VAX2

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

Basic information

Region (hg38): 2:70900575-70965373

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 provided (30 variants)
• Inborn genetic diseases (23 variants)
• Renal tubular acidosis with progressive nerve deafness (13 variants)
• not specified (4 variants)
• Distal renal tubular acidosis (1 variants)
• Usher syndrome (1 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17	4	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1				1
non coding	1	4	12	13	2	32
Total	1	4	29	17	3

Highest pathogenic variant AF is 0.0000263

Variants in VAX2

This is a list of pathogenic ClinVar variants found in the VAX2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-70900676-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-70900691-C-G			Benign (Dec 31, 2019)
2-70900694-T-G		not specified	Likely benign (Jan 18, 2022)
2-70900736-G-A		not specified	Uncertain significance (Aug 10, 2023)
2-70900767-C-G		not specified	Uncertain significance (Oct 26, 2022)
2-70921139-C-A		not specified	Uncertain significance (Jun 06, 2023)
2-70921151-C-T		not specified	Uncertain significance (Apr 08, 2022)
2-70921161-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-70921196-C-T		not specified	Uncertain significance (Jun 12, 2023)
2-70921221-G-C		not specified	Uncertain significance (Oct 23, 2023)
2-70921241-G-A		not specified	Uncertain significance (Dec 15, 2023)
2-70921248-C-T		Anophthalmia-microphthalmia syndrome	Likely benign (Jan 01, 2013)
2-70921277-G-A		not specified	Uncertain significance (Apr 12, 2022)
2-70932788-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-70932789-G-A		not specified	Uncertain significance (Aug 17, 2022)
2-70932814-G-C		not specified	Uncertain significance (Oct 28, 2023)
2-70932833-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-70932856-G-T		not specified	Uncertain significance (Dec 06, 2023)
2-70932881-C-T		not specified	Uncertain significance (Aug 15, 2023)
2-70932890-G-A		not specified	Uncertain significance (Oct 30, 2023)
2-70932933-T-A		not specified	Uncertain significance (Nov 08, 2022)
2-70932960-T-C			Likely benign (Jun 26, 2018)
2-70932981-C-T		not specified	Uncertain significance (Nov 13, 2023)
2-70933022-C-G		not specified	Uncertain significance (Jun 07, 2023)
2-70933023-C-A		not specified	Uncertain significance (Nov 27, 2023)

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