VEZT

protein-coding

vezatin, adherens junctions transmembrane protein

Gene summary

This gene encodes a transmembrane protein which has been localized to adherens junctions and shown to bind to myosin VIIA. Examination of expression of this gene in gastric cancer tissues have shown that expression is decreased which appears to be related to hypermethylation of the promoter. Expression of this gene may also be inhibited by binding of a specific microRNA to a target sequence in the 3' UTR of the transcripts. A pseudogene of this gene is located on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

MANE transcript

NM_017599.4

Inheritance

—

ClinVar variants

U:100B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr12:95,217,746-95,302,799

External References & Databases

Ensembl (ENSG00000028203)

Transcript & Mutation Effects

hg38 • Region Span ~85.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VEZT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017599.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar			3
missense			92 clinvar	2 clinvar		94
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	100	2	0	102

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 128 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017599.4	RefSeq	NP_060069.3	12	MANE Select
ENST00000436874.6	Ensembl	ENSP00000410083.1	12	MANE Select
NM_001352088.2	RefSeq	NP_001339017.1	13	Standard
NM_001352089.2	RefSeq	NP_001339018.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

cell-cell adhesion

Molecular Function

myosin binding

Cellular Component

acrosomal vesicle
stereocilia ankle link complex
nucleoplasm
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000436874
Coding exons: 12
Length: 85045
Individuals with no LoFs: 124610
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 124637
p: 0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.698	338	376	0.899	0.0000185	5048
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000074	0.000065	rare
Latino/Admixed American	0.000090	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.000066	0.000065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.845
RVIS EVS: 1.38
RVIS percentile EVS: 94.57

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.723

Gene Damage Prediction

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