPS11
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See VAX1 in Genome Data Viewer
Location:
10q25.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (117128520..117138270, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (118023007..118032756, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (118888031..118897781, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene heat shock protein family A (Hsp70) member 12A Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:118595447-118596082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4095 Neighboring gene microRNA 9851 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:118665638-118666837 Neighboring gene enolase 4 Neighboring gene shootin 1 Neighboring gene Sharpr-MPRA regulatory region 1976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2857 Neighboring gene VISTA enhancer hs841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118885664-118886164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118890627-118891154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118891155-118891681 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118899364-118899950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118899951-118900536 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:118918871-118919627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118925104-118925658 Neighboring gene MIR3663 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4096 Neighboring gene microRNA 3663 Neighboring gene ribosomal protein L12 pseudogene 26

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. The potential up-regulation risk of 3' UTR SNP (rs10787760 G > A) for the VAX1 gene is associated with NSCLP in the northwest Chinese population. Feng H, et al. Gene, 2024 Sep 5. PMID 38608796
  2. Target sequencing reveals the association between variants in VAX1 and NSCL/P in Chinese population. You Y, et al. Oral Dis, 2023 Jul. PMID 35419918
  3. The risk of nonsyndromic cleft lip with or without cleft palate and Vax1 rs7078160 polymorphisms in southern Han Chinese. Wang Q, et al. Braz J Otorhinolaryngol, 2021 Nov-Dec. PMID 33132092, Free PMC Article
  4. Molecular Screening of VAX1 Gene Polymorphisms Uncovered the Genetic Heterogeneity of Nonsyndromic Orofacial Cleft Among Saudi Arabian Patients. Sabbagh HJ, et al. Genet Test Mol Biomarkers, 2019 Jan. PMID 30633559
  5. VAX1 gene associated non-syndromic cleft lip with or without palate in Western Han Chinese. Zhang BH, et al. Arch Oral Biol, 2018 Nov. PMID 30048854

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The potential up-regulation risk of 3' UTR SNP (rs10787760 G > A) for the VAX1 gene is associated with NSCLP in the northwest Chinese population.
    Title: The potential up-regulation risk of 3' UTR SNP (rs10787760 G > A) for the VAX1 gene is associated with NSCLP in the northwest Chinese population.
  2. Target sequencing reveals the association between variants in VAX1 and NSCL/P in Chinese population.
    Title: Target sequencing reveals the association between variants in VAX1 and NSCL/P in Chinese population.
  3. Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis.
    Title: Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis.
  4. The risk of nonsyndromic cleft lip with or without cleft palate and Vax1 rs7078160 polymorphisms in southern Han Chinese.
    Title: The risk of nonsyndromic cleft lip with or without cleft palate and Vax1 rs7078160 polymorphisms in southern Han Chinese.
  5. This is the first study to find a relationship between these two loci on 10q25 (rs4752028 and rs7078160) and Nonsyndromic Orofacial Cleft in a population with high levels of consanguinity.
    Title: Molecular Screening of VAX1 Gene Polymorphisms Uncovered the Genetic Heterogeneity of Nonsyndromic Orofacial Cleft Among Saudi Arabian Patients.
  6. Our study first revealed VAX1 gene could contribute to the etiology of NSCL/P and have a paternal-special transmission in Western Han Chinese. Additionally, the study also implied that rs7078160 might be associated with NSCLP.
    Title: VAX1 gene associated non-syndromic cleft lip with or without palate in Western Han Chinese.
  7. rs4752028 weakly associated with nonsyndromic cleft lip with or without cleft palate in northern Chinese Han population
    Title: Polymorphic variants in VAX1 and the risk of nonsyndromic cleft lip with or without cleft palate in a population from northern China.
  8. Our study replicated previous GWAS findings for markers in VAX1 in the Asian population, and identified rare variants in PAX7 and VAX1 that may contribute to the etiology of CL(P).
    Title: 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).
  9. VAX1 rs10787760, rs6585429 and rs1871345 polymorphisms may be involved in nonsyndromic cleft lip with or without cleft palate in Brazilian patients, but there is no association with polymorphisms in FGF12, VCL, or CX43
    Title: Polymorphisms in FGF12, VCL, CX43 and VAX1 in Brazilian patients with nonsyndromic cleft lip with or without cleft palate.
  10. The data do not support the hypothesis that highly penetrant rare variants in VAX1 are a cause of nonsyndromic cleft lip with or without cleft palate.
    Title: Resequencing of VAX1 in patients with nonsyndromic cleft lip with or without cleft palate.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Anophthalmia-microphthalmia syndrome
MedGen: C5680330 GeneReviews: Not available
Compare labs
Microphthalmia, syndromic 11
MedGen: C3553077 OMIM: 614402 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC126743, MGC126745

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in astrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in axon guidance IEA
Inferred from Electronic Annotation
more info
  
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in camera-type eye development IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuroepithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
  
involved_in skeletal muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ventral anterior homeobox 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012317.1 RefSeqGene

    Range
    5032..10012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001112704.2 → NP_001106175.1  ventral anterior homeobox 1 isoform a

    See identical proteins and their annotated locations for NP_001106175.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AK127095, AL731557
    Consensus CDS
    CCDS44483.1
    UniProtKB/Swiss-Prot
    B1AVW5, Q5SQQ9, Q6ZSX0
    Related
    ENSP00000358207.4, ENST00000369206.6
    Conserved Domains (2) summary
    COG5576
    Location:66 → 184
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:103 → 157
    Homeobox; Homeobox domain

  2. NM_199131.3 → NP_954582.1  ventral anterior homeobox 1 isoform b

    See identical proteins and their annotated locations for NP_954582.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and UTR compared to variant 1. The resulting isoform (b) has a shorter C-terminus compared to isoform a.
    Source sequence(s)
    AK127095, AL731557
    Consensus CDS
    CCDS7597.1
    UniProtKB/Swiss-Prot
    Q5SQQ9
    Related
    ENSP00000277905.2, ENST00000277905.6
    Conserved Domains (1) summary
    pfam00046
    Location:103 → 143
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    117128520..117138270 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    118023007..118032756 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SQQ9.1 GenPept UniProtKB/Swiss-Prot:Q5SQQ9

Gene LinkOut

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