VAX1

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

Basic information

Region (hg38): 10:117128520-117138301

Links

ENSG00000148704 ∙ NCBI:11023 ∙ OMIM:604294 ∙ HGNC:12660 ∙ Uniprot:Q5SQQ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the VAX1 gene.

• Microphthalmia, syndromic 11 (22 variants)
• not provided (13 variants)
• Inborn genetic diseases (8 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.

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			2	10	2	14
missense			15	1		16
nonsense						0
start loss						0
frameshift		1	2			3
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	2	3
Total	0	1	20	12	5

Variants in VAX1

This is a list of pathogenic ClinVar variants found in the VAX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-117133720-A-G			Benign (Jun 19, 2021)
10-117134019-C-CT		Microphthalmia, syndromic 11	Uncertain significance (Apr 30, 2017)
10-117134068-G-A		Microphthalmia, syndromic 11 • VAX1-related disorder	Benign (Dec 20, 2023)
10-117134074-G-A			Likely benign (Oct 23, 2017)
10-117134094-A-C		not specified	Uncertain significance (Jan 03, 2022)
10-117134130-T-C		Microphthalmia, syndromic 11 • not specified	Uncertain significance (Dec 21, 2023)
10-117134160-C-A		Microphthalmia, syndromic 11	Uncertain significance (Nov 10, 2023)
10-117134180-G-T		not specified	Uncertain significance (Nov 27, 2023)
10-117134192-C-A		Microphthalmia, syndromic 11	Uncertain significance (May 16, 2022)
10-117134209-C-G			Uncertain significance (Oct 20, 2015)
10-117134292-A-T		not specified	Uncertain significance (Feb 15, 2023)
10-117134298-C-A		not specified	Uncertain significance (Jul 05, 2023)
10-117134299-G-A		Microphthalmia, syndromic 11	Likely benign (Dec 06, 2022)
10-117134319-C-A		not specified	Uncertain significance (Jan 23, 2023)
10-117134320-G-GGCGGCGGCT		Microphthalmia, syndromic 11	Benign (Dec 18, 2023)
10-117134325-C-T		Microphthalmia, syndromic 11	Likely benign (Dec 07, 2023)
10-117134327-G-GCTGCGGCGGCCGAGC		Microphthalmia, syndromic 11	Uncertain significance (Oct 24, 2021)
10-117134333-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-117134335-G-A		Microphthalmia, syndromic 11 • VAX1-related disorder	Likely benign (Dec 31, 2023)
10-117134338-C-A		Microphthalmia, syndromic 11	Likely benign (Nov 12, 2023)
10-117134347-A-G			Likely benign (Dec 05, 2018)
10-117134362-C-G		Microphthalmia, syndromic 11	Benign (Jan 02, 2024)
10-117134369-G-T		not specified	Uncertain significance (Mar 02, 2023)
10-117134371-C-G		Microphthalmia, syndromic 11	Uncertain significance (Dec 09, 2021)
10-117134371-C-T		Microphthalmia, syndromic 11 • VAX1-related disorder	Conflicting classifications of pathogenicity (Apr 12, 2023)

GnomAD

Source: gnomAD

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: 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

	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