VAX1

ventral anterior homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:117128521-117138301

Links

ENSG00000148704NCBI:11023OMIM:604294HGNC:12660Uniprot:Q5SQQ9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • microphthalmia, syndromic 11 (Limited), mode of inheritance: AR
  • microphthalmia, syndromic 11 (Limited), mode of inheritance: AR
  • microphthalmia, syndromic 11 (Limited), mode of inheritance: AR
  • microphthalmia, syndromic 11 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Microphthalmia, syndromic 11ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Neurologic; Ophthalmologic22095910

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VAX1 gene.

  • Microphthalmia,_syndromic_11 (37 variants)
  • not_specified (36 variants)
  • not_provided (12 variants)
  • VAX1-related_disorder (7 variants)
  • Microphthalmia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001112704.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
15
clinvar
3
clinvar
20
missense
1
clinvar
44
clinvar
1
clinvar
46
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
0
Total 1 1 50 16 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VAX1protein_codingprotein_codingENST00000369206 39781
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7700.228124206011242070.00000403
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8691151440.7960.000007712069
Missense in Polyphen25.71680.34984111
Synonymous0.1047071.10.9840.00000392772
Loss of Function2.5119.220.1084.56e-7111

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008940.00000894
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
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). {ECO:0000250}.;
Disease
DISEASE: 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.;

Recessive Scores

pRec
0.111

Intolerance Scores

loftool
0.151
rvis_EVS
-0.27
rvis_percentile_EVS
33.97

Haploinsufficiency Scores

pHI
0.155
hipred
Y
hipred_score
0.684
ghis
0.481

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.424

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Vax1
Phenotype
skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype; craniofacial phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;neuron migration;negative regulation of neuroblast proliferation;axon guidance;brain development;skeletal muscle cell differentiation;camera-type eye development;roof of mouth development
Cellular component
nucleus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin DNA binding