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

Summary

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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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).
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.
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

Go to the top of the page Help

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	not available
Microphthalmia, syndromic 11 MedGen: C3553077 OMIM: 614402 GeneReviews: Not available	not available

EBI GWAS Catalog

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

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

NoName (e-PCR)
- UniSTS:485016

SHGC-13026 (e-PCR)
- UniSTS:41385

VAX1__5061 (e-PCR)
- UniSTS:463347

NoName (e-PCR)
- UniSTS:485875

Vax1 (e-PCR), detects polymorphism
- UniSTS:527604

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

Go to the top of the page Help

Preferred Names: ventral anterior homeobox 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

NG_012317.1 RefSeqGene

Range

5032..10012

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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