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

    Gene ID: 11023, updated on 2-Nov-2024

    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
    mouse all
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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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    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. Resequencing of VAX1 in patients with nonsyndromic cleft lip with or without cleft palate. Nasser E, et al. Birth Defects Res A Clin Mol Teratol, 2012 Nov. PMID 23081944
    5. 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

    See all (26) 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)

    Genotypes

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools