VAX2

ventral anterior homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 2:70900576-70965373

Links

ENSG00000116035

∙ NCBI:25806 ∙ OMIM:604295 ∙ HGNC:12661 ∙ Uniprot:Q9UIW0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VAX2 gene.

not_specified (71 variants)
not_provided (4 variants)
Anophthalmia-microphthalmia_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012476.3. 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				1 clinvar		1
missense			69 clinvar	4 clinvar	1 clinvar	74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	69	5	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAX2	protein_coding	protein_coding	ENST00000234392	3	32857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.160	0.781	125596	0	43	125639	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.650	176	153	1.15	0.0000104	1785
Missense in Polyphen		48	51.006	0.94107		500
Synonymous	0.158	68	69.7	0.976	0.00000445	676
Loss of Function	1.55	2	6.13	0.326	2.60e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000968	0.0000949
Ashkenazi Jewish	0.000237	0.000199
East Asian	0.000449	0.000435
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000112	0.000106
Middle Eastern	0.000449	0.000435
South Asian	0.000475	0.000457
Other	0.000352	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcription factor that may function in dorsoventral specification of the forebrain. Regulates the expression of Wnt signaling antagonists including the expression of a truncated TCF7L2 isoform that cannot bind CTNNB1 and acts therefore as a potent dominant-negative Wnt antagonist. Plays a crucial role in eye development and, in particular, in the specification of the ventral optic vesicle (By similarity). May be a regulator of axial polarization in the retina. {ECO:0000250}.;
Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

pRec: 0.119

Intolerance Scores

loftool: 0.143
rvis_EVS: 0.33
rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

pHI: 0.185
hipred: N
hipred_score: 0.318
ghis: 0.540

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.626

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Vax2
Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye 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); 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);

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;ectoderm development;axonogenesis;visual perception;dorsal/ventral axis specification;Wnt signaling pathway;forebrain development;embryonic eye morphogenesis;retina development in camera-type eye
Cellular component: nucleus;cytoplasm
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;DNA-binding transcription factor activity;chromatin DNA binding