VAX1
Basic information
Region (hg38): 10:117128521-117138301
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Microphthalmia, syndromic 11 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Neurologic; Ophthalmologic | 22095910 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 15 | 20 | ||||
missense | 44 | 46 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 1 | 1 | 50 | 16 | 3 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
VAX1 | protein_coding | protein_coding | ENST00000369206 | 3 | 9781 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.770 | 0.228 | 124206 | 0 | 1 | 124207 | 0.00000403 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.869 | 115 | 144 | 0.796 | 0.00000771 | 2069 |
Missense in Polyphen | 2 | 5.7168 | 0.34984 | 111 | ||
Synonymous | 0.104 | 70 | 71.1 | 0.984 | 0.00000392 | 772 |
Loss of Function | 2.51 | 1 | 9.22 | 0.108 | 4.56e-7 | 111 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000894 | 0.00000894 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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