VEZT

vezatin, adherens junctions transmembrane protein

Basic information

Region (hg38): 12:95217746-95302799

Links

ENSG00000028203 ∙ NCBI:55591 ∙ OMIM:619749 ∙ HGNC:18258 ∙ Uniprot:Q9HBM0 ∙ 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 VEZT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VEZT 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	0	0

Variants in VEZT

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

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

Position	Type	Phenotype	Significance	ClinVar
12-95252001-C-T		not specified	Uncertain significance (Dec 13, 2023)
12-95252051-C-G		not specified	Uncertain significance (Nov 09, 2023)
12-95257156-A-G		not specified	Uncertain significance (Mar 07, 2024)
12-95262981-A-C		not specified	Uncertain significance (Mar 31, 2024)
12-95262988-T-C		not specified	Uncertain significance (Apr 08, 2024)
12-95266368-T-A		not specified	Uncertain significance (May 08, 2024)
12-95266434-T-C		not specified	Uncertain significance (Apr 20, 2023)
12-95266509-C-A		not specified	Uncertain significance (Jan 03, 2024)
12-95270109-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-95270121-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-95282469-C-G		not specified	Uncertain significance (Nov 05, 2021)
12-95282512-A-G		not specified	Uncertain significance (Sep 26, 2023)
12-95282514-C-T		not specified	Uncertain significance (Mar 28, 2024)
12-95282515-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-95282570-G-C		not specified	Uncertain significance (May 07, 2024)
12-95287717-A-C		not specified	Uncertain significance (Jul 13, 2021)
12-95287779-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-95287827-A-C		not specified	Uncertain significance (May 16, 2024)
12-95287837-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-95287854-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-95294276-G-T		not specified	Uncertain significance (Jun 10, 2022)
12-95296064-A-G		not specified	Uncertain significance (Oct 14, 2023)
12-95296082-T-C		not specified	Uncertain significance (Nov 08, 2022)
12-95296255-C-G		not specified	Uncertain significance (Mar 08, 2024)
12-95300228-T-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VEZT	protein_coding	protein_coding	ENST00000436874	12	85045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.110	0.890	124610	0	27	124637	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.698	338	376	0.899	0.0000185	5048
Missense in Polyphen		95	139.73	0.6799		1869
Synonymous	0.653	130	140	0.930	0.00000664	1485
Loss of Function	4.14	9	35.6	0.252	0.00000176	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000164	0.000155
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000111
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.000155	0.000142
Middle Eastern	0.000116	0.000111
South Asian	0.0000657	0.0000654
Other	0.000335	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a pivotal role in the establishment of adherens junctions and their maintenance in adult life. In case of Listeria infection, promotes bacterial internalization by participating in myosin VIIa recruitment to the entry site. {ECO:0000269|PubMed:15090598}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.845
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.57

Haploinsufficiency Scores

• pHI: 0.305
• hipred: N
• hipred_score: 0.426
• ghis: 0.484

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.723

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vezt
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; normal 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; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell-cell adhesion
• Cellular component: acrosomal vesicle;stereocilia ankle link complex;nucleoplasm;cytosol;plasma membrane;adherens junction;integral component of membrane
• Molecular function: myosin binding